@article{ozmen_proximity_2025,
	title = {Proximity labeling techniques for protein–protein interaction mapping in plants},
	volume = {301},
	issn = {0021-9258},
	url = {https://www.sciencedirect.com/science/article/pii/S0021925825023518},
	doi = {10.1016/j.jbc.2025.110501},
	abstract = {Protein–protein interactions (PPIs) are fundamental to understanding cellular processes, serving as the cornerstone of biological signaling, structural organization, and metabolic regulation. However, capturing PPIs in living organisms remains a significant challenge, particularly in complex and compartmentalized cellular environments. Research in this area has been greatly accelerated by the invention of proximity labeling (PL) techniques. By employing engineered enzymes capable of tagging proteins and other molecules in vivo, PL allows real-time mapping of biomolecular interactions within native environments. In plants, the implementation of PL presents unique challenges but has nonetheless emerged as a powerful tool. Here, we summarize the mechanisms, strengths, and weaknesses of different enzyme-based PL methods. We also highlight key considerations to optimize PL experiments in plants and propose targets for development to further improve their efficiency and flexibility.},
	number = {8},
	urldate = {2026-01-30},
	journal = {Journal of Biological Chemistry},
	author = {Özmen, Beyza and Blaschek, Leonard and Ogden, Michael and San Segundo, Marcos and Persson, Staffan and Zheng, Shuai},
	month = aug,
	year = {2025},
	keywords = {TOR complex, cellulose, plants, protein-protein interactions (PPIs), proximity labeling (PL)},
	pages = {110501},
}

Protein–protein interactions (PPIs) are fundamental to understanding cellular processes, serving as the cornerstone of biological signaling, structural organization, and metabolic regulation. However, capturing PPIs in living organisms remains a significant challenge, particularly in complex and compartmentalized cellular environments. Research in this area has been greatly accelerated by the invention of proximity labeling (PL) techniques. By employing engineered enzymes capable of tagging proteins and other molecules in vivo, PL allows real-time mapping of biomolecular interactions within native environments. In plants, the implementation of PL presents unique challenges but has nonetheless emerged as a powerful tool. Here, we summarize the mechanisms, strengths, and weaknesses of different enzyme-based PL methods. We also highlight key considerations to optimize PL experiments in plants and propose targets for development to further improve their efficiency and flexibility.

@article{zheng_pupylation-based_2025,
	title = {Pupylation-{Based} {Proximity} {Labeling} {Unravels} a {Comprehensive} {Protein} and {Phosphoprotein} {Interactome} of the {Arabidopsis} {TOR} {Complex}},
	volume = {12},
	copyright = {© 2025 The Author(s). Advanced Science published by Wiley-VCH GmbH},
	issn = {2198-3844},
	url = {https://onlinelibrary.wiley.com/doi/abs/10.1002/advs.202414496},
	doi = {10.1002/advs.202414496},
	abstract = {Target of rapamycin (TOR) is a signaling hub that integrates developmental, hormonal, and environmental signals to optimize carbon allocation and plant growth. In plant cells, TOR acts together with the proteins LST8-1 and RAPTOR1 to form a core TOR complex (TORC). While these proteins comprise a functional TORC, they engage with many other proteins to ensure precise signal outputs. Although TORC interactions have attracted significant attention in the recent past, large parts of the interactome are still unknown. In this resource study, PUP-IT is adapted, a fully endogenously expressed protein proximity labeling toolbox, to map TORC protein–protein interactions using the core set of TORC as baits. It is outlined how this interactome is differentially phosphorylated during changes in carbon availability, uncovering putative direct TOR kinase targets. An AlphaFold-Multimer approach is further used to validate many interactors, thus outlining a comprehensive TORC interactome that includes over a hundred new candidate interactors and provides an invaluable resource to the plant cell signaling community.},
	language = {en},
	number = {19},
	urldate = {2026-01-30},
	journal = {Advanced Science},
	author = {Zheng, Shuai and Blaschek, Leonard and Pottier, Delphine and Dijkhof, Luuk Robin Hoegen and Özmen, Beyza and Lim, Peng Ken and Tan, Qiao Wen and Mutwil, Marek and Hauser, Alexander Sebastian and Persson, Staffan},
	year = {2025},
	note = {\_eprint: https://advanced.onlinelibrary.wiley.com/doi/pdf/10.1002/advs.202414496},
	keywords = {AlphaFold, PUP-IT, proximity labeling, sugar signaling, target of rapamycin},
	pages = {2414496},
}

Target of rapamycin (TOR) is a signaling hub that integrates developmental, hormonal, and environmental signals to optimize carbon allocation and plant growth. In plant cells, TOR acts together with the proteins LST8-1 and RAPTOR1 to form a core TOR complex (TORC). While these proteins comprise a functional TORC, they engage with many other proteins to ensure precise signal outputs. Although TORC interactions have attracted significant attention in the recent past, large parts of the interactome are still unknown. In this resource study, PUP-IT is adapted, a fully endogenously expressed protein proximity labeling toolbox, to map TORC protein–protein interactions using the core set of TORC as baits. It is outlined how this interactome is differentially phosphorylated during changes in carbon availability, uncovering putative direct TOR kinase targets. An AlphaFold-Multimer approach is further used to validate many interactors, thus outlining a comprehensive TORC interactome that includes over a hundred new candidate interactors and provides an invaluable resource to the plant cell signaling community.

@article{low_zinc_2025,
	title = {{ZINC} {FINGER} {PROTEIN2} suppresses funiculus lignification to ensure seed loading efficiency in \textit{{Arabidopsis}}},
	volume = {60},
	issn = {1534-5807},
	url = {https://www.sciencedirect.com/science/article/pii/S1534580725000620},
	doi = {10.1016/j.devcel.2025.01.021},
	abstract = {The plant funiculus anchors the developing seed to the placenta within the inner dorsal pod strands of the silique wall and directly transports nutrients to the seeds. The lignified vasculature critically supports nutrient transport through the funiculus. However, molecular mechanisms underlying lignified secondary cell wall (SCW) biosynthesis in the funiculus remain elusive. Here, we show that the transcription factor ZINC FINGER PROTEIN2 (ZFP2) represses SCW formation in the cortex cells that surround the vasculature. This function is essential for efficient nutrient loading into the seeds. Notably, ZFP2 directly acts on the SCW transcription factor NAC SECONDARY WALL THICKENING PROMOTING FACTOR1 (NST1) to repress cortex cell lignification, providing a mechanism of how SCW biosynthesis is restricted to the vasculature of the funiculus to ensure proper seed loading in Arabidopsis.},
	number = {12},
	urldate = {2026-01-30},
	journal = {Developmental Cell},
	author = {Low, Pui Man and Kong, Que and Blaschek, Leonard and Ma, Zhiming and Lim, Peng Ken and Yang, Yuzhou and Quek, Trisha and Lim, Cuithbert J. R. and Singh, Sanjay K. and Crocoll, Christoph and Engquist, Ellen and Thorsen, Jakob S. and Pattanaik, Sitakanta and Tee, Wan Ting and Mutwil, Marek and Miao, Yansong and Yuan, Ling and Xu, Deyang and Persson, Staffan and Ma, Wei},
	month = jun,
	year = {2025},
	keywords = {ZINC FINGER PROTEIN2, funiculus, secondary cell wall biosynthesis, transcription factor, transcriptional repression},
	pages = {1719--1729.e6},
}

The plant funiculus anchors the developing seed to the placenta within the inner dorsal pod strands of the silique wall and directly transports nutrients to the seeds. The lignified vasculature critically supports nutrient transport through the funiculus. However, molecular mechanisms underlying lignified secondary cell wall (SCW) biosynthesis in the funiculus remain elusive. Here, we show that the transcription factor ZINC FINGER PROTEIN2 (ZFP2) represses SCW formation in the cortex cells that surround the vasculature. This function is essential for efficient nutrient loading into the seeds. Notably, ZFP2 directly acts on the SCW transcription factor NAC SECONDARY WALL THICKENING PROMOTING FACTOR1 (NST1) to repress cortex cell lignification, providing a mechanism of how SCW biosynthesis is restricted to the vasculature of the funiculus to ensure proper seed loading in Arabidopsis.

@incollection{pesquet_bulk_2024,
	address = {New York, NY},
	title = {Bulk and {In} {Situ} {Quantification} of {Coniferaldehyde} {Residues} in {Lignin}},
	isbn = {978-1-0716-3477-6},
	url = {https://doi.org/10.1007/978-1-0716-3477-6_14},
	doi = {10.1007/978-1-0716-3477-6_14},
	abstract = {Lignin is a group of cell wall localised heterophenolic polymers varying in the chemistry of the aromatic and aliphatic parts of its units. The lignin residues common to all vascular plants have an aromatic ring with one para hydroxy group and one meta methoxy group, also called guaiacyl (G). The terminal function of the aliphatic part of these G units, however, varies from alcohols, which are generally abundant, to aldehydes, which represent a smaller proportion of lignin monomers. The proportions of aldehyde to alcohol G units in lignin are, nevertheless, precisely controlled to respond to environmental and development cues. These G aldehyde to alcohol unit proportions differ between each cell wall layer of each cell type to fine-tune the cell wall biomechanical and physico-chemical properties. To precisely determine changes in lignin composition, we, herein, describe the various methods to detect and quantify the levels and positions of G aldehyde units, also called coniferaldehyde residues, of lignin polymers in ground plant samples as well as in situ in histological cross-sections.},
	language = {en},
	urldate = {2026-01-30},
	booktitle = {Xylem: {Methods} and {Protocols}},
	publisher = {Springer US},
	author = {Pesquet, Edouard and Blaschek, Leonard and Takahashi, Junko and Yamamoto, Masanobu and Champagne, Antoine and {Nuoendagula} and Subbotina, Elena and Dimotakis, Charilaos and Bacisk, Zoltán and Kajita, Shinya},
	editor = {Agusti, Javier},
	year = {2024},
	keywords = {Coniferaldehyde residues, In situ quantitative chemical imaging, Lignin, Pyrolysis-GC/MS, Raman microspectroscopy, Thioacidolysis-GC/MS, Wiesner test, Xylem cell types},
	pages = {201--226},
}

Lignin is a group of cell wall localised heterophenolic polymers varying in the chemistry of the aromatic and aliphatic parts of its units. The lignin residues common to all vascular plants have an aromatic ring with one para hydroxy group and one meta methoxy group, also called guaiacyl (G). The terminal function of the aliphatic part of these G units, however, varies from alcohols, which are generally abundant, to aldehydes, which represent a smaller proportion of lignin monomers. The proportions of aldehyde to alcohol G units in lignin are, nevertheless, precisely controlled to respond to environmental and development cues. These G aldehyde to alcohol unit proportions differ between each cell wall layer of each cell type to fine-tune the cell wall biomechanical and physico-chemical properties. To precisely determine changes in lignin composition, we, herein, describe the various methods to detect and quantify the levels and positions of G aldehyde units, also called coniferaldehyde residues, of lignin polymers in ground plant samples as well as in situ in histological cross-sections.

@article{blaschek_functional_2024,
	title = {Functional {Complexity} on a {Cellular} {Scale}: {Why} {In} {Situ} {Analyses} {Are} {Indispensable} for {Our} {Understanding} of {Lignified} {Tissues}},
	volume = {72},
	issn = {0021-8561},
	shorttitle = {Functional {Complexity} on a {Cellular} {Scale}},
	url = {https://doi.org/10.1021/acs.jafc.4c01999},
	doi = {10.1021/acs.jafc.4c01999},
	abstract = {Lignins are a key adaptation that enables vascular plants to thrive in terrestrial habitats. Lignin is heterogeneous, containing upward of 30 different monomers, and its function is multifarious: It provides structural support, predetermined breaking points, ultraviolet protection, diffusion barriers, pathogen resistance, and drought resilience. Recent studies, carefully characterizing lignin in situ, have started to identify specific lignin compositions and ultrastructures with distinct cellular functions, but our understanding remains fractional. We summarize recent works and highlight where further in situ lignin analysis could provide valuable insights into plant growth and adaptation. We also summarize strengths and weaknesses of lignin in situ analysis methods.},
	number = {24},
	urldate = {2024-07-01},
	journal = {Journal of Agricultural and Food Chemistry},
	publisher = {American Chemical Society},
	author = {Blaschek, Leonard and Serk, Henrik and Pesquet, Edouard},
	month = jun,
	year = {2024},
	pages = {13552--13560},
}

Lignins are a key adaptation that enables vascular plants to thrive in terrestrial habitats. Lignin is heterogeneous, containing upward of 30 different monomers, and its function is multifarious: It provides structural support, predetermined breaking points, ultraviolet protection, diffusion barriers, pathogen resistance, and drought resilience. Recent studies, carefully characterizing lignin in situ, have started to identify specific lignin compositions and ultrastructures with distinct cellular functions, but our understanding remains fractional. We summarize recent works and highlight where further in situ lignin analysis could provide valuable insights into plant growth and adaptation. We also summarize strengths and weaknesses of lignin in situ analysis methods.

@article{pedersen_cellulose_2023,
	series = {“{Celebrating} 15 {Years} of {Publication}” {Special} {Issue}},
	title = {Cellulose synthesis in land plants},
	volume = {16},
	issn = {1674-2052},
	url = {https://www.sciencedirect.com/science/article/pii/S1674205222004506},
	doi = {10.1016/j.molp.2022.12.015},
	abstract = {All plant cells are surrounded by a cell wall that provides cohesion, protection, and a means of directional growth to plants. Cellulose microfibrils contribute the main biomechanical scaffold for most of these walls. The biosynthesis of cellulose, which typically is the most prominent constituent of the cell wall and therefore Earth’s most abundant biopolymer, is finely attuned to developmental and environmental cues. Our understanding of the machinery that catalyzes and regulates cellulose biosynthesis has substantially improved due to recent technological advances in, for example, structural biology and microscopy. Here, we provide a comprehensive overview of the structure, function, and regulation of the cellulose synthesis machinery and its regulatory interactors. We aim to highlight important knowledge gaps in the field, and outline emerging approaches that promise a means to close those gaps.},
	number = {1},
	urldate = {2026-01-30},
	journal = {Molecular Plant},
	author = {Pedersen, Gustav B. and Blaschek, Leonard and Frandsen, Kristian E. H. and Noack, Lise C. and Persson, Staffan},
	month = jan,
	year = {2023},
	keywords = {cellulose microfibrils, cellulose synthases, cytoskeleton, membrane proteins, plant cell wall, protein interaction},
	pages = {206--231},
}

All plant cells are surrounded by a cell wall that provides cohesion, protection, and a means of directional growth to plants. Cellulose microfibrils contribute the main biomechanical scaffold for most of these walls. The biosynthesis of cellulose, which typically is the most prominent constituent of the cell wall and therefore Earth’s most abundant biopolymer, is finely attuned to developmental and environmental cues. Our understanding of the machinery that catalyzes and regulates cellulose biosynthesis has substantially improved due to recent technological advances in, for example, structural biology and microscopy. Here, we provide a comprehensive overview of the structure, function, and regulation of the cellulose synthesis machinery and its regulatory interactors. We aim to highlight important knowledge gaps in the field, and outline emerging approaches that promise a means to close those gaps.

@article{blaschek_different_2023,
	title = {Different combinations of laccase paralogs nonredundantly control the amount and composition of lignin in specific cell types and cell wall layers in {Arabidopsis}},
	volume = {35},
	issn = {1040-4651},
	url = {https://doi.org/10.1093/plcell/koac344},
	doi = {10.1093/plcell/koac344},
	abstract = {Vascular plants reinforce the cell walls of the different xylem cell types with lignin phenolic polymers. Distinct lignin chemistries differ between each cell wall layer and each cell type to support their specific functions. Yet the mechanisms controlling the tight spatial localization of specific lignin chemistries remain unclear. Current hypotheses focus on control by monomer biosynthesis and/or export, while cell wall polymerization is viewed as random and nonlimiting. Here, we show that combinations of multiple individual laccases (LACs) are nonredundantly and specifically required to set the lignin chemistry in different cell types and their distinct cell wall layers. We dissected the roles of Arabidopsis thaliana LAC4, 5, 10, 12, and 17 by generating quadruple and quintuple loss-of-function mutants. Loss of these LACs in different combinations led to specific changes in lignin chemistry affecting both residue ring structures and/or aliphatic tails in specific cell types and cell wall layers. Moreover, we showed that LAC-mediated lignification has distinct functions in specific cell types, waterproofing fibers, and strengthening vessels. Altogether, we propose that the spatial control of lignin chemistry depends on different combinations of LACs with nonredundant activities immobilized in specific cell types and cell wall layers.},
	number = {2},
	urldate = {2026-01-30},
	journal = {The Plant Cell},
	author = {Blaschek, Leonard and Murozuka, Emiko and Serk, Henrik and Ménard, Delphine and Pesquet, Edouard},
	month = feb,
	year = {2023},
	pages = {889--909},
}

Vascular plants reinforce the cell walls of the different xylem cell types with lignin phenolic polymers. Distinct lignin chemistries differ between each cell wall layer and each cell type to support their specific functions. Yet the mechanisms controlling the tight spatial localization of specific lignin chemistries remain unclear. Current hypotheses focus on control by monomer biosynthesis and/or export, while cell wall polymerization is viewed as random and nonlimiting. Here, we show that combinations of multiple individual laccases (LACs) are nonredundantly and specifically required to set the lignin chemistry in different cell types and their distinct cell wall layers. We dissected the roles of Arabidopsis thaliana LAC4, 5, 10, 12, and 17 by generating quadruple and quintuple loss-of-function mutants. Loss of these LACs in different combinations led to specific changes in lignin chemistry affecting both residue ring structures and/or aliphatic tails in specific cell types and cell wall layers. Moreover, we showed that LAC-mediated lignification has distinct functions in specific cell types, waterproofing fibers, and strengthening vessels. Altogether, we propose that the spatial control of lignin chemistry depends on different combinations of LACs with nonredundant activities immobilized in specific cell types and cell wall layers.

@article{menard_plant_2022,
	title = {Plant biomechanics and resilience to environmental changes are controlled by specific lignin chemistries in each vascular cell type and morphotype},
	volume = {34},
	issn = {1040-4651},
	url = {https://doi.org/10.1093/plcell/koac284},
	doi = {10.1093/plcell/koac284},
	abstract = {The biopolymer lignin is deposited in the cell walls of vascular cells and is essential for long-distance water conduction and structural support in plants. Different vascular cell types contain distinct and conserved lignin chemistries, each with specific aromatic and aliphatic substitutions. Yet, the biological role of this conserved and specific lignin chemistry in each cell type remains unclear. Here, we investigated the roles of this lignin biochemical specificity for cellular functions by producing single cell analyses for three cell morphotypes of tracheary elements, which all allow sap conduction but differ in their morphology. We determined that specific lignin chemistries accumulate in each cell type. Moreover, lignin accumulated dynamically, increasing in quantity and changing in composition, to alter the cell wall biomechanics during cell maturation. For similar aromatic substitutions, residues with alcohol aliphatic functions increased stiffness whereas aldehydes increased flexibility of the cell wall. Modifying this lignin biochemical specificity and the sequence of its formation impaired the cell wall biomechanics of each morphotype and consequently hindered sap conduction and drought recovery. Together, our results demonstrate that each sap-conducting vascular cell type distinctly controls their lignin biochemistry to adjust their biomechanics and hydraulic properties to face developmental and environmental constraints.},
	number = {12},
	urldate = {2026-01-30},
	journal = {The Plant Cell},
	author = {Ménard, Delphine and Blaschek, Leonard and Kriechbaum, Konstantin and Lee, Cheng Choo and Serk, Henrik and Zhu, Chuantao and Lyubartsev, Alexander and {Nuoendagula} and Bacsik, Zoltán and Bergström, Lennart and Mathew, Aji and Kajita, Shinya and Pesquet, Edouard},
	month = dec,
	year = {2022},
	pages = {4877--4896},
}

The biopolymer lignin is deposited in the cell walls of vascular cells and is essential for long-distance water conduction and structural support in plants. Different vascular cell types contain distinct and conserved lignin chemistries, each with specific aromatic and aliphatic substitutions. Yet, the biological role of this conserved and specific lignin chemistry in each cell type remains unclear. Here, we investigated the roles of this lignin biochemical specificity for cellular functions by producing single cell analyses for three cell morphotypes of tracheary elements, which all allow sap conduction but differ in their morphology. We determined that specific lignin chemistries accumulate in each cell type. Moreover, lignin accumulated dynamically, increasing in quantity and changing in composition, to alter the cell wall biomechanics during cell maturation. For similar aromatic substitutions, residues with alcohol aliphatic functions increased stiffness whereas aldehydes increased flexibility of the cell wall. Modifying this lignin biochemical specificity and the sequence of its formation impaired the cell wall biomechanics of each morphotype and consequently hindered sap conduction and drought recovery. Together, our results demonstrate that each sap-conducting vascular cell type distinctly controls their lignin biochemistry to adjust their biomechanics and hydraulic properties to face developmental and environmental constraints.

@article{blaschek_phenoloxidases_2021,
	title = {Phenoloxidases in {Plants}—{How} {Structural} {Diversity} {Enables} {Functional} {Specificity}},
	volume = {12},
	issn = {1664-462X},
	url = {https://www.frontiersin.org/journals/plant-science/articles/10.3389/fpls.2021.754601/full},
	doi = {10.3389/fpls.2021.754601},
	abstract = {The metabolism of polyphenolic polymers is essential to the development and response to environmental changes of organisms from all kingdoms of life, but shows particular diversity in plants. In contrast to other biopolymers, whose polymerisation is catalysed by homologous gene families, polyphenolic metabolism depends on phenoloxidases, a group of heterogeneous oxidases that share little beyond the eponymous common substrate. In this review, we provide an overview of the differences and similarities between phenoloxidases in their protein structure, reaction mechanism, substrate specificity, and functional roles. Using the example of laccases, we also performed a meta-analysis of enzyme kinetics, a comprehensive phylogenetic analysis and machine-learning based protein structure modelling to link functions, evolution, and structures in this group of phenoloxidases. With these approaches, we generated a framework to explain the reported functional differences between paralogs, while also hinting at the likely diversity of yet undescribed laccase functions. Altogether, this review provides a basis to better understand the functional overlaps and specificities between and within the three major families of phenoloxidases, their evolutionary trajectories, and their importance for plant primary and secondary metabolism.},
	language = {English},
	urldate = {2026-01-30},
	journal = {Frontiers in Plant Science},
	publisher = {Frontiers},
	author = {Blaschek, Leonard and Pesquet, Edouard},
	month = oct,
	year = {2021},
	keywords = {Bayesian phylogeny, Laccase, Lignin, Peroxidase, Polyphenol oxidase, Polyphenolic polymers, Protein modelling},
}

The metabolism of polyphenolic polymers is essential to the development and response to environmental changes of organisms from all kingdoms of life, but shows particular diversity in plants. In contrast to other biopolymers, whose polymerisation is catalysed by homologous gene families, polyphenolic metabolism depends on phenoloxidases, a group of heterogeneous oxidases that share little beyond the eponymous common substrate. In this review, we provide an overview of the differences and similarities between phenoloxidases in their protein structure, reaction mechanism, substrate specificity, and functional roles. Using the example of laccases, we also performed a meta-analysis of enzyme kinetics, a comprehensive phylogenetic analysis and machine-learning based protein structure modelling to link functions, evolution, and structures in this group of phenoloxidases. With these approaches, we generated a framework to explain the reported functional differences between paralogs, while also hinting at the likely diversity of yet undescribed laccase functions. Altogether, this review provides a basis to better understand the functional overlaps and specificities between and within the three major families of phenoloxidases, their evolutionary trajectories, and their importance for plant primary and secondary metabolism.

@article{blaschek_cellular_2020,
	title = {Cellular and {Genetic} {Regulation} of {Coniferaldehyde} {Incorporation} in {Lignin} of {Herbaceous} and {Woody} {Plants} by {Quantitative} {Wiesner} {Staining}},
	volume = {11},
	issn = {1664-462X},
	url = {https://www.frontiersin.org/article/10.3389/fpls.2020.00109/full},
	doi = {10.3389/fpls.2020.00109},
	urldate = {2021-06-07},
	journal = {Frontiers in Plant Science},
	author = {Blaschek, Leonard and Champagne, Antoine and Dimotakis, Charilaos and {Nuoendagula} and Decou, Raphaël and Hishiyama, Shojiro and Kratzer, Susanne and Kajita, Shinya and Pesquet, Edouard},
	month = mar,
	year = {2020},
	pages = {109},
}

@article{blaschek_determining_2020,
	title = {Determining the {Genetic} {Regulation} and {Coordination} of {Lignification} in {Stem} {Tissues} of {Arabidopsis} {Using} {Semiquantitative} {Raman} {Microspectroscopy}},
	volume = {8},
	url = {https://doi.org/10.1021/acssuschemeng.0c00194},
	doi = {10.1021/acssuschemeng.0c00194},
	abstract = {Lignin is a phenolic polymer accumulating in the cell walls of specific plant cell types to confer unique properties such as hydrophobicity, mechanical strengthening, and resistance to degradation. Different cell types accumulate lignin with specific concentration and composition to support their specific roles in the different plant tissues. Yet the genetic mechanisms controlling lignin quantity and composition differently between the different lignified cell types and tissues still remain poorly understood. To investigate this tissue-specific genetic regulation, we validated both the target molecular structures as well as the linear semiquantitative capacity of Raman microspectroscopy to characterize the total lignin amount, S/G ratio, and coniferyl alcohol content in situ directly in plant biopsies. Using the optimized method on stems of multiple lignin biosynthesis loss-of-function mutants revealed that the genetic regulation of lignin is tissue specific, with distinct genes establishing nonredundant check-points to trigger specific compensatory adjustments affecting either lignin composition and/or cell wall polymer concentrations.},
	number = {12},
	urldate = {2026-01-30},
	journal = {ACS Sustainable Chemistry \& Engineering},
	publisher = {American Chemical Society},
	author = {Blaschek, Leonard and {Nuoendagula} and Bacsik, Zoltán and Kajita, Shinya and Pesquet, Edouard},
	month = mar,
	year = {2020},
	pages = {4900--4909},
}

Lignin is a phenolic polymer accumulating in the cell walls of specific plant cell types to confer unique properties such as hydrophobicity, mechanical strengthening, and resistance to degradation. Different cell types accumulate lignin with specific concentration and composition to support their specific roles in the different plant tissues. Yet the genetic mechanisms controlling lignin quantity and composition differently between the different lignified cell types and tissues still remain poorly understood. To investigate this tissue-specific genetic regulation, we validated both the target molecular structures as well as the linear semiquantitative capacity of Raman microspectroscopy to characterize the total lignin amount, S/G ratio, and coniferyl alcohol content in situ directly in plant biopsies. Using the optimized method on stems of multiple lignin biosynthesis loss-of-function mutants revealed that the genetic regulation of lignin is tissue specific, with distinct genes establishing nonredundant check-points to trigger specific compensatory adjustments affecting either lignin composition and/or cell wall polymer concentrations.

@article{yamamoto_importance_2020,
	title = {Importance of {Lignin} {Coniferaldehyde} {Residues} for {Plant} {Properties} and {Sustainable} {Uses}},
	volume = {13},
	copyright = {© 2020 The Authors. Published by Wiley-VCH GmbH},
	issn = {1864-564X},
	url = {https://onlinelibrary.wiley.com/doi/abs/10.1002/cssc.202001242},
	doi = {10.1002/cssc.202001242},
	abstract = {Increases in coniferaldehyde content, a minor lignin residue, significantly improves the sustainable use of plant biomass for feed, pulping, and biorefinery without affecting plant growth and yields. Herein, different analytical methods are compared and validated to distinguish coniferaldehyde from other lignin residues. It is shown that specific genetic pathways regulate amount, linkage, and position of coniferaldehyde within the lignin polymer for each cell type. This specific cellular regulation offers new possibilities for designing plant lignin for novel and targeted industrial uses.},
	language = {en},
	number = {17},
	urldate = {2026-01-30},
	journal = {ChemSusChem},
	author = {Yamamoto, Masanobu and Blaschek, Leonard and Subbotina, Elena and Kajita, Shinya and Pesquet, Edouard},
	year = {2020},
	note = {\_eprint: https://chemistry-europe.onlinelibrary.wiley.com/doi/pdf/10.1002/cssc.202001242},
	keywords = {analytical methods, biomass, coniferaldehyde, mutagenesis, polymers},
	pages = {4400--4408},
}

Increases in coniferaldehyde content, a minor lignin residue, significantly improves the sustainable use of plant biomass for feed, pulping, and biorefinery without affecting plant growth and yields. Herein, different analytical methods are compared and validated to distinguish coniferaldehyde from other lignin residues. It is shown that specific genetic pathways regulate amount, linkage, and position of coniferaldehyde within the lignin polymer for each cell type. This specific cellular regulation offers new possibilities for designing plant lignin for novel and targeted industrial uses.

@article{pinosio_forgenius_2026,
	title = {The {FORGENIUS} {Genomic} {Resources}: {New} {Genotyping} {Tools} and {Genomic} {Data} for 23 {Forest} {Tree} {Species} and {Their} {Genetic} {Conservation} {Units}},
	volume = {26},
	issn = {1755-0998},
	shorttitle = {The {FORGENIUS} {Genomic} {Resources}},
	url = {https://onlinelibrary.wiley.com/doi/abs/10.1111/1755-0998.70115},
	doi = {10.1111/1755-0998.70115},
	abstract = {Genetic diversity is a critical but often overlooked component of biological diversity. The European H2020 FORGENIUS project is aimed at increasing the quality and quantity of genetic data to start monitoring the European network of forest Genetic Conservation Units (GCUs). A first step in this direction was developing standardised genomic resources for 23 forest tree species, spanning from rare and scattered (e.g., Abies nebrodensis and Torminalis glaberrima) to widespread and stand-forming, economically relevant ones (e.g., Fagus sylvatica, Picea abies and Pinus sylvestris). Here, we describe the development and application of targeted genotyping tools, primarily based on Single Primer Enrichment Technology (SPET), along with existing SNP arrays for the selected species. The SPET panels developed in FORGENIUS were designed to capture ⁓10,000 loci per species, balancing species-specific and randomly distributed regions to ensure broad genome coverage and minimise ascertainment bias. Across 7220 genotyped trees, we identified over 1.8 million single nucleotide polymorphisms (SNPs) covering approximately 50 Mb of DNA sequence. SPET panels demonstrated high genotyping efficiency and cross-species transferability, especially within genera such as Quercus and Abies. They represent a cost-effective, flexible, and scalable solution for population-level genetic assessments across diverse taxa, enabling standardised, genome-wide characterisation of the GCU network. These resources not only promote the establishment of genetic monitoring, support genetically informed conservation strategies and improve our understanding of adaptive responses in European forests, but also enhance species delimitation and hybrid detection, and enable the characterisation of phylogenetically related but previously underexplored species.},
	language = {en},
	number = {3},
	urldate = {2026-03-09},
	journal = {Molecular Ecology Resources},
	author = {Pinosio, Sara and Bagnoli, Francesca and Avanzi, Camilla and Castellani, Maria B. and Frascella, Arcangela and McEvoy, Susan L. and Olsson, Sanna and Spanu, Ilaria and Vajana, Elia and Consortium, the FORGENIUS and González-Martínez, Santiago C. and Pyhäjärvi, Tanja and Scotti, Ivan and Vendramin, Giovanni G. and Piotti, Andrea},
	year = {2026},
	note = {\_eprint: https://onlinelibrary.wiley.com/doi/pdf/10.1111/1755-0998.70115},
	keywords = {forest tree species, genetic conservation units, genetic diversity, genetic monitoring, single primer enrichment technology, targeted genotyping},
	pages = {e70115},
}

Genetic diversity is a critical but often overlooked component of biological diversity. The European H2020 FORGENIUS project is aimed at increasing the quality and quantity of genetic data to start monitoring the European network of forest Genetic Conservation Units (GCUs). A first step in this direction was developing standardised genomic resources for 23 forest tree species, spanning from rare and scattered (e.g., Abies nebrodensis and Torminalis glaberrima) to widespread and stand-forming, economically relevant ones (e.g., Fagus sylvatica, Picea abies and Pinus sylvestris). Here, we describe the development and application of targeted genotyping tools, primarily based on Single Primer Enrichment Technology (SPET), along with existing SNP arrays for the selected species. The SPET panels developed in FORGENIUS were designed to capture ⁓10,000 loci per species, balancing species-specific and randomly distributed regions to ensure broad genome coverage and minimise ascertainment bias. Across 7220 genotyped trees, we identified over 1.8 million single nucleotide polymorphisms (SNPs) covering approximately 50 Mb of DNA sequence. SPET panels demonstrated high genotyping efficiency and cross-species transferability, especially within genera such as Quercus and Abies. They represent a cost-effective, flexible, and scalable solution for population-level genetic assessments across diverse taxa, enabling standardised, genome-wide characterisation of the GCU network. These resources not only promote the establishment of genetic monitoring, support genetically informed conservation strategies and improve our understanding of adaptive responses in European forests, but also enhance species delimitation and hybrid detection, and enable the characterisation of phylogenetically related but previously underexplored species.

@article{castellano_genome_2025,
	title = {Genome {Assembly} of a {Living} {Fossil}, the {Atlantic} {Horseshoe} {Crab} {Limulus} polyphemus, {Reveals} {Lineage}-{Specific} {Whole}-{Genome} {Duplications}, {Transposable} {Element}-{Based} {Centromeres}, and a {ZW} {Sex} {Chromosome} {System}},
	volume = {42},
	issn = {1537-1719},
	url = {https://doi.org/10.1093/molbev/msaf021},
	doi = {10.1093/molbev/msaf021},
	abstract = {Horseshoe crabs, considered living fossils with a stable morphotype spanning ∼445 million years, are evolutionarily, ecologically, and biomedically important species experiencing rapid population decline. Of the four extant species of horseshoe crabs, the Atlantic horseshoe crab, Limulus polyphemus, has become an essential component of the modern medicine toolkit. Here, we present the first chromosome-level genome assembly, and the most contiguous and complete assembly to date, for L. polyphemus using nanopore long-read sequencing and chromatin conformation analysis. We find support for three horseshoe crab-specific whole-genome duplications, but none shared with Arachnopulmonata (spiders and scorpions). Moreover, we discovered tandem duplicates of endotoxin detection pathway components Factors C and G, identify candidate centromeres consisting of Gypsy retroelements, and classify the ZW sex chromosome system for this species and a sister taxon, Carcinoscorpius rotundicauda. Finally, we revealed this species has been experiencing a steep population decline over the last 5 million years, highlighting the need for international conservation interventions and fisheries-based management for this critical species.},
	number = {2},
	urldate = {2026-01-16},
	journal = {Molecular Biology and Evolution},
	author = {Castellano, Kate R and Neitzey, Michelle L and Starovoitov, Andrew and Barrett, Gabriel A and Reid, Noah M and Vuruputoor, Vidya S and Webster, Cynthia N and Storer, Jessica M and Pauloski, Nicole R and Ameral, Natalie J and McEvoy, Susan L and McManus, M Conor and Puritz, Jonathan B and Wegrzyn, Jill L and O’Neill, Rachel J},
	month = feb,
	year = {2025},
	pages = {msaf021},
}

Horseshoe crabs, considered living fossils with a stable morphotype spanning ∼445 million years, are evolutionarily, ecologically, and biomedically important species experiencing rapid population decline. Of the four extant species of horseshoe crabs, the Atlantic horseshoe crab, Limulus polyphemus, has become an essential component of the modern medicine toolkit. Here, we present the first chromosome-level genome assembly, and the most contiguous and complete assembly to date, for L. polyphemus using nanopore long-read sequencing and chromatin conformation analysis. We find support for three horseshoe crab-specific whole-genome duplications, but none shared with Arachnopulmonata (spiders and scorpions). Moreover, we discovered tandem duplicates of endotoxin detection pathway components Factors C and G, identify candidate centromeres consisting of Gypsy retroelements, and classify the ZW sex chromosome system for this species and a sister taxon, Carcinoscorpius rotundicauda. Finally, we revealed this species has been experiencing a steep population decline over the last 5 million years, highlighting the need for international conservation interventions and fisheries-based management for this critical species.

@article{mcevoy_profiling_2024,
	title = {Profiling genome-wide methylation in two maples: {Fine}-scale approaches to detection with nanopore technology},
	volume = {17},
	copyright = {© 2024 The Authors. Evolutionary Applications published by John Wiley \& Sons Ltd.},
	issn = {1752-4571},
	shorttitle = {Profiling genome-wide methylation in two maples},
	url = {https://onlinelibrary.wiley.com/doi/abs/10.1111/eva.13669},
	doi = {10.1111/eva.13669},
	abstract = {DNA methylation is critical to the regulation of transposable elements and gene expression and can play an important role in the adaptation of stress response mechanisms in plants. Traditional methods of methylation quantification rely on bisulfite conversion that can compromise accuracy. Recent advances in long-read sequencing technologies allow for methylation detection in real time. The associated algorithms that interpret these modifications have evolved from strictly statistical approaches to Hidden Markov Models and, recently, deep learning approaches. Much of the existing software focuses on methylation in the CG context, but methylation in other contexts is important to quantify, as it is extensively leveraged in plants. Here, we present methylation profiles for two maple species across the full range of 5mC sequence contexts using Oxford Nanopore Technologies (ONT) long-reads. Hybrid and reference-guided assemblies were generated for two new Acer accessions: Acer negundo (box elder; 65x ONT and 111X Illumina) and Acer saccharum (sugar maple; 93x ONT and 148X Illumina). The ONT reads generated for these assemblies were re-basecalled, and methylation detection was conducted in a custom pipeline with the published Acer references (PacBio assemblies) and hybrid assemblies reported herein to generate four epigenomes. Examination of the transposable element landscape revealed the dominance of LTR Copia elements and patterns of methylation associated with different classes of TEs. Methylation distributions were examined at high resolution across gene and repeat density and described within the broader angiosperm context, and more narrowly in the context of gene family dynamics and candidate nutrient stress genes.},
	language = {en},
	number = {4},
	urldate = {2025-11-12},
	journal = {Evolutionary Applications},
	author = {McEvoy, Susan L. and Grady, Patrick G. S. and Pauloski, Nicole and O'Neill, Rachel J. and Wegrzyn, Jill L.},
	year = {2024},
	note = {\_eprint: https://onlinelibrary.wiley.com/doi/pdf/10.1111/eva.13669},
	keywords = {Acer negundo, Acer saccharum, methylome, nanopore, nutrient stress, transposable elements},
	pages = {e13669},
}

DNA methylation is critical to the regulation of transposable elements and gene expression and can play an important role in the adaptation of stress response mechanisms in plants. Traditional methods of methylation quantification rely on bisulfite conversion that can compromise accuracy. Recent advances in long-read sequencing technologies allow for methylation detection in real time. The associated algorithms that interpret these modifications have evolved from strictly statistical approaches to Hidden Markov Models and, recently, deep learning approaches. Much of the existing software focuses on methylation in the CG context, but methylation in other contexts is important to quantify, as it is extensively leveraged in plants. Here, we present methylation profiles for two maple species across the full range of 5mC sequence contexts using Oxford Nanopore Technologies (ONT) long-reads. Hybrid and reference-guided assemblies were generated for two new Acer accessions: Acer negundo (box elder; 65x ONT and 111X Illumina) and Acer saccharum (sugar maple; 93x ONT and 148X Illumina). The ONT reads generated for these assemblies were re-basecalled, and methylation detection was conducted in a custom pipeline with the published Acer references (PacBio assemblies) and hybrid assemblies reported herein to generate four epigenomes. Examination of the transposable element landscape revealed the dominance of LTR Copia elements and patterns of methylation associated with different classes of TEs. Methylation distributions were examined at high resolution across gene and repeat density and described within the broader angiosperm context, and more narrowly in the context of gene family dynamics and candidate nutrient stress genes.

@article{mcevoy_reference_2024,
	title = {The reference genome of an endangered {Asteraceae}, {Deinandra} increscens subsp. villosa, endemic to the {Central} {Coast} of {California}},
	volume = {14},
	issn = {2160-1836},
	url = {https://doi.org/10.1093/g3journal/jkae117},
	doi = {10.1093/g3journal/jkae117},
	abstract = {We present a reference genome for the federally endangered Gaviota tarplant, Deinandra increscens subsp. villosa (Madiinae, Asteraceae), an annual herb endemic to the Central California coast. Generating PacBio HiFi, Oxford Nanopore Technologies, and Dovetail Omni-C data, we assembled a haploid consensus genome of 1.67 Gb as 28.7 K scaffolds with a scaffold N50 of 74.9 Mb. We annotated repeat content in 74.8\% of the genome. Long terminal repeats (LTRs) covered 44.0\% of the genome with Copia families predominant at 22.9\% followed by Gypsy at 14.2\%. Both Gypsy and Copia elements were common in ancestral peaks of LTRs, and the most abundant element was a Gypsy element containing nested Copia/Angela sequence similarity, reflecting a complex evolutionary history of repeat activity. Gene annotation produced 33,257 genes and 68,942 transcripts, of which 99\% were functionally annotated. BUSCO scores for the annotated proteins were 96.0\% complete of which 77.6\% was single copy and 18.4\% duplicates. Whole genome duplication synonymous mutation rates of Gaviota tarplant and sunflower (Helianthus annuus) shared peaks that correspond to the last Asteraceae polyploidization event and subsequent divergence from a common ancestor at ∼27 MYA. Regions of high-density tandem genes were identified, pointing to potentially important loci of environmental adaptation in this species.},
	number = {8},
	urldate = {2025-11-12},
	journal = {G3 Genes Genomes Genetics},
	author = {McEvoy, Susan L and Meyer, Rachel S and Hasenstab-Lehman, Kristen E and Guilliams, C Matt},
	month = aug,
	year = {2024},
	pages = {jkae117},
}

We present a reference genome for the federally endangered Gaviota tarplant, Deinandra increscens subsp. villosa (Madiinae, Asteraceae), an annual herb endemic to the Central California coast. Generating PacBio HiFi, Oxford Nanopore Technologies, and Dovetail Omni-C data, we assembled a haploid consensus genome of 1.67 Gb as 28.7 K scaffolds with a scaffold N50 of 74.9 Mb. We annotated repeat content in 74.8% of the genome. Long terminal repeats (LTRs) covered 44.0% of the genome with Copia families predominant at 22.9% followed by Gypsy at 14.2%. Both Gypsy and Copia elements were common in ancestral peaks of LTRs, and the most abundant element was a Gypsy element containing nested Copia/Angela sequence similarity, reflecting a complex evolutionary history of repeat activity. Gene annotation produced 33,257 genes and 68,942 transcripts, of which 99% were functionally annotated. BUSCO scores for the annotated proteins were 96.0% complete of which 77.6% was single copy and 18.4% duplicates. Whole genome duplication synonymous mutation rates of Gaviota tarplant and sunflower (Helianthus annuus) shared peaks that correspond to the last Asteraceae polyploidization event and subsequent divergence from a common ancestor at ∼27 MYA. Regions of high-density tandem genes were identified, pointing to potentially important loci of environmental adaptation in this species.

@article{mcevoy_chromosome-level_2023,
	title = {Chromosome-level reference genome of stinkwort, {Dittrichia} graveolens ({L}.) {Greuter}: {A} resource for studies on invasion, range expansion, and evolutionary adaptation under global change},
	volume = {114},
	issn = {1465-7333},
	shorttitle = {Chromosome-level reference genome of stinkwort, {Dittrichia} graveolens ({L}.) {Greuter}},
	url = {https://doi.org/10.1093/jhered/esad033},
	doi = {10.1093/jhered/esad033},
	abstract = {Dittrichia graveolens (L.) Greuter, or stinkwort, is a weedy annual plant within the family Asteraceae. The species is recognized for the rapid expansion of both its native and introduced ranges: in Europe, it has expanded its native distribution northward from the Mediterranean basin by nearly 7 °C latitude since the mid-20th century, while in California and Australia the plant is an invasive weed of concern. Here, we present the first de novo D. graveolens genome assembly (1N = 9 chromosomes), including complete chloroplast (151,013 bp) and partial mitochondrial genomes (22,084 bp), created using Pacific Biosciences HiFi reads and Dovetail Omni-C data. The final primary assembly is 835 Mbp in length, of which 98.1\% are represented by 9 scaffolds ranging from 66 to 119 Mbp. The contig N50 is 74.9 Mbp and the scaffold N50 is 96.9 Mbp, which, together with a 98.8\% completeness based on the BUSCO embryophyta10 database containing 1,614 orthologs, underscores the high quality of this assembly. This pseudo-molecule-scale genome assembly is a valuable resource for our fundamental understanding of the genomic consequences of range expansion under global change, as well as comparative genomic studies in the Asteraceae.},
	number = {5},
	urldate = {2026-01-16},
	journal = {Journal of Heredity},
	author = {McEvoy, Susan L and Lustenhouwer, Nicky and Melen, Miranda K and Nguyen, Oanh and Marimuthu, Mohan P A and Chumchim, Noravit and Beraut, Eric and Parker, Ingrid M and Meyer, Rachel S},
	month = sep,
	year = {2023},
	pages = {561--569},
}

Dittrichia graveolens (L.) Greuter, or stinkwort, is a weedy annual plant within the family Asteraceae. The species is recognized for the rapid expansion of both its native and introduced ranges: in Europe, it has expanded its native distribution northward from the Mediterranean basin by nearly 7 °C latitude since the mid-20th century, while in California and Australia the plant is an invasive weed of concern. Here, we present the first de novo D. graveolens genome assembly (1N = 9 chromosomes), including complete chloroplast (151,013 bp) and partial mitochondrial genomes (22,084 bp), created using Pacific Biosciences HiFi reads and Dovetail Omni-C data. The final primary assembly is 835 Mbp in length, of which 98.1% are represented by 9 scaffolds ranging from 66 to 119 Mbp. The contig N50 is 74.9 Mbp and the scaffold N50 is 96.9 Mbp, which, together with a 98.8% completeness based on the BUSCO embryophyta10 database containing 1,614 orthologs, underscores the high quality of this assembly. This pseudo-molecule-scale genome assembly is a valuable resource for our fundamental understanding of the genomic consequences of range expansion under global change, as well as comparative genomic studies in the Asteraceae.

@article{vuruputoor_welcome_2023,
	title = {Welcome to the big leaves: {Best} practices for improving genome annotation in non-model plant genomes},
	volume = {11},
	copyright = {© 2023 The Authors. Applications in Plant Sciences published by Wiley Periodicals LLC on behalf of Botanical Society of America.},
	issn = {2168-0450},
	shorttitle = {Welcome to the big leaves},
	url = {https://onlinelibrary.wiley.com/doi/abs/10.1002/aps3.11533},
	doi = {10.1002/aps3.11533},
	abstract = {Premise Robust standards to evaluate quality and completeness are lacking in eukaryotic structural genome annotation, as genome annotation software is developed using model organisms and typically lacks benchmarking to comprehensively evaluate the quality and accuracy of the final predictions. The annotation of plant genomes is particularly challenging due to their large sizes, abundant transposable elements, and variable ploidies. This study investigates the impact of genome quality, complexity, sequence read input, and method on protein-coding gene predictions. Methods The impact of repeat masking, long-read and short-read inputs, and de novo and genome-guided protein evidence was examined in the context of the popular BRAKER and MAKER workflows for five plant genomes. The annotations were benchmarked for structural traits and sequence similarity. Results Benchmarks that reflect gene structures, reciprocal similarity search alignments, and mono-exonic/multi-exonic gene counts provide a more complete view of annotation accuracy. Transcripts derived from RNA-read alignments alone are not sufficient for genome annotation. Gene prediction workflows that combine evidence-based and ab initio approaches are recommended, and a combination of short and long reads can improve genome annotation. Adding protein evidence from de novo assemblies, genome-guided transcriptome assemblies, or full-length proteins from OrthoDB generates more putative false positives as implemented in the current workflows. Post-processing with functional and structural filters is highly recommended. Discussion While the annotation of non-model plant genomes remains complex, this study provides recommendations for inputs and methodological approaches. We discuss a set of best practices to generate an optimal plant genome annotation and present a more robust set of metrics to evaluate the resulting predictions.},
	language = {en},
	number = {4},
	urldate = {2026-01-16},
	journal = {Applications in Plant Sciences},
	author = {Vuruputoor, Vidya S. and Monyak, Daniel and Fetter, Karl C. and Webster, Cynthia and Bhattarai, Akriti and Shrestha, Bikash and Zaman, Sumaira and Bennett, Jeremy and McEvoy, Susan L. and Caballero, Madison and Wegrzyn, Jill L.},
	year = {2023},
	note = {\_eprint: https://bsapubs.onlinelibrary.wiley.com/doi/pdf/10.1002/aps3.11533},
	keywords = {BRAKER, MAKER, StringTie2, TSEBRA, gene identification, genome annotation, plant genomes},
	pages = {e11533},
}

Premise Robust standards to evaluate quality and completeness are lacking in eukaryotic structural genome annotation, as genome annotation software is developed using model organisms and typically lacks benchmarking to comprehensively evaluate the quality and accuracy of the final predictions. The annotation of plant genomes is particularly challenging due to their large sizes, abundant transposable elements, and variable ploidies. This study investigates the impact of genome quality, complexity, sequence read input, and method on protein-coding gene predictions. Methods The impact of repeat masking, long-read and short-read inputs, and de novo and genome-guided protein evidence was examined in the context of the popular BRAKER and MAKER workflows for five plant genomes. The annotations were benchmarked for structural traits and sequence similarity. Results Benchmarks that reflect gene structures, reciprocal similarity search alignments, and mono-exonic/multi-exonic gene counts provide a more complete view of annotation accuracy. Transcripts derived from RNA-read alignments alone are not sufficient for genome annotation. Gene prediction workflows that combine evidence-based and ab initio approaches are recommended, and a combination of short and long reads can improve genome annotation. Adding protein evidence from de novo assemblies, genome-guided transcriptome assemblies, or full-length proteins from OrthoDB generates more putative false positives as implemented in the current workflows. Post-processing with functional and structural filters is highly recommended. Discussion While the annotation of non-model plant genomes remains complex, this study provides recommendations for inputs and methodological approaches. We discuss a set of best practices to generate an optimal plant genome annotation and present a more robust set of metrics to evaluate the resulting predictions.

@article{mcevoy_strategies_2022,
	title = {Strategies of tolerance reflected in two {North} {American} maple genomes},
	volume = {109},
	copyright = {© 2021 The Authors. The Plant Journal published by Society for Experimental Biology and John Wiley \& Sons Ltd.},
	issn = {1365-313X},
	url = {https://onlinelibrary.wiley.com/doi/abs/10.1111/tpj.15657},
	doi = {10.1111/tpj.15657},
	abstract = {Maples (the genus Acer) represent important and beloved forest, urban, and ornamental trees distributed throughout the Northern hemisphere. They exist in a diverse array of native ranges and distributions, across spectrums of tolerance or decline, and have varying levels of susceptibility to biotic and abiotic stress. Among Acer species, several stand out in their importance to economic interest. Here we report the first two chromosome-scale genomes for North American species, Acer negundo and Acer saccharum. Both assembled genomes contain scaffolds corresponding to 13 chromosomes, with A. negundo at a length of 442 Mb, an N50 of 32 Mb, and 30 491 genes, and A. saccharum at a length of 626 Mb, an N50 of 46 Mb, and 40 074 genes. No recent whole genome duplications were detected, though A. saccharum has local gene duplication and more recent bursts of transposable elements, as well as a large-scale translocation between two chromosomes. Genomic comparison revealed that A. negundo has a smaller genome with recent gene family evolution that is predominantly contracted and expansions that are potentially related to invasive tendencies and tolerance to abiotic stress. Examination of RNA sequencing data obtained from A. saccharum given long-term aluminum and calcium soil treatments at the Hubbard Brook Experimental Forest provided insights into genes involved in the aluminum stress response at the systemic level, as well as signs of compromised processes upon calcium deficiency, a condition contributing to maple decline.},
	language = {de},
	number = {6},
	urldate = {2026-01-16},
	journal = {The Plant Journal},
	author = {McEvoy, Susan L. and Sezen, U. Uzay and Trouern-Trend, Alexander and McMahon, Sean M. and Schaberg, Paul G. and Yang, Jie and Wegrzyn, Jill L. and Swenson, Nathan G.},
	year = {2022},
	note = {\_eprint: https://onlinelibrary.wiley.com/doi/pdf/10.1111/tpj.15657},
	keywords = {Acer negundo, Acer saccharum, abiotic stress, aluminum, calcium, differential expression, genome, nutrient stress, plasticity, tolerance},
	pages = {1591--1613},
}

Maples (the genus Acer) represent important and beloved forest, urban, and ornamental trees distributed throughout the Northern hemisphere. They exist in a diverse array of native ranges and distributions, across spectrums of tolerance or decline, and have varying levels of susceptibility to biotic and abiotic stress. Among Acer species, several stand out in their importance to economic interest. Here we report the first two chromosome-scale genomes for North American species, Acer negundo and Acer saccharum. Both assembled genomes contain scaffolds corresponding to 13 chromosomes, with A. negundo at a length of 442 Mb, an N50 of 32 Mb, and 30 491 genes, and A. saccharum at a length of 626 Mb, an N50 of 46 Mb, and 40 074 genes. No recent whole genome duplications were detected, though A. saccharum has local gene duplication and more recent bursts of transposable elements, as well as a large-scale translocation between two chromosomes. Genomic comparison revealed that A. negundo has a smaller genome with recent gene family evolution that is predominantly contracted and expansions that are potentially related to invasive tendencies and tolerance to abiotic stress. Examination of RNA sequencing data obtained from A. saccharum given long-term aluminum and calcium soil treatments at the Hubbard Brook Experimental Forest provided insights into genes involved in the aluminum stress response at the systemic level, as well as signs of compromised processes upon calcium deficiency, a condition contributing to maple decline.

@article{alonso-serra_growth_2026,
	title = {On growth and flow: hydraulic aspects of aboveground meristems},
	volume = {249},
	copyright = {© 2025 The Author(s). New Phytologist © 2025 New Phytologist Foundation.},
	issn = {1469-8137},
	shorttitle = {On growth and flow},
	url = {https://onlinelibrary.wiley.com/doi/abs/10.1111/nph.70713},
	doi = {10.1111/nph.70713},
	abstract = {Water is essential for plant growth under both normal and stress conditions. Aboveground, two key meristems control plant development: the shoot apical meristem and the vascular cambium. Here, stem cell maintenance and cell differentiation are affected by hydraulic fluctuations across seasons, days, or even hours. Water fluxes, turgor pressure, osmotic gradients, and tissue mechanics are integrated by molecular signals to provide a robust control of meristematic activity. Despite this fundamental connection, our understanding of how meristems sense and respond to hydraulic changes is only beginning to emerge. Thus, integrating insights from research on plant stress and development opens exciting avenues to study meristem plasticity.},
	language = {en},
	number = {2},
	urldate = {2026-03-18},
	journal = {New Phytologist},
	author = {Alonso-Serra, Juan},
	year = {2026},
	note = {\_eprint: https://nph.onlinelibrary.wiley.com/doi/pdf/10.1111/nph.70713},
	keywords = {biomechanics, cambium, hydraulics, meristem, shoot apical meristem, water},
	pages = {722--728},
}

Water is essential for plant growth under both normal and stress conditions. Aboveground, two key meristems control plant development: the shoot apical meristem and the vascular cambium. Here, stem cell maintenance and cell differentiation are affected by hydraulic fluctuations across seasons, days, or even hours. Water fluxes, turgor pressure, osmotic gradients, and tissue mechanics are integrated by molecular signals to provide a robust control of meristematic activity. Despite this fundamental connection, our understanding of how meristems sense and respond to hydraulic changes is only beginning to emerge. Thus, integrating insights from research on plant stress and development opens exciting avenues to study meristem plasticity.

@article{alonso-serra_water_2024,
	title = {Water fluxes pattern growth and identity in shoot meristems},
	volume = {15},
	copyright = {2024 The Author(s)},
	issn = {2041-1723},
	url = {https://www.nature.com/articles/s41467-024-51099-x},
	doi = {10.1038/s41467-024-51099-x},
	abstract = {In multicellular organisms, tissue outgrowth creates a new water sink, modifying local hydraulic patterns. Although water fluxes are often considered passive by-products of development, their contribution to morphogenesis remains largely unexplored. Here, we mapped cell volumetric growth across the shoot apex in Arabidopsis thaliana. We found that, as organs grow, a subpopulation of cells at the organ-meristem boundary shrinks. Growth simulations using a model that integrates hydraulics and mechanics revealed water fluxes and predicted a water deficit for boundary cells. In planta, a water-soluble dye preferentially allocated to fast-growing tissues and failed to enter the boundary domain. Cell shrinkage next to fast-growing domains was also robust to different growth conditions and different topographies. Finally, a molecular signature of water deficit at the boundary confirmed our conclusion. Taken together, we propose that the differential sink strength of emerging organs prescribes the hydraulic patterns that define boundary domains at the shoot apex.},
	language = {en},
	number = {1},
	urldate = {2025-10-08},
	journal = {Nature Communications},
	publisher = {Nature Publishing Group},
	author = {Alonso-Serra, Juan and Cheddadi, Ibrahim and Kiss, Annamaria and Cerutti, Guillaume and Lang, Marianne and Dieudonné, Sana and Lionnet, Claire and Godin, Christophe and Hamant, Olivier},
	month = aug,
	year = {2024},
	keywords = {Computational biophysics, Patterning, Plant morphogenesis},
	pages = {6944},
}

In multicellular organisms, tissue outgrowth creates a new water sink, modifying local hydraulic patterns. Although water fluxes are often considered passive by-products of development, their contribution to morphogenesis remains largely unexplored. Here, we mapped cell volumetric growth across the shoot apex in Arabidopsis thaliana. We found that, as organs grow, a subpopulation of cells at the organ-meristem boundary shrinks. Growth simulations using a model that integrates hydraulics and mechanics revealed water fluxes and predicted a water deficit for boundary cells. In planta, a water-soluble dye preferentially allocated to fast-growing tissues and failed to enter the boundary domain. Cell shrinkage next to fast-growing domains was also robust to different growth conditions and different topographies. Finally, a molecular signature of water deficit at the boundary confirmed our conclusion. Taken together, we propose that the differential sink strength of emerging organs prescribes the hydraulic patterns that define boundary domains at the shoot apex.

@article{bourdon_ectopic_2023,
	title = {Ectopic callose deposition into woody biomass modulates the nano-architecture of macrofibrils},
	volume = {9},
	copyright = {2023 The Author(s)},
	issn = {2055-0278},
	url = {https://www.nature.com/articles/s41477-023-01459-0},
	doi = {10.1038/s41477-023-01459-0},
	abstract = {Plant biomass plays an increasingly important role in the circular bioeconomy, replacing non-renewable fossil resources. Genetic engineering of this lignocellulosic biomass could benefit biorefinery transformation chains by lowering economic and technological barriers to industrial processing. However, previous efforts have mostly targeted the major constituents of woody biomass: cellulose, hemicellulose and lignin. Here we report the engineering of wood structure through the introduction of callose, a polysaccharide novel to most secondary cell walls. Our multiscale analysis of genetically engineered poplar trees shows that callose deposition modulates cell wall porosity, water and lignin contents and increases the lignin–cellulose distance, ultimately resulting in substantially decreased biomass recalcitrance. We provide a model of the wood cell wall nano-architecture engineered to accommodate the hydrated callose inclusions. Ectopic polymer introduction into biomass manifests in new physico-chemical properties and offers new avenues when considering lignocellulose engineering.},
	language = {en},
	number = {9},
	urldate = {2023-09-22},
	journal = {Nature Plants},
	publisher = {Nature Publishing Group},
	author = {Bourdon, Matthieu and Lyczakowski, Jan J. and Cresswell, Rosalie and Amsbury, Sam and Vilaplana, Francisco and Le Guen, Marie-Joo and Follain, Nadège and Wightman, Raymond and Su, Chang and Alatorre-Cobos, Fulgencio and Ritter, Maximilian and Liszka, Aleksandra and Terrett, Oliver M. and Yadav, Shri Ram and Vatén, Anne and Nieminen, Kaisa and Eswaran, Gugan and Alonso-Serra, Juan and Müller, Karin H. and Iuga, Dinu and Miskolczi, Pal Csaba and Kalmbach, Lothar and Otero, Sofia and Mähönen, Ari Pekka and Bhalerao, Rishikesh and Bulone, Vincent and Mansfield, Shawn D. and Hill, Stefan and Burgert, Ingo and Beaugrand, Johnny and Benitez-Alfonso, Yoselin and Dupree, Ray and Dupree, Paul and Helariutta, Ykä},
	month = sep,
	year = {2023},
	note = {Number: 9},
	keywords = {Biofuels, Molecular engineering in plants},
	pages = {1530--1546},
}

Plant biomass plays an increasingly important role in the circular bioeconomy, replacing non-renewable fossil resources. Genetic engineering of this lignocellulosic biomass could benefit biorefinery transformation chains by lowering economic and technological barriers to industrial processing. However, previous efforts have mostly targeted the major constituents of woody biomass: cellulose, hemicellulose and lignin. Here we report the engineering of wood structure through the introduction of callose, a polysaccharide novel to most secondary cell walls. Our multiscale analysis of genetically engineered poplar trees shows that callose deposition modulates cell wall porosity, water and lignin contents and increases the lignin–cellulose distance, ultimately resulting in substantially decreased biomass recalcitrance. We provide a model of the wood cell wall nano-architecture engineered to accommodate the hydrated callose inclusions. Ectopic polymer introduction into biomass manifests in new physico-chemical properties and offers new avenues when considering lignocellulose engineering.

@article{su_tree_2023,
	title = {Tree architecture: {A} strigolactone-deficient mutant reveals a connection between branching order and auxin gradient along the tree stem},
	volume = {120},
	shorttitle = {Tree architecture},
	url = {https://www.pnas.org/doi/10.1073/pnas.2308587120},
	doi = {10.1073/pnas.2308587120},
	abstract = {Due to their long lifespan, trees and bushes develop higher order of branches in a perennial manner. In contrast to a tall tree, with a clearly defined main stem and branching order, a bush is shorter and has a less apparent main stem and branching pattern. To address the developmental basis of these two forms, we studied several naturally occurring architectural variants in silver birch (Betula pendula). Using a candidate gene approach, we identified a bushy kanttarelli variant with a loss-of-function mutation in the BpMAX1 gene required for strigolactone (SL) biosynthesis. While kanttarelli is shorter than the wild type (WT), it has the same number of primary branches, whereas the number of secondary branches is increased, contributing to its bush-like phenotype. To confirm that the identified mutation was responsible for the phenotype, we phenocopied kanttarelli in transgenic BpMAX1::RNAi birch lines. SL profiling confirmed that both kanttarelli and the transgenic lines produced very limited amounts of SL. Interestingly, the auxin (IAA) distribution along the main stem differed between WT and BpMAX1::RNAi. In the WT, the auxin concentration formed a gradient, being higher in the uppermost internodes and decreasing toward the basal part of the stem, whereas in the transgenic line, this gradient was not observed. Through modeling, we showed that the different IAA distribution patterns may result from the difference in the number of higher-order branches and plant height. Future studies will determine whether the IAA gradient itself regulates aspects of plant architecture.},
	number = {48},
	urldate = {2023-11-24},
	journal = {Proceedings of the National Academy of Sciences},
	publisher = {Proceedings of the National Academy of Sciences},
	author = {Su, Chang and Kokosza, Andrzej and Xie, Xiaonan and Pěnčík, Aleš and Zhang, Youjun and Raumonen, Pasi and Shi, Xueping and Muranen, Sampo and Topcu, Melis Kucukoglu and Immanen, Juha and Hagqvist, Risto and Safronov, Omid and Alonso-Serra, Juan and Eswaran, Gugan and Venegas, Mirko Pavicic and Ljung, Karin and Ward, Sally and Mähönen, Ari Pekka and Himanen, Kristiina and Salojärvi, Jarkko and Fernie, Alisdair R. and Novák, Ondřej and Leyser, Ottoline and Pałubicki, Wojtek and Helariutta, Ykä and Nieminen, Kaisa},
	month = nov,
	year = {2023},
	pages = {e2308587120},
}

Due to their long lifespan, trees and bushes develop higher order of branches in a perennial manner. In contrast to a tall tree, with a clearly defined main stem and branching order, a bush is shorter and has a less apparent main stem and branching pattern. To address the developmental basis of these two forms, we studied several naturally occurring architectural variants in silver birch (Betula pendula). Using a candidate gene approach, we identified a bushy kanttarelli variant with a loss-of-function mutation in the BpMAX1 gene required for strigolactone (SL) biosynthesis. While kanttarelli is shorter than the wild type (WT), it has the same number of primary branches, whereas the number of secondary branches is increased, contributing to its bush-like phenotype. To confirm that the identified mutation was responsible for the phenotype, we phenocopied kanttarelli in transgenic BpMAX1::RNAi birch lines. SL profiling confirmed that both kanttarelli and the transgenic lines produced very limited amounts of SL. Interestingly, the auxin (IAA) distribution along the main stem differed between WT and BpMAX1::RNAi. In the WT, the auxin concentration formed a gradient, being higher in the uppermost internodes and decreasing toward the basal part of the stem, whereas in the transgenic line, this gradient was not observed. Through modeling, we showed that the different IAA distribution patterns may result from the difference in the number of higher-order branches and plant height. Future studies will determine whether the IAA gradient itself regulates aspects of plant architecture.

@article{alonso-serra_carbon_2021,
	title = {Carbon sequestration: counterintuitive feedback of plant growth},
	volume = {2},
	issn = {2632-8828},
	shorttitle = {Carbon sequestration},
	url = {https://pmc.ncbi.nlm.nih.gov/articles/PMC10095961/},
	doi = {10.1017/qpb.2021.11},
	abstract = {Interaction between the atmosphere, plants and soils plays an important role in the carbon cycle. Soils contain vast amounts of carbon, but their capacity to keep it belowground depends on the long-term ecosystem dynamics. Plant growth has the potential of adding or releasing carbon from soil stocks. Since plant growth is also stimulated by higher CO2 levels, understanding its impact on soils becomes crucial for estimating carbon sequestration at the ecosystem level. A recent meta-analysis explored the effect CO2 levels have in plant versus soil carbon sequestration. The integration of 108 experiments performed across different environments revealed that the magnitude of plant growth and the nutrient acquisition strategy result in counterintuitive feedback for soil carbon sequestration.},
	urldate = {2025-10-08},
	journal = {Quantitative Plant Biology},
	author = {Alonso-Serra, Juan},
	month = sep,
	year = {2021},
	pages = {e11},
}

Interaction between the atmosphere, plants and soils plays an important role in the carbon cycle. Soils contain vast amounts of carbon, but their capacity to keep it belowground depends on the long-term ecosystem dynamics. Plant growth has the potential of adding or releasing carbon from soil stocks. Since plant growth is also stimulated by higher CO2 levels, understanding its impact on soils becomes crucial for estimating carbon sequestration at the ecosystem level. A recent meta-analysis explored the effect CO2 levels have in plant versus soil carbon sequestration. The integration of 108 experiments performed across different environments revealed that the magnitude of plant growth and the nutrient acquisition strategy result in counterintuitive feedback for soil carbon sequestration.

@article{trinh_how_2021,
	title = {How {Mechanical} {Forces} {Shape} {Plant} {Organs}},
	volume = {31},
	issn = {0960-9822},
	url = {https://www.sciencedirect.com/science/article/pii/S0960982220318200},
	doi = {10.1016/j.cub.2020.12.001},
	abstract = {Plants produce organs of various shapes and sizes. While much has been learned about genetic regulation of organogenesis, the integration of mechanics in the process is also gaining attention. Here, we consider the role of forces as instructive signals in organ morphogenesis. Turgor pressure is the primary cause of mechanical signals in developing organs. Because plant cells are glued to each other, mechanical signals act, in essence, at multiple scales, through cell wall contiguity and water flux. In turn, cells use such signals to resist mechanical stress, for instance, by reinforcing their cell walls. We show that the three elemental shapes behind plant organs — spheres, cylinders and lamina — can be actively maintained by such a mechanical feedback. Combinations of this 3-letter alphabet can generate more complex shapes. Furthermore, mechanical conflicts emerge at the boundary between domains exhibiting different growth rates or directions. These secondary mechanical signals contribute to three other organ shape features — folds, shape reproducibility and growth arrest. The further integration of mechanical signals with the molecular network offers many fruitful prospects for the scientific community, including the role of proprioception in organ shape robustness or the definition of cell and organ identities as a result of an interplay between biochemical and mechanical signals.},
	number = {3},
	urldate = {2025-10-08},
	journal = {Current Biology},
	author = {Trinh, Duy-Chi and Alonso-Serra, Juan and Asaoka, Mariko and Colin, Leia and Cortes, Matthieu and Malivert, Alice and Takatani, Shogo and Zhao, Feng and Traas, Jan and Trehin, Christophe and Hamant, Olivier},
	month = feb,
	year = {2021},
	pages = {R143--R159},
}

Plants produce organs of various shapes and sizes. While much has been learned about genetic regulation of organogenesis, the integration of mechanics in the process is also gaining attention. Here, we consider the role of forces as instructive signals in organ morphogenesis. Turgor pressure is the primary cause of mechanical signals in developing organs. Because plant cells are glued to each other, mechanical signals act, in essence, at multiple scales, through cell wall contiguity and water flux. In turn, cells use such signals to resist mechanical stress, for instance, by reinforcing their cell walls. We show that the three elemental shapes behind plant organs — spheres, cylinders and lamina — can be actively maintained by such a mechanical feedback. Combinations of this 3-letter alphabet can generate more complex shapes. Furthermore, mechanical conflicts emerge at the boundary between domains exhibiting different growth rates or directions. These secondary mechanical signals contribute to three other organ shape features — folds, shape reproducibility and growth arrest. The further integration of mechanical signals with the molecular network offers many fruitful prospects for the scientific community, including the role of proprioception in organ shape robustness or the definition of cell and organ identities as a result of an interplay between biochemical and mechanical signals.

@article{fal_tissue_2021,
	title = {Tissue folding at the organ–meristem boundary results in nuclear compression and chromatin compaction},
	volume = {118},
	url = {https://www.pnas.org/doi/10.1073/pnas.2017859118},
	doi = {10.1073/pnas.2017859118},
	abstract = {Artificial mechanical perturbations affect chromatin in animal cells in culture. Whether this is also relevant to growing tissues in living organisms remains debated. In plants, aerial organ emergence occurs through localized outgrowth at the periphery of the shoot apical meristem, which also contains a stem cell niche. Interestingly, organ outgrowth has been proposed to generate compression in the saddle-shaped organ–meristem boundary domain. Yet whether such growth-induced mechanical stress affects chromatin in plant tissues is unknown. Here, by imaging the nuclear envelope in vivo over time and quantifying nucleus deformation, we demonstrate the presence of active nuclear compression in that domain. We developed a quantitative pipeline amenable to identifying a subset of very deformed nuclei deep in the boundary and in which nuclei become gradually narrower and more elongated as the cell contracts transversely. In this domain, we find that the number of chromocenters is reduced, as shown by chromatin staining and labeling, and that the expression of linker histone H1.3 is induced. As further evidence of the role of forces on chromatin changes, artificial compression with a MicroVice could induce the ectopic expression of H1.3 in the rest of the meristem. Furthermore, while the methylation status of chromatin was correlated with nucleus deformation at the meristem boundary, such correlation was lost in the h1.3 mutant. Altogether, we reveal that organogenesis in plants generates compression that is able to have global effects on chromatin in individual cells.},
	number = {8},
	urldate = {2025-10-08},
	journal = {Proceedings of the National Academy of Sciences},
	publisher = {Proceedings of the National Academy of Sciences},
	author = {Fal, Kateryna and Korsbo, Niklas and Alonso-Serra, Juan and Teles, Jose and Liu, Mengying and Refahi, Yassin and Chabouté, Marie-Edith and Jönsson, Henrik and Hamant, Olivier},
	month = feb,
	year = {2021},
	pages = {e2017859118},
}

Artificial mechanical perturbations affect chromatin in animal cells in culture. Whether this is also relevant to growing tissues in living organisms remains debated. In plants, aerial organ emergence occurs through localized outgrowth at the periphery of the shoot apical meristem, which also contains a stem cell niche. Interestingly, organ outgrowth has been proposed to generate compression in the saddle-shaped organ–meristem boundary domain. Yet whether such growth-induced mechanical stress affects chromatin in plant tissues is unknown. Here, by imaging the nuclear envelope in vivo over time and quantifying nucleus deformation, we demonstrate the presence of active nuclear compression in that domain. We developed a quantitative pipeline amenable to identifying a subset of very deformed nuclei deep in the boundary and in which nuclei become gradually narrower and more elongated as the cell contracts transversely. In this domain, we find that the number of chromocenters is reduced, as shown by chromatin staining and labeling, and that the expression of linker histone H1.3 is induced. As further evidence of the role of forces on chromatin changes, artificial compression with a MicroVice could induce the ectopic expression of H1.3 in the rest of the meristem. Furthermore, while the methylation status of chromatin was correlated with nucleus deformation at the meristem boundary, such correlation was lost in the h1.3 mutant. Altogether, we reveal that organogenesis in plants generates compression that is able to have global effects on chromatin in individual cells.

@article{alonso-serra_elimaki_2020,
	title = {{ELIMÄKI} {Locus} {Is} {Required} for {Vertical} {Proprioceptive} {Response} in {Birch} {Trees}},
	volume = {30},
	issn = {09609822},
	url = {https://linkinghub.elsevier.com/retrieve/pii/S0960982219316112},
	doi = {10.1016/j.cub.2019.12.016},
	language = {en},
	number = {4},
	urldate = {2021-06-07},
	journal = {Current Biology},
	author = {Alonso-Serra, Juan and Shi, Xueping and Peaucelle, Alexis and Rastas, Pasi and Bourdon, Matthieu and Immanen, Juha and Takahashi, Junko and Koivula, Hanna and Eswaran, Gugan and Muranen, Sampo and Help, Hanna and Smolander, Olli-Pekka and Su, Chang and Safronov, Omid and Gerber, Lorenz and Salojärvi, Jarkko and Hagqvist, Risto and Mähönen, Ari Pekka and Helariutta, Ykä and Nieminen, Kaisa},
	month = feb,
	year = {2020},
	pages = {589--599.e5},
}

@inproceedings{hyvonen_coded_2019,
	title = {Coded {Acoustic} {Microscopy} to {Study} {Wood} {Mechanics} and {Development}},
	issn = {1948-5727},
	url = {https://ieeexplore.ieee.org/document/8926285},
	doi = {10.1109/ULTSYM.2019.8926285},
	abstract = {We have developed a coded excitation scanning acoustic microscope (CESAM) that operates in range of 0.1 to 1 GHz. We used a focusing transducer with 375 MHz central frequency to image two different tree species (birch and hybrid aspen) at different stem height to study their micromechanical difference. The method was able to capture the fresh wood anatomy with cellular resolution. A full stem section scan revealed the heterogeneity of micromechanical properties throughout tissues, and highlighted the higher stiffness of the phloem fibers compared to other vascular cells. This demonstrates the applicability of the method for plant developmental biology.},
	urldate = {2025-10-08},
	booktitle = {2019 {IEEE} {International} {Ultrasonics} {Symposium} ({IUS})},
	author = {Hyvönen, Jere and Serra, Juan Alonso and Meriläinen, Antti and Help-Rinta-Rahko, Hanna and Nieminen, Kaisa and Salmi, Ari and Svedström, Kirsi and Helariutta, Yrjö and Haeggström, Edward},
	month = oct,
	year = {2019},
	keywords = {Acoustic impedance, Acoustic microscopy, Acoustics, Image resolution, Imaging, Impedance, Microscopy, Optical microscopy, Vegetation, Wood developmental biology},
	pages = {1989--1991},
}

We have developed a coded excitation scanning acoustic microscope (CESAM) that operates in range of 0.1 to 1 GHz. We used a focusing transducer with 375 MHz central frequency to image two different tree species (birch and hybrid aspen) at different stem height to study their micromechanical difference. The method was able to capture the fresh wood anatomy with cellular resolution. A full stem section scan revealed the heterogeneity of micromechanical properties throughout tissues, and highlighted the higher stiffness of the phloem fibers compared to other vascular cells. This demonstrates the applicability of the method for plant developmental biology.

@article{alonso-serra_tissue-specific_2019,
	title = {Tissue-specific study across the stem reveals the chemistry and transcriptome dynamics of birch bark},
	volume = {222},
	copyright = {© 2019 The Authors. New Phytologist © 2019 New Phytologist Trust},
	issn = {1469-8137},
	url = {https://onlinelibrary.wiley.com/doi/abs/10.1111/nph.15725},
	doi = {10.1111/nph.15725},
	abstract = {Tree bark is a highly specialized array of tissues that plays important roles in plant protection and development. Bark tissues develop from two lateral meristems; the phellogen (cork cambium) produces the outermost stem–environment barrier called the periderm, while the vascular cambium contributes with phloem tissues. Although bark is diverse in terms of tissues, functions and species, it remains understudied at higher resolution. We dissected the stem of silver birch (Betula pendula) into eight major tissue types, and characterized these by a combined transcriptomics and metabolomics approach. We further analyzed the varying bark types within the Betulaceae family. The two meristems had a distinct contribution to the stem transcriptomic landscape. Furthermore, inter- and intraspecies analyses illustrated the unique molecular profile of the phellem. We identified multiple tissue-specific metabolic pathways, such as the mevalonate/betulin biosynthesis pathway, that displayed differential evolution within the Betulaceae. A detailed analysis of suberin and betulin biosynthesis pathways identified a set of underlying regulators and highlighted the important role of local, small-scale gene duplication events in the evolution of metabolic pathways. This work reveals the transcriptome and metabolic diversity among bark tissues and provides insights to its development and evolution, as well as its biotechnological applications.},
	language = {en},
	number = {4},
	urldate = {2025-10-08},
	journal = {New Phytologist},
	author = {Alonso-Serra, Juan and Safronov, Omid and Lim, Kean-Jin and Fraser-Miller, Sara J. and Blokhina, Olga B. and Campilho, Ana and Chong, Sun-Li and Fagerstedt, Kurt and Haavikko, Raisa and Helariutta, Ykä and Immanen, Juha and Kangasjärvi, Jaakko and Kauppila, Tiina J. and Lehtonen, Mari and Ragni, Laura and Rajaraman, Sitaram and Räsänen, Riikka-Marjaana and Safdari, Pezhman and Tenkanen, Maija and Yli-Kauhaluoma, Jari T. and Teeri, Teemu H. and Strachan, Clare J. and Nieminen, Kaisa and Salojärvi, Jarkko},
	year = {2019},
	note = {\_eprint: https://nph.onlinelibrary.wiley.com/doi/pdf/10.1111/nph.15725},
	keywords = {Betula pendula (silver birch), bark, cambium, genome evolution, metabolic pathways, periderm, phellem, phellogen},
	pages = {1816--1831},
}

Tree bark is a highly specialized array of tissues that plays important roles in plant protection and development. Bark tissues develop from two lateral meristems; the phellogen (cork cambium) produces the outermost stem–environment barrier called the periderm, while the vascular cambium contributes with phloem tissues. Although bark is diverse in terms of tissues, functions and species, it remains understudied at higher resolution. We dissected the stem of silver birch (Betula pendula) into eight major tissue types, and characterized these by a combined transcriptomics and metabolomics approach. We further analyzed the varying bark types within the Betulaceae family. The two meristems had a distinct contribution to the stem transcriptomic landscape. Furthermore, inter- and intraspecies analyses illustrated the unique molecular profile of the phellem. We identified multiple tissue-specific metabolic pathways, such as the mevalonate/betulin biosynthesis pathway, that displayed differential evolution within the Betulaceae. A detailed analysis of suberin and betulin biosynthesis pathways identified a set of underlying regulators and highlighted the important role of local, small-scale gene duplication events in the evolution of metabolic pathways. This work reveals the transcriptome and metabolic diversity among bark tissues and provides insights to its development and evolution, as well as its biotechnological applications.

@article{zhang_transcriptional_2019,
	title = {Transcriptional regulatory framework for vascular cambium development in {Arabidopsis} roots},
	volume = {5},
	copyright = {2019 The Author(s), under exclusive licence to Springer Nature Limited},
	issn = {2055-0278},
	url = {https://www.nature.com/articles/s41477-019-0522-9},
	doi = {10.1038/s41477-019-0522-9},
	abstract = {Vascular cambium, a lateral plant meristem, is a central producer of woody biomass. Although a few transcription factors have been shown to regulate cambial activity1, the phenotypes of the corresponding loss-of-function mutants are relatively modest, highlighting our limited understanding of the underlying transcriptional regulation. Here, we use cambium cell-specific transcript profiling followed by a combination of transcription factor network and genetic analyses to identify 62 new transcription factor genotypes displaying an array of cambial phenotypes. This approach culminated in virtual loss of cambial activity when both WUSCHEL-RELATED HOMEOBOX 4 (WOX4) and KNOTTED-like from Arabidopsis thaliana 1 (KNAT1; also known as BREVIPEDICELLUS) were mutated, thereby unlocking the genetic redundancy in the regulation of cambium development. We also identified transcription factors with dual functions in cambial cell proliferation and xylem differentiation, including WOX4, SHORT VEGETATIVE PHASE (SVP) and PETAL LOSS (PTL). Using the transcription factor network information, we combined overexpression of the cambial activator WOX4 and removal of the putative inhibitor PTL to engineer Arabidopsis for enhanced radial growth. This line also showed ectopic cambial activity, thus further highlighting the central roles of WOX4 and PTL in cambium development.},
	language = {en},
	number = {10},
	urldate = {2025-10-08},
	journal = {Nature Plants},
	publisher = {Nature Publishing Group},
	author = {Zhang, Jing and Eswaran, Gugan and Alonso-Serra, Juan and Kucukoglu, Melis and Xiang, Jiale and Yang, Weibing and Elo, Annakaisa and Nieminen, Kaisa and Damén, Teddy and Joung, Je-Gun and Yun, Jae-Young and Lee, Jung-Hun and Ragni, Laura and Barbier de Reuille, Pierre and Ahnert, Sebastian E. and Lee, Ji-Young and Mähönen, Ari Pekka and Helariutta, Ykä},
	month = oct,
	year = {2019},
	keywords = {Plant development, Plant genetics},
	pages = {1033--1042},
}

Vascular cambium, a lateral plant meristem, is a central producer of woody biomass. Although a few transcription factors have been shown to regulate cambial activity1, the phenotypes of the corresponding loss-of-function mutants are relatively modest, highlighting our limited understanding of the underlying transcriptional regulation. Here, we use cambium cell-specific transcript profiling followed by a combination of transcription factor network and genetic analyses to identify 62 new transcription factor genotypes displaying an array of cambial phenotypes. This approach culminated in virtual loss of cambial activity when both WUSCHEL-RELATED HOMEOBOX 4 (WOX4) and KNOTTED-like from Arabidopsis thaliana 1 (KNAT1; also known as BREVIPEDICELLUS) were mutated, thereby unlocking the genetic redundancy in the regulation of cambium development. We also identified transcription factors with dual functions in cambial cell proliferation and xylem differentiation, including WOX4, SHORT VEGETATIVE PHASE (SVP) and PETAL LOSS (PTL). Using the transcription factor network information, we combined overexpression of the cambial activator WOX4 and removal of the putative inhibitor PTL to engineer Arabidopsis for enhanced radial growth. This line also showed ectopic cambial activity, thus further highlighting the central roles of WOX4 and PTL in cambium development.

@article{salojarvi_genome_2017,
	title = {Genome sequencing and population genomic analyses provide insights into the adaptive landscape of silver birch},
	volume = {49},
	issn = {1061-4036, 1546-1718},
	url = {http://www.nature.com/articles/ng.3862},
	doi = {10/f96grj},
	abstract = {Abstract
            
              Silver birch (
              Betula pendula
              ) is a pioneer boreal tree that can be induced to flower within 1 year. Its rapid life cycle, small (440-Mb) genome, and advanced germplasm resources make birch an attractive model for forest biotechnology. We assembled and chromosomally anchored the nuclear genome of an inbred
              B. pendula
              individual. Gene duplicates from the paleohexaploid event were enriched for transcriptional regulation, whereas tandem duplicates were overrepresented by environmental responses. Population resequencing of 80 individuals showed effective population size crashes at major points of climatic upheaval. Selective sweeps were enriched among polyploid duplicates encoding key developmental and physiological triggering functions, suggesting that local adaptation has tuned the timing of and cross-talk between fundamental plant processes. Variation around the tightly-linked light response genes
              PHYC
              and
              FRS10
              correlated with latitude and longitude and temperature, and with precipitation for
              PHYC
              . Similar associations characterized the growth-promoting cytokinin response regulator ARR1, and the wood development genes
              KAK
              and
              MED5A
              .},
	language = {en},
	number = {6},
	urldate = {2021-06-07},
	journal = {Nature Genetics},
	author = {Salojärvi, Jarkko and Smolander, Olli-Pekka and Nieminen, Kaisa and Rajaraman, Sitaram and Safronov, Omid and Safdari, Pezhman and Lamminmäki, Airi and Immanen, Juha and Lan, Tianying and Tanskanen, Jaakko and Rastas, Pasi and Amiryousefi, Ali and Jayaprakash, Balamuralikrishna and Kammonen, Juhana I and Hagqvist, Risto and Eswaran, Gugan and Ahonen, Viivi Helena and Serra, Juan Alonso and Asiegbu, Fred O and de Dios Barajas-Lopez, Juan and Blande, Daniel and Blokhina, Olga and Blomster, Tiina and Broholm, Suvi and Brosché, Mikael and Cui, Fuqiang and Dardick, Chris and Ehonen, Sanna E and Elomaa, Paula and Escamez, Sacha and Fagerstedt, Kurt V and Fujii, Hiroaki and Gauthier, Adrien and Gollan, Peter J and Halimaa, Pauliina and Heino, Pekka I and Himanen, Kristiina and Hollender, Courtney and Kangasjärvi, Saijaliisa and Kauppinen, Leila and Kelleher, Colin T and Kontunen-Soppela, Sari and Koskinen, J Patrik and Kovalchuk, Andriy and Kärenlampi, Sirpa O and Kärkönen, Anna K and Lim, Kean-Jin and Leppälä, Johanna and Macpherson, Lee and Mikola, Juha and Mouhu, Katriina and Mähönen, Ari Pekka and Niinemets, Ülo and Oksanen, Elina and Overmyer, Kirk and Palva, E Tapio and Pazouki, Leila and Pennanen, Ville and Puhakainen, Tuula and Poczai, Péter and Possen, Boy J H M and Punkkinen, Matleena and Rahikainen, Moona M and Rousi, Matti and Ruonala, Raili and van der Schoot, Christiaan and Shapiguzov, Alexey and Sierla, Maija and Sipilä, Timo P and Sutela, Suvi and Teeri, Teemu H and Tervahauta, Arja I and Vaattovaara, Aleksia and Vahala, Jorma and Vetchinnikova, Lidia and Welling, Annikki and Wrzaczek, Michael and Xu, Enjun and Paulin, Lars G and Schulman, Alan H and Lascoux, Martin and Albert, Victor A and Auvinen, Petri and Helariutta, Ykä and Kangasjärvi, Jaakko},
	month = jun,
	year = {2017},
	pages = {904--912},
}

Abstract Silver birch ( Betula pendula ) is a pioneer boreal tree that can be induced to flower within 1 year. Its rapid life cycle, small (440-Mb) genome, and advanced germplasm resources make birch an attractive model for forest biotechnology. We assembled and chromosomally anchored the nuclear genome of an inbred B. pendula individual. Gene duplicates from the paleohexaploid event were enriched for transcriptional regulation, whereas tandem duplicates were overrepresented by environmental responses. Population resequencing of 80 individuals showed effective population size crashes at major points of climatic upheaval. Selective sweeps were enriched among polyploid duplicates encoding key developmental and physiological triggering functions, suggesting that local adaptation has tuned the timing of and cross-talk between fundamental plant processes. Variation around the tightly-linked light response genes PHYC and FRS10 correlated with latitude and longitude and temperature, and with precipitation for PHYC . Similar associations characterized the growth-promoting cytokinin response regulator ARR1, and the wood development genes KAK and MED5A .

@article{fagerstedt_determining_2015,
	title = {Determining the {Composition} of {Lignins} in {Different} {Tissues} of {Silver} {Birch}},
	volume = {4},
	copyright = {http://creativecommons.org/licenses/by/3.0/},
	issn = {2223-7747},
	url = {https://www.mdpi.com/2223-7747/4/2/183},
	doi = {10.3390/plants4020183},
	abstract = {Quantitative and qualitative lignin analyses were carried out on material from the trunks of silver birch (Betula pendula Roth) trees. Two types of material were analyzed. First, whole birch trunk pieces were cryosectioned into cork cambium, non-conductive phloem, the cambial zone (conductive phloem, cambium and differentiating xylem), lignified xylem and the previous year’s xylem; material that would show differences in lignin amount and quality. Second, clonal material from one natural birch population was analyzed to show variations between individuals and between the lignin analysis methods. The different tissues showed marked differences in lignin amount and the syringyl:guaiacyl (S/G) ratio. In the non-conductive phloem tissue containing sclereids, the S/G ratio was very low, and typical for phloem fibers and in the newly-formed xylem, as well as in the previous year’s xylem, the ratio lay between five and seven, typical for broadleaf tree xylem. Clonal material consisting of 88 stems was used to calculate the S/G ratios from the thioacidolysis and CuO methods, which correlated positively with an R2 value of 0.43. Comparisons of the methods indicate clearly that the CuO method is a good alternative to study the monomeric composition and S/G ratio of wood lignins.},
	language = {en},
	number = {2},
	urldate = {2025-10-08},
	journal = {Plants},
	publisher = {Multidisciplinary Digital Publishing Institute},
	author = {Fagerstedt, Kurt V. and Saranpää, Pekka and Tapanila, Tarja and Immanen, Juha and Serra, Juan Antonio Alonso and Nieminen, Kaisa},
	month = jun,
	year = {2015},
	keywords = {\textit{Betula pendula}, acetyl bromide, cupric oxide, lignin analysis methods, phloem, thioacidolysis, xylem},
	pages = {183--195},
}

Quantitative and qualitative lignin analyses were carried out on material from the trunks of silver birch (Betula pendula Roth) trees. Two types of material were analyzed. First, whole birch trunk pieces were cryosectioned into cork cambium, non-conductive phloem, the cambial zone (conductive phloem, cambium and differentiating xylem), lignified xylem and the previous year’s xylem; material that would show differences in lignin amount and quality. Second, clonal material from one natural birch population was analyzed to show variations between individuals and between the lignin analysis methods. The different tissues showed marked differences in lignin amount and the syringyl:guaiacyl (S/G) ratio. In the non-conductive phloem tissue containing sclereids, the S/G ratio was very low, and typical for phloem fibers and in the newly-formed xylem, as well as in the previous year’s xylem, the ratio lay between five and seven, typical for broadleaf tree xylem. Clonal material consisting of 88 stems was used to calculate the S/G ratios from the thioacidolysis and CuO methods, which correlated positively with an R2 value of 0.43. Comparisons of the methods indicate clearly that the CuO method is a good alternative to study the monomeric composition and S/G ratio of wood lignins.

@article{zhang_wood_2015,
	title = {Wood development: {Growth} through knowledge},
	volume = {1},
	copyright = {2015 Macmillan Publishers Limited},
	issn = {2055-0278},
	shorttitle = {Wood development},
	url = {https://www.nature.com/articles/nplants201560},
	doi = {10.1038/nplants.2015.60},
	abstract = {Overexpressing a receptor–ligand pair specifically in their native tissue domains dramatically promotes wood formation and biomass production in trees.},
	language = {en},
	number = {5},
	urldate = {2025-10-08},
	journal = {Nature Plants},
	publisher = {Nature Publishing Group},
	author = {Zhang, Jing and Serra, Juan Antonio Alonso and Helariutta, Ykä},
	month = may,
	year = {2015},
	keywords = {Patterning, Plant biotechnology, Plant stem cell},
	pages = {15060},
}

Overexpressing a receptor–ligand pair specifically in their native tissue domains dramatically promotes wood formation and biomass production in trees.

@article{zhang_formation_2014,
	series = {Growth and development},
	title = {The formation of wood and its control},
	volume = {17},
	issn = {1369-5266},
	url = {https://www.sciencedirect.com/science/article/pii/S1369526613001660},
	doi = {10.1016/j.pbi.2013.11.003},
	abstract = {Wood continues to increase in importance as a sustainable source of energy and shelter. Wood formation is a dynamic process derived from plant secondary (radial) growth. Several experimental systems have been employed to study wood formation and its regulation. The use of genetic manipulation approaches and genome-wide analyses in model plants have significantly advanced our understanding of wood formation. In this review, we provide an update of our knowledge of the genetic and hormonal regulation of wood formation based on research in different plants systems, as well as considering the subject from an evo-devo perspective.},
	urldate = {2025-10-08},
	journal = {Current Opinion in Plant Biology},
	author = {Zhang, Jing and Nieminen, Kaisa and Serra, Juan Antonio Alonso and Helariutta, Ykä},
	month = feb,
	year = {2014},
	pages = {56--63},
}

Wood continues to increase in importance as a sustainable source of energy and shelter. Wood formation is a dynamic process derived from plant secondary (radial) growth. Several experimental systems have been employed to study wood formation and its regulation. The use of genetic manipulation approaches and genome-wide analyses in model plants have significantly advanced our understanding of wood formation. In this review, we provide an update of our knowledge of the genetic and hormonal regulation of wood formation based on research in different plants systems, as well as considering the subject from an evo-devo perspective.

@article{wu_population_2025,
	title = {Population genomics of \textit{{Marchantia} polymorpha} subsp. \textit{ruderalis} reveals evidence of climate adaptation},
	volume = {35},
	issn = {0960-9822},
	url = {https://www.sciencedirect.com/science/article/pii/S0960982225000089},
	doi = {10.1016/j.cub.2025.01.008},
	abstract = {Sexual reproduction results in the development of haploid and diploid cell states during the life cycle. In bryophytes, the dominant multicellular haploid phase produces motile sperm that swim through water to the egg to effect fertilization from which a relatively small diploid phase develops. In angiosperms, the reduced multicellular haploid phase produces non-motile sperm that is delivered to the egg through a pollen tube to effect fertilization from which the dominant diploid phase develops. These different life cycle characteristics are likely to impact the distribution of genetic variation among populations. However, little is known about the distribution of genetic variation among wild populations of bryophytes. To investigate how genetic variation is distributed among populations of a bryophyte and to establish the foundation for population genetics research in bryophytes, we described the genetic diversity of collections of Marchantia polymorpha subsp. ruderalis, a cosmopolitan ruderal liverwort. We identified 78 genetically unique (non-clonal) from a total of 209 sequenced accessions collected from 37 sites in Europe and Japan. There was no detectable population structure among European populations but significant genetic differentiation between Japanese and European populations. By associating genetic variation across the genome with global climate data, we showed that temperature and precipitation influence the frequency of potentially adaptive alleles. This collection establishes the core of an experimental platform that exploits natural genetic variation to answer diverse questions in biology.},
	number = {5},
	urldate = {2025-03-28},
	journal = {Current Biology},
	author = {Wu, Shuangyang and Jandrasits, Katharina and Swarts, Kelly and Roetzer, Johannes and Akimcheva, Svetlana and Shimamura, Masaki and Hisanaga, Tetsuya and Berger, Frédéric and Dolan, Liam},
	month = mar,
	year = {2025},
	pages = {970--980.e3},
}

Sexual reproduction results in the development of haploid and diploid cell states during the life cycle. In bryophytes, the dominant multicellular haploid phase produces motile sperm that swim through water to the egg to effect fertilization from which a relatively small diploid phase develops. In angiosperms, the reduced multicellular haploid phase produces non-motile sperm that is delivered to the egg through a pollen tube to effect fertilization from which the dominant diploid phase develops. These different life cycle characteristics are likely to impact the distribution of genetic variation among populations. However, little is known about the distribution of genetic variation among wild populations of bryophytes. To investigate how genetic variation is distributed among populations of a bryophyte and to establish the foundation for population genetics research in bryophytes, we described the genetic diversity of collections of Marchantia polymorpha subsp. ruderalis, a cosmopolitan ruderal liverwort. We identified 78 genetically unique (non-clonal) from a total of 209 sequenced accessions collected from 37 sites in Europe and Japan. There was no detectable population structure among European populations but significant genetic differentiation between Japanese and European populations. By associating genetic variation across the genome with global climate data, we showed that temperature and precipitation influence the frequency of potentially adaptive alleles. This collection establishes the core of an experimental platform that exploits natural genetic variation to answer diverse questions in biology.

@article{polacek_automation_2023,
	title = {Automation of tree-ring detection and measurements using deep learning},
	volume = {14},
	copyright = {© 2023 GMI - Gregor Mendel Institute of Molecular Plant Biology. Methods in Ecology and Evolution published by John Wiley \& Sons Ltd on behalf of British Ecological Society.},
	issn = {2041-210X},
	url = {https://onlinelibrary.wiley.com/doi/abs/10.1111/2041-210X.14183},
	doi = {10.1111/2041-210X.14183},
	abstract = {Core samples from trees are a critical reservoir of ecological information, informing our understanding of past climates, as well as contemporary ecosystem responses to global change. Manual measurements of annual growth rings in trees are slow, labour-intensive and subject to human bias, hindering the generation of big datasets. We present an alternative, neural network-based implementation that automates detection and measurement of tree-ring boundaries from coniferous species. We trained our Mask R-CNN extensively on over 8000 manually annotated ring boundaries from microscope-imaged Norway Spruce Picea abies increment cores. We assessed the performance of the trained model after post-processing on real-world data generated from our core processing pipeline. The CNN after post-processing performed well, with recognition of over 98\% of ring boundaries (recall) with a precision in detection of 96\% when tested on real-world data. Additionally, we have implemented automatic measurements based on minimum distance between rings. With minimal editing for missed ring detections, these measurements were 98\% correlated with human measurements of the same samples. Tests on other three conifer species demonstrate that the CNN generalizes well to other species with similar structure. We demonstrate the efficacy of automating the measurement of growth increment in tree core samples. Our CNN-based system provides high predictive performance in terms of both tree-ring detection and growth rate determination. Our application is readily deployable as a Docker container and requires only basic command line skills. Additionally, an easy re-training option allows users to expand capabilities to other wood types. Application outputs include both editable annotations of predictions as well as ring-width measurements in a commonly used .pos format, facilitating the efficient generation of large ring-width measurement datasets from increment core samples, an important source of environmental data.},
	language = {en},
	number = {9},
	urldate = {2024-03-22},
	journal = {Methods in Ecology and Evolution},
	author = {Poláček, Miroslav and Arizpe, Alexis and Hüther, Patrick and Weidlich, Lisa and Steindl, Sonja and Swarts, Kelly},
	year = {2023},
	note = {\_eprint: https://onlinelibrary.wiley.com/doi/pdf/10.1111/2041-210X.14183},
	keywords = {automation, computer vision, mask R-CNN, phenotyping, tree rings},
	pages = {2233--2242},
}

Core samples from trees are a critical reservoir of ecological information, informing our understanding of past climates, as well as contemporary ecosystem responses to global change. Manual measurements of annual growth rings in trees are slow, labour-intensive and subject to human bias, hindering the generation of big datasets. We present an alternative, neural network-based implementation that automates detection and measurement of tree-ring boundaries from coniferous species. We trained our Mask R-CNN extensively on over 8000 manually annotated ring boundaries from microscope-imaged Norway Spruce Picea abies increment cores. We assessed the performance of the trained model after post-processing on real-world data generated from our core processing pipeline. The CNN after post-processing performed well, with recognition of over 98% of ring boundaries (recall) with a precision in detection of 96% when tested on real-world data. Additionally, we have implemented automatic measurements based on minimum distance between rings. With minimal editing for missed ring detections, these measurements were 98% correlated with human measurements of the same samples. Tests on other three conifer species demonstrate that the CNN generalizes well to other species with similar structure. We demonstrate the efficacy of automating the measurement of growth increment in tree core samples. Our CNN-based system provides high predictive performance in terms of both tree-ring detection and growth rate determination. Our application is readily deployable as a Docker container and requires only basic command line skills. Additionally, an easy re-training option allows users to expand capabilities to other wood types. Application outputs include both editable annotations of predictions as well as ring-width measurements in a commonly used .pos format, facilitating the efficient generation of large ring-width measurement datasets from increment core samples, an important source of environmental data.

@article{vallebueno-estrada_domestication_2023,
	title = {Domestication and lowland adaptation of coastal preceramic maize from {Paredones}, {Peru}},
	volume = {12},
	issn = {2050-084X},
	url = {https://doi.org/10.7554/eLife.83149},
	doi = {10.7554/eLife.83149},
	abstract = {Archaeological cobs from Paredones and Huaca Prieta (Peru) represent some of the oldest maize known to date, yet they present relevant phenotypic traits corresponding to domesticated maize. This contrasts with the earliest Mexican macro-specimens from Guila Naquitz and San Marcos, which are phenotypically intermediate for these traits, even though they date more recently in time. To gain insights into the origins of ancient Peruvian maize, we sequenced DNA from three Paredones specimens dating {\textasciitilde}6700–5000 calibrated years before present (BP), conducting comparative analyses with two teosinte subspecies (Zea mays ssp. mexicana and parviglumis) and extant maize, that include highland and lowland landraces from Mesoamerica and South America. We show that Paredones maize originated from the same domestication event as Mexican maize and was domesticated by {\textasciitilde}6700 BP, implying rapid dispersal followed by improvement. Paredones maize shows no relevant gene flow from mexicana, smaller than that observed in teosinte parviglumis. Thus, Paredones samples represent the only maize without confounding mexicana variation found to date. It also harbors significantly fewer alleles previously found to be adaptive to highlands, but not of alleles adaptive to lowlands, supporting a lowland migration route. Our overall results imply that Paredones maize originated in Mesoamerica, arrived in Peru without mexicana introgression through a rapid lowland migration route, and underwent improvements in both Mesoamerica and South America.},
	urldate = {2024-03-22},
	journal = {eLife},
	publisher = {eLife Sciences Publications, Ltd},
	author = {Vallebueno-Estrada, Miguel and Hernández-Robles, Guillermo G and González-Orozco, Eduardo and Lopez-Valdivia, Ivan and Rosales Tham, Teresa and Vásquez Sánchez, Víctor and Swarts, Kelly and Dillehay, Tom D and Vielle-Calzada, Jean-Philippe and Montiel, Rafael},
	editor = {Weigel, Detlef},
	month = apr,
	year = {2023},
	keywords = {domestication, lowlands, paleogenomics, paredones},
	pages = {e83149},
}

Archaeological cobs from Paredones and Huaca Prieta (Peru) represent some of the oldest maize known to date, yet they present relevant phenotypic traits corresponding to domesticated maize. This contrasts with the earliest Mexican macro-specimens from Guila Naquitz and San Marcos, which are phenotypically intermediate for these traits, even though they date more recently in time. To gain insights into the origins of ancient Peruvian maize, we sequenced DNA from three Paredones specimens dating ~6700–5000 calibrated years before present (BP), conducting comparative analyses with two teosinte subspecies (Zea mays ssp. mexicana and parviglumis) and extant maize, that include highland and lowland landraces from Mesoamerica and South America. We show that Paredones maize originated from the same domestication event as Mexican maize and was domesticated by ~6700 BP, implying rapid dispersal followed by improvement. Paredones maize shows no relevant gene flow from mexicana, smaller than that observed in teosinte parviglumis. Thus, Paredones samples represent the only maize without confounding mexicana variation found to date. It also harbors significantly fewer alleles previously found to be adaptive to highlands, but not of alleles adaptive to lowlands, supporting a lowland migration route. Our overall results imply that Paredones maize originated in Mesoamerica, arrived in Peru without mexicana introgression through a rapid lowland migration route, and underwent improvements in both Mesoamerica and South America.

@article{morales_heritable_2022,
	title = {Heritable and {Climatic} {Sources} of {Variation} in {Juvenile} {Tree} {Growth} in an {Austrian} {Common} {Garden} {Experiment} of {Central} {European} {Norway} {Spruce} {Populations}},
	volume = {13},
	copyright = {http://creativecommons.org/licenses/by/3.0/},
	issn = {1999-4907},
	url = {https://www.mdpi.com/1999-4907/13/5/809},
	doi = {10.3390/f13050809},
	abstract = {We leveraged publicly available data on juvenile tree height of 299 Central European Norway spruce populations grown in a common garden experiment across 24 diverse trial locations in Austria and weather data from the trial locations and population provenances to parse the heritable and climatic components of juvenile tree height variation. Principal component analysis of geospatial and weather variables demonstrated high interannual variation among trial environments, largely driven by differences in precipitation, and separation of population provenances based on altitude, temperature, and snowfall. Tree height was highly heritable and modeling the covariance between populations and trial environments based on climatic data led to more stable estimation of heritability and population × environment variance. Climatic similarity among population provenances was highly predictive of population × environment estimates for tree height.},
	language = {en},
	number = {5},
	urldate = {2024-03-22},
	journal = {Forests},
	publisher = {Multidisciplinary Digital Publishing Institute},
	author = {Morales, Laura and Swarts, Kelly},
	month = may,
	year = {2022},
	note = {Number: 5},
	keywords = {Norway spruce, climate, genotype-by-environment, prediction, tree height},
	pages = {809},
}

We leveraged publicly available data on juvenile tree height of 299 Central European Norway spruce populations grown in a common garden experiment across 24 diverse trial locations in Austria and weather data from the trial locations and population provenances to parse the heritable and climatic components of juvenile tree height variation. Principal component analysis of geospatial and weather variables demonstrated high interannual variation among trial environments, largely driven by differences in precipitation, and separation of population provenances based on altitude, temperature, and snowfall. Tree height was highly heritable and modeling the covariance between populations and trial environments based on climatic data led to more stable estimation of heritability and population × environment variance. Climatic similarity among population provenances was highly predictive of population × environment estimates for tree height.

@article{korolyova_last_2022,
	title = {The {Last} {Trees} {Standing}: {Climate} modulates tree survival factors during a prolonged bark beetle outbreak in {Europe}},
	volume = {322},
	issn = {0168-1923},
	shorttitle = {The {Last} {Trees} {Standing}},
	url = {https://www.sciencedirect.com/science/article/pii/S0168192322002143},
	doi = {10.1016/j.agrformet.2022.109025},
	abstract = {Plant traits are an expression of strategic tradeoffs in plant performance that determine variation in allocation of finite resources to alternate physiological functions. Climate factors interact with plant traits to mediate tree survival. This study investigated survival dynamics in Norway spruce (Picea abies) in relation to tree-level morphological traits during a prolonged multi-year outbreak of the bark beetle, Ips typographus, in Central Europe. We acquired datasets describing the trait attributes of individual spruce using remote sensing and field surveys. We used nonlinear regression in a hypothesis-driven framework to quantify survival probability as a function of tree size, crown morphology, intraspecific competition and a growing season water balance. Extant spruce trees that persisted through the outbreak were spatially clustered, suggesting that survival was a non-random process. Larger diameter trees were more susceptible to bark beetles, reflecting either life history tradeoffs or a dynamic interaction between defense capacity and insect aggregation behavior. Competition had a strong negative effect on survival, presumably through resource limitation. Trees with more extensive crowns were buffered against bark beetles, ostensibly by a more robust photosynthetic capability and greater carbon reserves. The outbreak spanned a warming trend and conditions of anomalous aridity. Sustained water limitation during this period amplified the consequences of other factors, rendering even smaller trees vulnerable to colonization by insects. Our results are in agreement with prior research indicating that climate change has the potential to intensify bark beetle activity. However, forest outcomes will depend on complex cross-scale interactions between global climate trends and tree-level trait factors, as well as feedback effects associated with landscape patterns of stand structural diversity.},
	urldate = {2024-03-22},
	journal = {Agricultural and Forest Meteorology},
	author = {Korolyova, Nataliya and Buechling, Arne and Ďuračiová, Renata and Zabihi, Khodabakhsh and Turčáni, Marek and Svoboda, Miroslav and Bláha, Jaromír and Swarts, Kelly and Poláček, Miroslav and Hradecký, Jaromir and Červenka, Jaroslav and Němčák, Pavel and Schlyter, Fredrik and Jakuš, Rastislav},
	month = jul,
	year = {2022},
	keywords = {Carbon, Climate change, Competition, Crown shading, Drought, Tree survival},
	pages = {109025},
}

Plant traits are an expression of strategic tradeoffs in plant performance that determine variation in allocation of finite resources to alternate physiological functions. Climate factors interact with plant traits to mediate tree survival. This study investigated survival dynamics in Norway spruce (Picea abies) in relation to tree-level morphological traits during a prolonged multi-year outbreak of the bark beetle, Ips typographus, in Central Europe. We acquired datasets describing the trait attributes of individual spruce using remote sensing and field surveys. We used nonlinear regression in a hypothesis-driven framework to quantify survival probability as a function of tree size, crown morphology, intraspecific competition and a growing season water balance. Extant spruce trees that persisted through the outbreak were spatially clustered, suggesting that survival was a non-random process. Larger diameter trees were more susceptible to bark beetles, reflecting either life history tradeoffs or a dynamic interaction between defense capacity and insect aggregation behavior. Competition had a strong negative effect on survival, presumably through resource limitation. Trees with more extensive crowns were buffered against bark beetles, ostensibly by a more robust photosynthetic capability and greater carbon reserves. The outbreak spanned a warming trend and conditions of anomalous aridity. Sustained water limitation during this period amplified the consequences of other factors, rendering even smaller trees vulnerable to colonization by insects. Our results are in agreement with prior research indicating that climate change has the potential to intensify bark beetle activity. However, forest outcomes will depend on complex cross-scale interactions between global climate trends and tree-level trait factors, as well as feedback effects associated with landscape patterns of stand structural diversity.

@article{yost_situ_2021,
	title = {An \textit{in situ} and morphometric study of maize (\textit{{Zea} mays} {L}.) cob rondel phytoliths from {Southwestern} {North} {American} landraces},
	volume = {35},
	issn = {2352-409X},
	url = {https://www.sciencedirect.com/science/article/pii/S2352409X2030523X},
	doi = {10.1016/j.jasrep.2020.102732},
	abstract = {We present the first comprehensive computer-assisted morphometric analysis of microscopic rondel11As per the International Code for Phytolith Nomenclature 2.0 the names of recognized phytolith morphotypes are written in small caps in this report (Neumann et al., 2019). phytoliths (plant opal microfossils) produced in the cobs of 24 historic Southwestern North American landraces of maize (Zea mays L.) after all were grown in a well-documented agronomic field study. We also present an in situ study of the location of rondel phytolith production within the maize cob and provide a detailed review of previous maize phytolith studies. We found that glumes contained abundant rondel phytoliths throughout the tissue; however, lemma/palea tissue contained no phytoliths. In contrast, cupule tissue had some areas with abundant phytoliths, some with fewer scattered phytoliths, and vast areas that contained no rondel phytoliths. The rondel-rich areas appear to be where the glumes had once attached to the cupule and may be remnants of glume tissue adhering to the cupule. From the morphometric study, we found there were significant differences in the size morphometries of glume rondels depending on their cob location (top, middle, base) but no significant differences in shape morphometries. Using shape morphometries, we could not discriminate reliably among maize cob rondel phytoliths produced by the diverse landraces considered. The inclusion of morphometrics from areas in addition to or in combination with the outer periclinal surface may allow for some discrimination of maize landraces and is an avenue that should be explored further. Although our approach was not successful at identifying differences between essentially modern landraces, there may be significant rondel phytolith morphometric differences between wild, progenitor, and domesticated Zea.},
	urldate = {2024-03-22},
	journal = {Journal of Archaeological Science: Reports},
	author = {Yost, Chad L. and Michas, McCaela and Adams, Karen R. and Swarts, Kelly and Puseman, Kathryn and Ball, Terry},
	month = feb,
	year = {2021},
	keywords = {Glumes, Landrace, Maize, Morphometrics, Phytoliths},
	pages = {102732},
}

We present the first comprehensive computer-assisted morphometric analysis of microscopic rondel11As per the International Code for Phytolith Nomenclature 2.0 the names of recognized phytolith morphotypes are written in small caps in this report (Neumann et al., 2019). phytoliths (plant opal microfossils) produced in the cobs of 24 historic Southwestern North American landraces of maize (Zea mays L.) after all were grown in a well-documented agronomic field study. We also present an in situ study of the location of rondel phytolith production within the maize cob and provide a detailed review of previous maize phytolith studies. We found that glumes contained abundant rondel phytoliths throughout the tissue; however, lemma/palea tissue contained no phytoliths. In contrast, cupule tissue had some areas with abundant phytoliths, some with fewer scattered phytoliths, and vast areas that contained no rondel phytoliths. The rondel-rich areas appear to be where the glumes had once attached to the cupule and may be remnants of glume tissue adhering to the cupule. From the morphometric study, we found there were significant differences in the size morphometries of glume rondels depending on their cob location (top, middle, base) but no significant differences in shape morphometries. Using shape morphometries, we could not discriminate reliably among maize cob rondel phytoliths produced by the diverse landraces considered. The inclusion of morphometrics from areas in addition to or in combination with the outer periclinal surface may allow for some discrimination of maize landraces and is an avenue that should be explored further. Although our approach was not successful at identifying differences between essentially modern landraces, there may be significant rondel phytolith morphometric differences between wild, progenitor, and domesticated Zea.

@article{hu_genome_2021,
	title = {Genome assembly and population genomic analysis provide insights into the evolution of modern sweet corn},
	volume = {12},
	copyright = {2021 The Author(s)},
	issn = {2041-1723},
	url = {https://www.nature.com/articles/s41467-021-21380-4},
	doi = {10.1038/s41467-021-21380-4},
	abstract = {Sweet corn is one of the most important vegetables in the United States and Canada. Here, we present a de novo assembly of a sweet corn inbred line Ia453 with the mutated shrunken2-reference allele (Ia453-sh2). This mutation accumulates more sugar and is present in most commercial hybrids developed for the processing and fresh markets. The ten pseudochromosomes cover 92\% of the total assembly and 99\% of the estimated genome size, with a scaffold N50 of 222.2 Mb. This reference genome completely assembles the large structural variation that created the mutant sh2-R allele. Furthermore, comparative genomics analysis with six field corn genomes highlights differences in single-nucleotide polymorphisms, structural variations, and transposon composition. Phylogenetic analysis of 5,381 diverse maize and teosinte accessions reveals genetic relationships between sweet corn and other types of maize. Our results show evidence for a common origin in northern Mexico for modern sweet corn in the U.S. Finally, population genomic analysis identifies regions of the genome under selection and candidate genes associated with sweet corn traits, such as early flowering, endosperm composition, plant and tassel architecture, and kernel row number. Our study provides a high-quality reference-genome sequence to facilitate comparative genomics, functional studies, and genomic-assisted breeding for sweet corn.},
	language = {en},
	number = {1},
	urldate = {2024-03-22},
	journal = {Nature Communications},
	publisher = {Nature Publishing Group},
	author = {Hu, Ying and Colantonio, Vincent and Müller, Bárbara S. F. and Leach, Kristen A. and Nanni, Adalena and Finegan, Christina and Wang, Bo and Baseggio, Matheus and Newton, Carter J. and Juhl, Emily M. and Hislop, Lillian and Gonzalez, Juan M. and Rios, Esteban F. and Hannah, L. Curtis and Swarts, Kelly and Gore, Michael A. and Hennen-Bierwagen, Tracie A. and Myers, Alan M. and Settles, A. Mark and Tracy, William F. and Resende, Marcio F. R.},
	month = feb,
	year = {2021},
	keywords = {Agricultural genetics, Evolutionary biology, Plant breeding},
	pages = {1227},
}

Sweet corn is one of the most important vegetables in the United States and Canada. Here, we present a de novo assembly of a sweet corn inbred line Ia453 with the mutated shrunken2-reference allele (Ia453-sh2). This mutation accumulates more sugar and is present in most commercial hybrids developed for the processing and fresh markets. The ten pseudochromosomes cover 92% of the total assembly and 99% of the estimated genome size, with a scaffold N50 of 222.2 Mb. This reference genome completely assembles the large structural variation that created the mutant sh2-R allele. Furthermore, comparative genomics analysis with six field corn genomes highlights differences in single-nucleotide polymorphisms, structural variations, and transposon composition. Phylogenetic analysis of 5,381 diverse maize and teosinte accessions reveals genetic relationships between sweet corn and other types of maize. Our results show evidence for a common origin in northern Mexico for modern sweet corn in the U.S. Finally, population genomic analysis identifies regions of the genome under selection and candidate genes associated with sweet corn traits, such as early flowering, endosperm composition, plant and tassel architecture, and kernel row number. Our study provides a high-quality reference-genome sequence to facilitate comparative genomics, functional studies, and genomic-assisted breeding for sweet corn.

@article{swarts_joint_2021,
	title = {Joint analysis of days to flowering reveals independent temperate adaptations in maize},
	volume = {126},
	copyright = {2021 The Author(s), under exclusive licence to The Genetics Society},
	issn = {1365-2540},
	url = {https://www.nature.com/articles/s41437-021-00422-z},
	doi = {10.1038/s41437-021-00422-z},
	abstract = {Domesticates are an excellent model for understanding biological consequences of rapid climate change. Maize (Zea mays ssp. mays) was domesticated from a tropical grass yet is widespread across temperate regions today. We investigate the biological basis of temperate adaptation in diverse structured nested association mapping (NAM) populations from China, Europe (Dent and Flint) and the United States as well as in the Ames inbred diversity panel, using days to flowering as a proxy. Using cross-population prediction, where high prediction accuracy derives from overall genomic relatedness, shared genetic architecture, and sufficient diversity in the training population, we identify patterns in predictive ability across the five populations. To identify the source of temperate adapted alleles in these populations, we predict top associated genome-wide association study (GWAS) identified loci in a Random Forest Classifier using independent temperate–tropical North American populations based on lines selected from Hapmap3 as predictors. We find that North American populations are well predicted (AUC equals 0.89 and 0.85 for Ames and USNAM, respectively), European populations somewhat well predicted (AUC equals 0.59 and 0.67 for the Dent and Flint panels, respectively) and that the Chinese population is not predicted well at all (AUC is 0.47), suggesting an independent adaptation process for early flowering in China. Multiple adaptations for the complex trait days to flowering in maize provide hope for similar natural systems under climate change.},
	language = {en},
	number = {6},
	urldate = {2024-03-22},
	journal = {Heredity},
	publisher = {Nature Publishing Group},
	author = {Swarts, Kelly and Bauer, Eva and Glaubitz, Jeffrey C. and Ho, Tiffany and Johnson, Lynn and Li, Yongxiang and Li, Yu and Miller, Zachary and Romay, Cinta and Schön, Chris-Carolin and Wang, Tianyu and Zhang, Zhiwu and Buckler, Edward S. and Bradbury, Peter},
	month = jun,
	year = {2021},
	keywords = {Evolutionary genetics, Quantitative trait},
	pages = {929--941},
}

Domesticates are an excellent model for understanding biological consequences of rapid climate change. Maize (Zea mays ssp. mays) was domesticated from a tropical grass yet is widespread across temperate regions today. We investigate the biological basis of temperate adaptation in diverse structured nested association mapping (NAM) populations from China, Europe (Dent and Flint) and the United States as well as in the Ames inbred diversity panel, using days to flowering as a proxy. Using cross-population prediction, where high prediction accuracy derives from overall genomic relatedness, shared genetic architecture, and sufficient diversity in the training population, we identify patterns in predictive ability across the five populations. To identify the source of temperate adapted alleles in these populations, we predict top associated genome-wide association study (GWAS) identified loci in a Random Forest Classifier using independent temperate–tropical North American populations based on lines selected from Hapmap3 as predictors. We find that North American populations are well predicted (AUC equals 0.89 and 0.85 for Ames and USNAM, respectively), European populations somewhat well predicted (AUC equals 0.59 and 0.67 for the Dent and Flint panels, respectively) and that the Chinese population is not predicted well at all (AUC is 0.47), suggesting an independent adaptation process for early flowering in China. Multiple adaptations for the complex trait days to flowering in maize provide hope for similar natural systems under climate change.

@article{bilinski_parallel_2018,
	title = {Parallel altitudinal clines reveal trends in adaptive evolution of genome size in {Zea} mays},
	volume = {14},
	issn = {1553-7404},
	url = {https://journals.plos.org/plosgenetics/article?id=10.1371/journal.pgen.1007162},
	doi = {10.1371/journal.pgen.1007162},
	abstract = {While the vast majority of genome size variation in plants is due to differences in repetitive sequence, we know little about how selection acts on repeat content in natural populations. Here we investigate parallel changes in intraspecific genome size and repeat content of domesticated maize (Zea mays) landraces and their wild relative teosinte across altitudinal gradients in Mesoamerica and South America. We combine genotyping, low coverage whole-genome sequence data, and flow cytometry to test for evidence of selection on genome size and individual repeat abundance. We find that population structure alone cannot explain the observed variation, implying that clinal patterns of genome size are maintained by natural selection. Our modeling additionally provides evidence of selection on individual heterochromatic knob repeats, likely due to their large individual contribution to genome size. To better understand the phenotypes driving selection on genome size, we conducted a growth chamber experiment using a population of highland teosinte exhibiting extensive variation in genome size. We find weak support for a positive correlation between genome size and cell size, but stronger support for a negative correlation between genome size and the rate of cell production. Reanalyzing published data of cell counts in maize shoot apical meristems, we then identify a negative correlation between cell production rate and flowering time. Together, our data suggest a model in which variation in genome size is driven by natural selection on flowering time across altitudinal clines, connecting intraspecific variation in repetitive sequence to important differences in adaptive phenotypes.},
	language = {en},
	number = {5},
	urldate = {2024-03-22},
	journal = {PLOS Genetics},
	publisher = {Public Library of Science},
	author = {Bilinski, Paul and Albert, Patrice S. and Berg, Jeremy J. and Birchler, James A. and Grote, Mark N. and Lorant, Anne and Quezada, Juvenal and Swarts, Kelly and Yang, Jinliang and Ross-Ibarra, Jeffrey},
	month = may,
	year = {2018},
	keywords = {Fish genomics, Inbreeding, Invertebrate genomics, Leaves, Maize, Natural selection, Plant genomics, Transposable elements},
	pages = {e1007162},
}

While the vast majority of genome size variation in plants is due to differences in repetitive sequence, we know little about how selection acts on repeat content in natural populations. Here we investigate parallel changes in intraspecific genome size and repeat content of domesticated maize (Zea mays) landraces and their wild relative teosinte across altitudinal gradients in Mesoamerica and South America. We combine genotyping, low coverage whole-genome sequence data, and flow cytometry to test for evidence of selection on genome size and individual repeat abundance. We find that population structure alone cannot explain the observed variation, implying that clinal patterns of genome size are maintained by natural selection. Our modeling additionally provides evidence of selection on individual heterochromatic knob repeats, likely due to their large individual contribution to genome size. To better understand the phenotypes driving selection on genome size, we conducted a growth chamber experiment using a population of highland teosinte exhibiting extensive variation in genome size. We find weak support for a positive correlation between genome size and cell size, but stronger support for a negative correlation between genome size and the rate of cell production. Reanalyzing published data of cell counts in maize shoot apical meristems, we then identify a negative correlation between cell production rate and flowering time. Together, our data suggest a model in which variation in genome size is driven by natural selection on flowering time across altitudinal clines, connecting intraspecific variation in repetitive sequence to important differences in adaptive phenotypes.

@article{romero_navarro_study_2017,
	title = {A study of allelic diversity underlying flowering-time adaptation in maize landraces},
	volume = {49},
	copyright = {2017 Springer Nature America, Inc.},
	issn = {1546-1718},
	url = {https://www.nature.com/articles/ng.3784},
	doi = {10.1038/ng.3784},
	abstract = {Edward Buckler, Sarah Hearne and colleagues integrate two approaches to characterize the genetic diversity of a large number of geographically distributed maize landraces. They examine flowering time and adaptation to altitude and find that the majority of the associated SNPs overlap both traits.},
	language = {en},
	number = {3},
	urldate = {2024-03-22},
	journal = {Nature Genetics},
	publisher = {Nature Publishing Group},
	author = {Romero Navarro, J. Alberto and Willcox, Martha and Burgueño, Juan and Romay, Cinta and Swarts, Kelly and Trachsel, Samuel and Preciado, Ernesto and Terron, Arturo and Delgado, Humberto Vallejo and Vidal, Victor and Ortega, Alejandro and Banda, Armando Espinoza and Montiel, Noel Orlando Gómez and Ortiz-Monasterio, Ivan and Vicente, Félix San and Espinoza, Armando Guadarrama and Atlin, Gary and Wenzl, Peter and Hearne, Sarah and Buckler, Edward S.},
	month = mar,
	year = {2017},
	keywords = {Plant breeding, Plant genetics},
	pages = {476--480},
}

Edward Buckler, Sarah Hearne and colleagues integrate two approaches to characterize the genetic diversity of a large number of geographically distributed maize landraces. They examine flowering time and adaptation to altitude and find that the majority of the associated SNPs overlap both traits.

@article{swarts_genomic_2017,
	title = {Genomic estimation of complex traits reveals ancient maize adaptation to temperate {North} {America}},
	volume = {357},
	url = {https://www.science.org/doi/10.1126/science.aam9425},
	doi = {10.1126/science.aam9425},
	abstract = {By 4000 years ago, people had introduced maize to the southwestern United States; full agriculture was established quickly in the lowland deserts but delayed in the temperate highlands for 2000 years. We test if the earliest upland maize was adapted for early flowering, a characteristic of modern temperate maize. We sequenced fifteen 1900-year-old maize cobs from Turkey Pen Shelter in the temperate Southwest. Indirectly validated genomic models predicted that Turkey Pen maize was marginally adapted with respect to flowering, as well as short, tillering, and segregating for yellow kernel color. Temperate adaptation drove modern population differentiation and was selected in situ from ancient standing variation. Validated prediction of polygenic traits improves our understanding of ancient phenotypes and the dynamics of environmental adaptation.},
	number = {6350},
	urldate = {2024-03-22},
	journal = {Science},
	publisher = {American Association for the Advancement of Science},
	author = {Swarts, Kelly and Gutaker, Rafal M. and Benz, Bruce and Blake, Michael and Bukowski, Robert and Holland, James and Kruse-Peeples, Melissa and Lepak, Nicholas and Prim, Lynda and Romay, M. Cinta and Ross-Ibarra, Jeffrey and Sanchez-Gonzalez, Jose de Jesus and Schmidt, Chris and Schuenemann, Verena J. and Krause, Johannes and Matson, R. G. and Weigel, Detlef and Buckler, Edward S. and Burbano, Hernán A.},
	month = aug,
	year = {2017},
	pages = {512--515},
}

By 4000 years ago, people had introduced maize to the southwestern United States; full agriculture was established quickly in the lowland deserts but delayed in the temperate highlands for 2000 years. We test if the earliest upland maize was adapted for early flowering, a characteristic of modern temperate maize. We sequenced fifteen 1900-year-old maize cobs from Turkey Pen Shelter in the temperate Southwest. Indirectly validated genomic models predicted that Turkey Pen maize was marginally adapted with respect to flowering, as well as short, tillering, and segregating for yellow kernel color. Temperate adaptation drove modern population differentiation and was selected in situ from ancient standing variation. Validated prediction of polygenic traits improves our understanding of ancient phenotypes and the dynamics of environmental adaptation.

@article{takuno_independent_2015,
	title = {Independent {Molecular} {Basis} of {Convergent} {Highland} {Adaptation} in {Maize}},
	volume = {200},
	issn = {1943-2631},
	url = {https://doi.org/10.1534/genetics.115.178327},
	doi = {10.1534/genetics.115.178327},
	abstract = {Convergent evolution is the independent evolution of similar traits in different species or lineages of the same species; this often is a result of adaptation to similar environments, a process referred to as convergent adaptation. We investigate here the molecular basis of convergent adaptation in maize to highland climates in Mesoamerica and South America, using genome-wide SNP data. Taking advantage of archaeological data on the arrival of maize to the highlands, we infer demographic models for both populations, identifying evidence of a strong bottleneck and rapid expansion in South America. We use these models to then identify loci showing an excess of differentiation as a means of identifying putative targets of natural selection and compare our results to expectations from recently developed theory on convergent adaptation. Consistent with predictions across a wide parameter space, we see limited evidence for convergent evolution at the nucleotide level in spite of strong similarities in overall phenotypes. Instead, we show that selection appears to have predominantly acted on standing genetic variation and that introgression from wild teosinte populations appears to have played a role in highland adaptation in Mexican maize.},
	number = {4},
	urldate = {2024-03-22},
	journal = {Genetics},
	author = {Takuno, Shohei and Ralph, Peter and Swarts, Kelly and Elshire, Rob J and Glaubitz, Jeffrey C and Buckler, Edward S and Hufford, Matthew B and Ross-Ibarra, Jeffrey},
	month = aug,
	year = {2015},
	pages = {1297--1312},
}

Convergent evolution is the independent evolution of similar traits in different species or lineages of the same species; this often is a result of adaptation to similar environments, a process referred to as convergent adaptation. We investigate here the molecular basis of convergent adaptation in maize to highland climates in Mesoamerica and South America, using genome-wide SNP data. Taking advantage of archaeological data on the arrival of maize to the highlands, we infer demographic models for both populations, identifying evidence of a strong bottleneck and rapid expansion in South America. We use these models to then identify loci showing an excess of differentiation as a means of identifying putative targets of natural selection and compare our results to expectations from recently developed theory on convergent adaptation. Consistent with predictions across a wide parameter space, we see limited evidence for convergent evolution at the nucleotide level in spite of strong similarities in overall phenotypes. Instead, we show that selection appears to have predominantly acted on standing genetic variation and that introgression from wild teosinte populations appears to have played a role in highland adaptation in Mexican maize.

@article{swarts_novel_2014,
	title = {Novel {Methods} to {Optimize} {Genotypic} {Imputation} for {Low}-{Coverage}, {Next}-{Generation} {Sequence} {Data} in {Crop} {Plants}},
	volume = {7},
	copyright = {© 2014 The Authors.},
	issn = {1940-3372},
	url = {https://onlinelibrary.wiley.com/doi/abs/10.3835/plantgenome2014.05.0023},
	doi = {10.3835/plantgenome2014.05.0023},
	abstract = {Next-generation sequencing technology such as genotyping-by-sequencing (GBS) made low-cost, but often low-coverage, whole-genome sequencing widely available. Extensive inbreeding in crop plants provides an untapped, high quality source of phased haplotypes for imputing missing genotypes. We introduce Full-Sib Family Haplotype Imputation (FSFHap), optimized for full-sib populations, and a generalized method, Fast Inbred Line Library ImputatioN (FILLIN), to rapidly and accurately impute missing genotypes in GBS-type data with ordered markers. FSFHap and FILLIN impute missing genotypes with high accuracy in GBS-genotyped maize (Zea mays L.) inbred lines and breeding populations, while Beagle v. 4 is still preferable for diverse heterozygous populations. FILLIN and FSFHap are implemented in TASSEL 5.0.},
	language = {en},
	number = {3},
	urldate = {2024-03-22},
	journal = {The Plant Genome},
	author = {Swarts, Kelly and Li, Huihui and Romero Navarro, J. Alberto and An, Dong and Romay, Maria Cinta and Hearne, Sarah and Acharya, Charlotte and Glaubitz, Jeffrey C. and Mitchell, Sharon and Elshire, Robert J. and Buckler, Edward S. and Bradbury, Peter J.},
	year = {2014},
	note = {\_eprint: https://onlinelibrary.wiley.com/doi/pdf/10.3835/plantgenome2014.05.0023},
	pages = {plantgenome2014.05.0023},
}

Next-generation sequencing technology such as genotyping-by-sequencing (GBS) made low-cost, but often low-coverage, whole-genome sequencing widely available. Extensive inbreeding in crop plants provides an untapped, high quality source of phased haplotypes for imputing missing genotypes. We introduce Full-Sib Family Haplotype Imputation (FSFHap), optimized for full-sib populations, and a generalized method, Fast Inbred Line Library ImputatioN (FILLIN), to rapidly and accurately impute missing genotypes in GBS-type data with ordered markers. FSFHap and FILLIN impute missing genotypes with high accuracy in GBS-genotyped maize (Zea mays L.) inbred lines and breeding populations, while Beagle v. 4 is still preferable for diverse heterozygous populations. FILLIN and FSFHap are implemented in TASSEL 5.0.

@book{swarts_structural_2012,
	address = {Center for Desert Archaeology},
	series = {Anthropological {Papers}},
	title = {Structural {Wood} {Choice} and {Cultural} {Meaning} at {Honey} {Bee} {Village}. {Life} in the valley of gold, archaeological investigations at {Honey} {Bee} {Village}, a prehistoric {Hohokam} ballcourt village in the {Canada} del {Oro} {Valley} of southern {Arizona}: introduction, chronology, material culture investigations and research results.},
	shorttitle = {Life in the {Valley} of {Gold}},
	abstract = {Honey Bee Village was a sizeable prehistoric Hohokam village complete with a plaza, mounds, and ballcourt located in the Cañada del Oro Valley north of Tucson, Arizona. In 2006 and 2007, nearly three-quarters of the village was intensively excavated under contract with Pima County and Vistoso Partners. The core of the site is a 13-acre preserve that was tested in the 1980s. Outside the core area, the full plan of the village was revealed, resulting in the identification of 2,004 cultural features. Occupation ranged from late in the Tortolita phase to the early Tanque Verde phase, roughly A.D. 650-1200. Overall, 947 cultural features were fully or partially excavated, including 183 pit structures, possible structures, and adobe rooms, 207 human burial features, 11 animal burials, 24 trash mounds or concentrations, and 522 extramural features. Particularly interesting remains uncovered include a golden eagle burial and a Late Rincon phase plaza and plaza cemetery. The wide excavation coverage permitted an unusually complete view of a Hohokam village and of surface-subsurface comparisons.

The archaeological features and artifacts recovered are documented in this two-volume report. A large set of radiocarbon and archaeomagnetic dates is discussed. Household economic specialization and architectural practices are addressed. Cremation mortuary practices are reconstructed, and Hohokam perspectives on death and the dead are considered. The history and shifting settlement structure of the village are considered in relation to its nearby sister village, Sleeping Snake. Of special interest is the discovery that logs obtained from the Santa Catalina Mountains were used in house construction.},
	language = {en-US},
	urldate = {2024-03-22},
	publisher = {Archaeology Southwest},
	author = {Swarts, Kelly},
	month = jun,
	year = {2012},
	note = {Edited by Henry D. Wallace},
}

Honey Bee Village was a sizeable prehistoric Hohokam village complete with a plaza, mounds, and ballcourt located in the Cañada del Oro Valley north of Tucson, Arizona. In 2006 and 2007, nearly three-quarters of the village was intensively excavated under contract with Pima County and Vistoso Partners. The core of the site is a 13-acre preserve that was tested in the 1980s. Outside the core area, the full plan of the village was revealed, resulting in the identification of 2,004 cultural features. Occupation ranged from late in the Tortolita phase to the early Tanque Verde phase, roughly A.D. 650-1200. Overall, 947 cultural features were fully or partially excavated, including 183 pit structures, possible structures, and adobe rooms, 207 human burial features, 11 animal burials, 24 trash mounds or concentrations, and 522 extramural features. Particularly interesting remains uncovered include a golden eagle burial and a Late Rincon phase plaza and plaza cemetery. The wide excavation coverage permitted an unusually complete view of a Hohokam village and of surface-subsurface comparisons. The archaeological features and artifacts recovered are documented in this two-volume report. A large set of radiocarbon and archaeomagnetic dates is discussed. Household economic specialization and architectural practices are addressed. Cremation mortuary practices are reconstructed, and Hohokam perspectives on death and the dead are considered. The history and shifting settlement structure of the village are considered in relation to its nearby sister village, Sleeping Snake. Of special interest is the discovery that logs obtained from the Santa Catalina Mountains were used in house construction.

@article{birkeland_updated_2025,
	title = {An updated perspective: what genes make a tree a tree?},
	issn = {1360-1385},
	shorttitle = {An updated perspective},
	url = {https://www.sciencedirect.com/science/article/pii/S1360138525002821},
	doi = {10.1016/j.tplants.2025.09.006},
	abstract = {We learn early on how to tell trees apart from other plants. However, it has proved hard to distinguish trees from other plants at the genetic level, and it is believed that there are no unique ‘tree genes’. With the rapid increase in available tree genomes, we can perform new comparative and evolutionary analyses of plant life histories and growth forms. Here we provide a fresh perspective on the genetic foundation for woodiness and perenniality in angiosperms by analyzing selection pressures and gene family evolution in the rosids using genomic data. We examine genes distinguishing trees from herbs and discuss future directions for uncovering the genetic factors that define a tree in this new era of tree genomics.},
	urldate = {2025-10-24},
	journal = {Trends in Plant Science},
	author = {Birkeland, Siri and Soldado, Eduardo R. and Ranade, Sonali S. and García-Gil, M. Rosario and Choudhary, Shruti and Kumar, Vikash and Tuominen, Hannele and Mellerowicz, Ewa J. and Street, Nathaniel R. and Hvidsten, Torgeir R.},
	month = oct,
	year = {2025},
	keywords = {comparative genomics, plant growth forms, plant life histories, rosids, tree genomics, woodiness},
}

We learn early on how to tell trees apart from other plants. However, it has proved hard to distinguish trees from other plants at the genetic level, and it is believed that there are no unique ‘tree genes’. With the rapid increase in available tree genomes, we can perform new comparative and evolutionary analyses of plant life histories and growth forms. Here we provide a fresh perspective on the genetic foundation for woodiness and perenniality in angiosperms by analyzing selection pressures and gene family evolution in the rosids using genomic data. We examine genes distinguishing trees from herbs and discuss future directions for uncovering the genetic factors that define a tree in this new era of tree genomics.

@article{gil-munoz_implications_2025,
	title = {Implications of {Breeding} for {Growth} on {Drought} {Tolerance} in {Scots} {Pine} ({Pinus} sylvestris {L}.)—{Insights} {From} {Metabolomics} and {High}-{Throughput} {Plant} {Architecture} {Analysis}},
	volume = {18},
	copyright = {© 2025 The Author(s). Evolutionary Applications published by John Wiley \& Sons Ltd.},
	issn = {1752-4571},
	url = {https://onlinelibrary.wiley.com/doi/abs/10.1111/eva.70122},
	doi = {10.1111/eva.70122},
	abstract = {Drought has been identified as one of the important environmental factors in the context of climate change due to its interaction with other biotic and abiotic stresses. However, only a few studies have reported the effect of breeding on forest adaptability to climate change. Using a common garden experiment with seedlings from families of Scots pine (Pinus sylvestris L.) from northern Sweden, we have found differences in drought tolerance between seedlings from breeding stands and those from natural forests. We performed a genetic analysis including high-throughput image-based phenotyping of seedling canopy and root traits and conducted metabolomic and hormone analyses with the aerial parts of the seedlings. Our results indicate that root architecture traits associated with drought tolerance exhibit moderate to high heritability. Analyses of seedling architecture reveal that families from breeding stands have higher drought resistance but lower genetic variation than the ones from natural forests, especially in the case of canopy traits. Metabolomic and hormone analyses of the aerial parts of the seedlings also support that the breeding stands may have a higher capacity to withstand or deal with drought conditions as compared to the natural forests. For example, increase in abscisic acid along with increase in tryptophan and auxin conjugates in the breeding stands compared to the natural forests under drought conditions may contribute to alleviation of drought response in the breeding stands. The methodology employed to evaluate drought tolerance and plant architecture in this study might be useful for future research and forest management focused on climate change adaptability.},
	language = {en},
	number = {6},
	urldate = {2025-06-27},
	journal = {Evolutionary Applications},
	author = {Gil-Muñoz, Francisco and Ranade, Sonali Sachin and Hayatgheibi, Haleh and Niemi, Juha and Östlund, Lars and García-Gil, María Rosario},
	year = {2025},
	note = {\_eprint: https://onlinelibrary.wiley.com/doi/pdf/10.1111/eva.70122},
	keywords = {abscisic acid, drought, metabolomics, root architecture, scots pine},
	pages = {e70122},
}

Drought has been identified as one of the important environmental factors in the context of climate change due to its interaction with other biotic and abiotic stresses. However, only a few studies have reported the effect of breeding on forest adaptability to climate change. Using a common garden experiment with seedlings from families of Scots pine (Pinus sylvestris L.) from northern Sweden, we have found differences in drought tolerance between seedlings from breeding stands and those from natural forests. We performed a genetic analysis including high-throughput image-based phenotyping of seedling canopy and root traits and conducted metabolomic and hormone analyses with the aerial parts of the seedlings. Our results indicate that root architecture traits associated with drought tolerance exhibit moderate to high heritability. Analyses of seedling architecture reveal that families from breeding stands have higher drought resistance but lower genetic variation than the ones from natural forests, especially in the case of canopy traits. Metabolomic and hormone analyses of the aerial parts of the seedlings also support that the breeding stands may have a higher capacity to withstand or deal with drought conditions as compared to the natural forests. For example, increase in abscisic acid along with increase in tryptophan and auxin conjugates in the breeding stands compared to the natural forests under drought conditions may contribute to alleviation of drought response in the breeding stands. The methodology employed to evaluate drought tolerance and plant architecture in this study might be useful for future research and forest management focused on climate change adaptability.

@article{ranade_metabolomic_2025,
	title = {Metabolomic profiling of shade response and in silico analysis of {PAL} homologs imply the potential presence of bifunctional ammonia lyases in conifers},
	volume = {177},
	copyright = {© 2025 The Author(s). Physiologia Plantarum published by John Wiley \& Sons Ltd on behalf of Scandinavian Plant Physiology Society.},
	issn = {1399-3054},
	url = {https://onlinelibrary.wiley.com/doi/abs/10.1111/ppl.70175},
	doi = {10.1111/ppl.70175},
	abstract = {Norway spruce and Scots pine show enhanced lignin synthesis under shade, along with differential expression of defense-related genes that render disease resilience. In general, phenylalanine (Phe) is the precursor for lignin synthesis in plants, and tyrosine (Tyr) forms an additional lignin precursor specifically in grasses. Phenylalanine ammonia-lyase (PAL) and tyrosine ammonia-lyase (TAL) from the lignin biosynthesis pathway use either Phe or Tyr as precursors for lignin production, respectively. Grasses possess a bifunctional phenylalanine/tyrosine ammonia-lyase (PTAL) that potentially can use both Phe and Tyr for lignin biosynthesis. Metabolomic profiles of seedlings revealed higher levels of Phe and Tyr under shade in Scots pine, while Norway spruce showed differential regulation of only Tyr under shade. Sequence analysis and phylogeny of PAL homologs in the two conifers, coupled with correlation of up-regulation of precursors for lignin synthesis (Phe/Tyr) and enhanced lignin synthesis along with differential expression of PAL homologs under shade, suggest the potential presence of a bifunctional ammonia-lyases (BAL) in conifers. This finding is novel and comparable to PTALs in grasses. Exome sequence analysis revealed a latitudinal variation in allele frequencies of SNPs from coding regions of putative PAL and BAL in Norway spruce, which may impact enzyme activity affecting lignin synthesis. Metabolomic analysis additionally identified metabolites involved in plant immunity, defense and stress response.},
	language = {en},
	number = {2},
	urldate = {2025-03-28},
	journal = {Physiologia Plantarum},
	author = {Ranade, Sonali Sachin and García-Gil, María Rosario},
	year = {2025},
	note = {\_eprint: https://onlinelibrary.wiley.com/doi/pdf/10.1111/ppl.70175},
	pages = {e70175},
}

Norway spruce and Scots pine show enhanced lignin synthesis under shade, along with differential expression of defense-related genes that render disease resilience. In general, phenylalanine (Phe) is the precursor for lignin synthesis in plants, and tyrosine (Tyr) forms an additional lignin precursor specifically in grasses. Phenylalanine ammonia-lyase (PAL) and tyrosine ammonia-lyase (TAL) from the lignin biosynthesis pathway use either Phe or Tyr as precursors for lignin production, respectively. Grasses possess a bifunctional phenylalanine/tyrosine ammonia-lyase (PTAL) that potentially can use both Phe and Tyr for lignin biosynthesis. Metabolomic profiles of seedlings revealed higher levels of Phe and Tyr under shade in Scots pine, while Norway spruce showed differential regulation of only Tyr under shade. Sequence analysis and phylogeny of PAL homologs in the two conifers, coupled with correlation of up-regulation of precursors for lignin synthesis (Phe/Tyr) and enhanced lignin synthesis along with differential expression of PAL homologs under shade, suggest the potential presence of a bifunctional ammonia-lyases (BAL) in conifers. This finding is novel and comparable to PTALs in grasses. Exome sequence analysis revealed a latitudinal variation in allele frequencies of SNPs from coding regions of putative PAL and BAL in Norway spruce, which may impact enzyme activity affecting lignin synthesis. Metabolomic analysis additionally identified metabolites involved in plant immunity, defense and stress response.

@article{ortiz_genomic_2024,
	title = {Genomic {Prediction} for {Inbred} and {Hybrid} {Polysomic} {Tetraploid} {Potato} {Offspring}},
	volume = {14},
	copyright = {http://creativecommons.org/licenses/by/3.0/},
	issn = {2077-0472},
	url = {https://www.mdpi.com/2077-0472/14/3/455},
	doi = {10.3390/agriculture14030455},
	abstract = {Potato genetic improvement begins with crossing cultivars or breeding clones which often have complementary characteristics for producing heritable variation in segregating offspring, in which phenotypic selection is used thereafter across various vegetative generations (Ti). The aim of this research was to determine whether tetrasomic genomic best linear unbiased predictors (GBLUPs) may facilitate selecting for tuber yield across early Ti within and across breeding sites in inbred (S1) and hybrid (F1) tetraploid potato offspring. This research used 858 breeding clones for a T1 trial at Umeå (Norrland, 63°49′30″ N 20°15′50″ E) in 2021, as well as 829 and 671 clones from the breeding population for T2 trials during 2022 at Umeå and Helgegården (Skåne, 56°01′46″ N 14°09′24″ E), respectively, along with their parents (S0) and check cultivars. The S1 and F1 were derived from selfing and crossing four S0. The experimental layout was an augmented design of four-plant plots across testing sites, where breeding clones were non-replicated, and the parents and cultivars were placed in all blocks between the former. The genomic prediction abilities (r) for tuber weight per plant were 0.5944 and 0.6776 in T2 at Helgegården and Umeå, respectively, when T1 at Umeå was used as the training population. On average, r was larger in inbred than in hybrid offspring at both breeding sites. The r was also estimated using multi-environment data (involving at least one S1 and one F1) for T2 performance at both breeding sites. The r was strongly influenced by the genotype in both S1 and F1 offspring irrespective of the breeding site.},
	language = {en},
	number = {3},
	urldate = {2024-04-04},
	journal = {Agriculture},
	publisher = {Multidisciplinary Digital Publishing Institute},
	author = {Ortiz, Rodomiro and Reslow, Fredrik and Vetukuri, Ramesh and García-Gil, M. Rosario and Pérez-Rodríguez, Paulino and Crossa, José},
	month = mar,
	year = {2024},
	note = {Number: 3},
	keywords = {\textit{Solanum tuberosum}, Nordic latitude, crossing, genomic estimated breeding values, linear models, polyploidy, selfing, tetrasomic inheritance},
	pages = {455},
}

Potato genetic improvement begins with crossing cultivars or breeding clones which often have complementary characteristics for producing heritable variation in segregating offspring, in which phenotypic selection is used thereafter across various vegetative generations (Ti). The aim of this research was to determine whether tetrasomic genomic best linear unbiased predictors (GBLUPs) may facilitate selecting for tuber yield across early Ti within and across breeding sites in inbred (S1) and hybrid (F1) tetraploid potato offspring. This research used 858 breeding clones for a T1 trial at Umeå (Norrland, 63°49′30″ N 20°15′50″ E) in 2021, as well as 829 and 671 clones from the breeding population for T2 trials during 2022 at Umeå and Helgegården (Skåne, 56°01′46″ N 14°09′24″ E), respectively, along with their parents (S0) and check cultivars. The S1 and F1 were derived from selfing and crossing four S0. The experimental layout was an augmented design of four-plant plots across testing sites, where breeding clones were non-replicated, and the parents and cultivars were placed in all blocks between the former. The genomic prediction abilities (r) for tuber weight per plant were 0.5944 and 0.6776 in T2 at Helgegården and Umeå, respectively, when T1 at Umeå was used as the training population. On average, r was larger in inbred than in hybrid offspring at both breeding sites. The r was also estimated using multi-environment data (involving at least one S1 and one F1) for T2 performance at both breeding sites. The r was strongly influenced by the genotype in both S1 and F1 offspring irrespective of the breeding site.

@article{hayatgheibi_implications_2024,
	title = {Implications of accounting for marker-based population structure in the quantitative genetic evaluation of genetic parameters related to growth and wood properties in {Norway} spruce},
	volume = {25},
	issn = {2730-6844},
	url = {https://doi.org/10.1186/s12863-024-01241-x},
	doi = {10.1186/s12863-024-01241-x},
	abstract = {Forest geneticists typically use provenances to account for population differences in their improvement schemes; however, the historical records of the imported materials might not be very precise or well-aligned with the genetic clusters derived from advanced molecular techniques. The main objective of this study was to assess the impact of marker-based population structure on genetic parameter estimates related to growth and wood properties and their trade-offs in Norway spruce, by either incorporating it as a fixed effect (model-A) or excluding it entirely from the analysis (model-B).},
	number = {1},
	urldate = {2024-07-01},
	journal = {BMC Genomic Data},
	author = {Hayatgheibi, Haleh and Hallingbäck, Henrik R. and Lundqvist, Sven-Olof and Grahn, Thomas and Scheepers, Gerhard and Nordström, Peter and Chen, Zhi-Qiang and Kärkkäinen, Katri and Wu, Harry X. and García-Gil, M. Rosario},
	month = jun,
	year = {2024},
	keywords = {Cross-validation, Norway spruce, Population structure, Prediction accuracy, Wood properties},
	pages = {60},
}

Forest geneticists typically use provenances to account for population differences in their improvement schemes; however, the historical records of the imported materials might not be very precise or well-aligned with the genetic clusters derived from advanced molecular techniques. The main objective of this study was to assess the impact of marker-based population structure on genetic parameter estimates related to growth and wood properties and their trade-offs in Norway spruce, by either incorporating it as a fixed effect (model-A) or excluding it entirely from the analysis (model-B).

@article{ranade_lignin_2024,
	title = {Lignin biosynthesis pathway repressors in gymnosperms: differential repressor domains as compared to angiosperms},
	volume = {4},
	copyright = {2024 The Author(s)},
	issn = {2767-3812},
	shorttitle = {Lignin biosynthesis pathway repressors in gymnosperms},
	url = {https://www.maxapress.com/article/doi/10.48130/forres-0024-0029},
	doi = {10.48130/forres-0024-0029},
	abstract = {{\textless}p{\textgreater}Lignin is a polyphenolic polymer present in the cell walls of specialized plant cell types in vascular plants that provides structural support and plays a major role in plant protection. The lignin biosynthesis pathway is regulated by transcription factors from the MYB (myeloblastosis) family. While several MYB members positively regulate lignin synthesis, only a few negatively regulate lignin synthesis. These lignin suppressors are well characterized in model plant species; however, their role has not been fully explored in gymnosperms. Lignin forms one of the major hurdles for the forest-based industry e.g. paper, pulp, and biofuel production. Therefore, the detailed mechanisms involved in the regulation of lignin synthesis are valuable, especially in conifers that form the major source of softwood for timber and paper production. In this review, the potential and differential domains present in the MYB suppressors in gymnosperms are discussed, along with their phylogenetic analysis. Sequence analysis revealed that the N-terminal regions of the MYB suppressor members were found to be conserved among the gymnosperms and angiosperms containing the R2, R3, and bHLH domains, while the C-terminal regions were found to be highly variable. The typical repressor motifs like the LxLxL-type EAR motif and the TLLLFR motif were absent from the C-terminal regions of MYB suppressors from most gymnosperms. However, although the gymnosperms lacked the characteristic repressor domains, a R2R3-type MYB member from \textit{Ginkgo} was reported to repress the lignin biosynthetic pathway. It is proposed that gymnosperms possess unique kinds of repressors that need further functional validation.{\textless}/p{\textgreater}},
	language = {en},
	number = {1},
	urldate = {2024-09-27},
	journal = {Forestry Research},
	publisher = {Maximum Academic Press},
	author = {Ranade, Sonali Sachin and García-Gil, María Rosario and Ranade, Sonali Sachin and García-Gil, María Rosario},
	month = sep,
	year = {2024},
	note = {Bandiera\_abtest: a
Cc\_license\_type: cc\_by
Cg\_type: Maximum Academic Press
Number: forres-0024-0029
Primary\_atype: Forestry Research
Subject\_term: MINI REVIEW
Subject\_term\_id: MINI REVIEW},
}

\textlessp\textgreaterLignin is a polyphenolic polymer present in the cell walls of specialized plant cell types in vascular plants that provides structural support and plays a major role in plant protection. The lignin biosynthesis pathway is regulated by transcription factors from the MYB (myeloblastosis) family. While several MYB members positively regulate lignin synthesis, only a few negatively regulate lignin synthesis. These lignin suppressors are well characterized in model plant species; however, their role has not been fully explored in gymnosperms. Lignin forms one of the major hurdles for the forest-based industry e.g. paper, pulp, and biofuel production. Therefore, the detailed mechanisms involved in the regulation of lignin synthesis are valuable, especially in conifers that form the major source of softwood for timber and paper production. In this review, the potential and differential domains present in the MYB suppressors in gymnosperms are discussed, along with their phylogenetic analysis. Sequence analysis revealed that the N-terminal regions of the MYB suppressor members were found to be conserved among the gymnosperms and angiosperms containing the R2, R3, and bHLH domains, while the C-terminal regions were found to be highly variable. The typical repressor motifs like the LxLxL-type EAR motif and the TLLLFR motif were absent from the C-terminal regions of MYB suppressors from most gymnosperms. However, although the gymnosperms lacked the characteristic repressor domains, a R2R3-type MYB member from Ginkgo was reported to repress the lignin biosynthetic pathway. It is proposed that gymnosperms possess unique kinds of repressors that need further functional validation.\textless/p\textgreater

@article{lecoy_analysis_2023,
	title = {Analysis of the {ASR} and {LP3} homologous gene families reveal positive selection acting on {LP3}-3 gene},
	volume = {850},
	issn = {0378-1119},
	url = {https://www.sciencedirect.com/science/article/pii/S0378111922007557},
	doi = {10.1016/j.gene.2022.146935},
	abstract = {Drought has long been established as a major environmental stress for plants which have in turn developed several coping strategies, ranging from physiological to molecular mechanisms. LP3 that was first discovered in loblolly pine (Pinus taeda L.) is a homolog of the Abscisic Acid, Stress and Ripening (ASR) gene belonging to the ABA/WDS gene family that was first detected in tomato. LP3 has been shown to be present in four different paralogs in loblolly pine called LP3-0, LP3-1, LP3-2 and LP3-3. LP3 in loblolly pine has not been as extensively studied as the ASR in tomato. Similar to ASR, the different LP3 paralogs have been shown to be upregulated in response to water deficit stress and to act as transcription factors for genes likely involved in hexose transport. In the current study, we have investigated the evolutionary history of LP3 gene family, with the aim of relating it to that of ASR from a phylogenetic perspective and comparing the differences in selective pressure and codon usage. Phylogenetic trees revealed that LP3 is less divergent across species than ASR even when the trees were solely based on the different sub-sections of the gene. Phylogenetic, GC content, codon usage and selective pressure analyses suggest that LP3-3 is undergoing positive selection.},
	language = {en},
	urldate = {2022-10-06},
	journal = {Gene},
	author = {Lecoy, Jonathan and Ranade, Sonali Sachin and García-Gil, María Rosario},
	month = jan,
	year = {2023},
	keywords = {ABA/WDS, Codon usage, Drought resistance, GC-content, Selective pressure},
	pages = {146935},
}

Drought has long been established as a major environmental stress for plants which have in turn developed several coping strategies, ranging from physiological to molecular mechanisms. LP3 that was first discovered in loblolly pine (Pinus taeda L.) is a homolog of the Abscisic Acid, Stress and Ripening (ASR) gene belonging to the ABA/WDS gene family that was first detected in tomato. LP3 has been shown to be present in four different paralogs in loblolly pine called LP3-0, LP3-1, LP3-2 and LP3-3. LP3 in loblolly pine has not been as extensively studied as the ASR in tomato. Similar to ASR, the different LP3 paralogs have been shown to be upregulated in response to water deficit stress and to act as transcription factors for genes likely involved in hexose transport. In the current study, we have investigated the evolutionary history of LP3 gene family, with the aim of relating it to that of ASR from a phylogenetic perspective and comparing the differences in selective pressure and codon usage. Phylogenetic trees revealed that LP3 is less divergent across species than ASR even when the trees were solely based on the different sub-sections of the gene. Phylogenetic, GC content, codon usage and selective pressure analyses suggest that LP3-3 is undergoing positive selection.

@article{ranade_clinal_2023,
	title = {Clinal variation in {PHY} ({PAS} domain) and {CRY} ({CCT} domain)—{Signs} of local adaptation to light quality in {Norway} spruce},
	volume = {n/a},
	copyright = {© 2023 The Authors. Plant, Cell \& Environment published by John Wiley \& Sons Ltd.},
	issn = {1365-3040},
	url = {https://onlinelibrary.wiley.com/doi/abs/10.1111/pce.14638},
	doi = {10.1111/pce.14638},
	abstract = {Detection of the genomic basis of local adaptation to environmental conditions is challenging in forest trees. Phytochromes (PHY) and cryptochromes (CRY) perceive the red (R)/far-red (FR) and blue light respectively, thus playing a fundamental role in regulating plant growth and development. PHYO and PHYP from conifers are the equivalents of PHYA/PHYC and PHYB in angiosperms, respectively. Norway spruce shows an adaptive latitudinal cline for shade (low R:FR or FR-enriched light) tolerance and requirement of FR light for its growth. We analyzed the exome capture data that included a uniquely large data set of 1654 Norway spruce trees sampled across many latitudes in Sweden to capture the natural clines for photoperiod and FR light exposure during the growth season. Statistically significant clinal variation was detected in allele and genotype frequencies of missense mutations in coding regions belonging to well-defined functional domains of PHYO (PAS-B), PHYP2 (PAS fold-2), CRY1 (CCT1) and CRY2 (CCT2) that strongly correlates with the latitudinal gradient in response to variable light quality in Norway spruce. The missense SNP in PHYO resulting in Asn835Ser, displayed the steepest cline among all other polymorphisms. We propose that these variations in the photoreceptors represent signs of local adaptation to light quality.},
	language = {en},
	number = {n/a},
	urldate = {2023-06-09},
	journal = {Plant, Cell \& Environment},
	author = {Ranade, Sonali Sachin and García-Gil, María Rosario},
	month = jun,
	year = {2023},
	note = {\_eprint: https://onlinelibrary.wiley.com/doi/pdf/10.1111/pce.14638},
	keywords = {SNP, cline, cryptochrome, missense mutation, photoreceptor, phytochrome, polymorphism},
}

Detection of the genomic basis of local adaptation to environmental conditions is challenging in forest trees. Phytochromes (PHY) and cryptochromes (CRY) perceive the red (R)/far-red (FR) and blue light respectively, thus playing a fundamental role in regulating plant growth and development. PHYO and PHYP from conifers are the equivalents of PHYA/PHYC and PHYB in angiosperms, respectively. Norway spruce shows an adaptive latitudinal cline for shade (low R:FR or FR-enriched light) tolerance and requirement of FR light for its growth. We analyzed the exome capture data that included a uniquely large data set of 1654 Norway spruce trees sampled across many latitudes in Sweden to capture the natural clines for photoperiod and FR light exposure during the growth season. Statistically significant clinal variation was detected in allele and genotype frequencies of missense mutations in coding regions belonging to well-defined functional domains of PHYO (PAS-B), PHYP2 (PAS fold-2), CRY1 (CCT1) and CRY2 (CCT2) that strongly correlates with the latitudinal gradient in response to variable light quality in Norway spruce. The missense SNP in PHYO resulting in Asn835Ser, displayed the steepest cline among all other polymorphisms. We propose that these variations in the photoreceptors represent signs of local adaptation to light quality.

@article{tiret_divergent_2023,
	title = {Divergent selection predating the {Last} {Glacial} {Maximum} mainly acted on macro-phenotypes in {Norway} spruce},
	volume = {16},
	issn = {1752-4571},
	url = {https://onlinelibrary.wiley.com/doi/abs/10.1111/eva.13519},
	doi = {10.1111/eva.13519},
	abstract = {The current distribution and population structure of many species were, to a large extent, shaped by cycles of isolation in glacial refugia and subsequent population expansions. Isolation in and postglacial expansion through heterogeneous environments led to either neutral or adaptive divergence. Norway spruce is no exception, and its current distribution is the consequence of a constant interplay between evolutionary and demographic processes. We investigated population differentiation and adaptation of Norway spruce for juvenile growth, diameter of the stem, wood density, and tracheid traits at breast height. Data from 4461 phenotyped and genotyped Norway spruce from 396 half-sib families in two progeny tests were used to test for divergent selection in the framework of QST vs. FST. We show that the macroscopic resultant trait (stem diameter), unlike its microscopic components (tracheid dimensions) and juvenile growth, was under divergent selection that predated the Last Glacial Maximum. Altogether, the current variation in these phenotypic traits in Norway spruce is better explained by local adaptation to ancestral environments than to current ones, where populations were partly preadapted, mainly through growth-related traits.},
	language = {en},
	number = {1},
	urldate = {2023-01-20},
	journal = {Evolutionary Applications},
	author = {Tiret, Mathieu and Olsson, Lars and Grahn, Thomas and Karlsson, Bo and Milesi, Pascal and Lascoux, Martin and Lundqvist, Sven-Olof and García-Gil, Maria Rosario},
	year = {2023},
	keywords = {Norway spruce, QST vs. FST, population structure, wood quality},
	pages = {163--172},
}

The current distribution and population structure of many species were, to a large extent, shaped by cycles of isolation in glacial refugia and subsequent population expansions. Isolation in and postglacial expansion through heterogeneous environments led to either neutral or adaptive divergence. Norway spruce is no exception, and its current distribution is the consequence of a constant interplay between evolutionary and demographic processes. We investigated population differentiation and adaptation of Norway spruce for juvenile growth, diameter of the stem, wood density, and tracheid traits at breast height. Data from 4461 phenotyped and genotyped Norway spruce from 396 half-sib families in two progeny tests were used to test for divergent selection in the framework of QST vs. FST. We show that the macroscopic resultant trait (stem diameter), unlike its microscopic components (tracheid dimensions) and juvenile growth, was under divergent selection that predated the Last Glacial Maximum. Altogether, the current variation in these phenotypic traits in Norway spruce is better explained by local adaptation to ancestral environments than to current ones, where populations were partly preadapted, mainly through growth-related traits.

@article{ortiz_inbreeding_2023,
	title = {Inbreeding {Effects} on the {Performance} and {Genomic} {Prediction} for {Polysomic} {Tetraploid} {Potato} {Offspring} {Grown} at {High} {Nordic} {Latitudes}},
	volume = {14},
	copyright = {http://creativecommons.org/licenses/by/3.0/},
	issn = {2073-4425},
	url = {https://www.mdpi.com/2073-4425/14/6/1302},
	doi = {10.3390/genes14061302},
	abstract = {Inbreeding depression (ID) is caused by increased homozygosity in the offspring after selfing. Although the self-compatible, highly heterozygous, tetrasomic polyploid potato (Solanum tuberosum L.) suffers from ID, some argue that the potential genetic gains from using inbred lines in a sexual propagation system of potato are too large to be ignored. The aim of this research was to assess the effects of inbreeding on potato offspring performance under a high latitude and the accuracy of the genomic prediction of breeding values (GEBVs) for further use in selection. Four inbred (S1) and two hybrid (F1) offspring and their parents (S0) were used in the experiment, with a field layout of an augmented design with the four S0 replicated in nine incomplete blocks comprising 100, four-plant plots at Umeå (63°49′30″ N 20°15′50″ E), Sweden. S0 was significantly (p {\textless} 0.01) better than both S1 and F1 offspring for tuber weight (total and according to five grading sizes), tuber shape and size uniformity, tuber eye depth and reducing sugars in the tuber flesh, while F1 was significantly (p {\textless} 0.01) better than S1 for all tuber weight and uniformity traits. Some F1 hybrid offspring (15–19\%) had better total tuber yield than the best-performing parent. The GEBV accuracy ranged from −0.3928 to 0.4436. Overall, tuber shape uniformity had the highest GEBV accuracy, while tuber weight traits exhibited the lowest accuracy. The F1 full sib’s GEBV accuracy was higher, on average, than that of S1. Genomic prediction may facilitate eliminating undesired inbred or hybrid offspring for further use in the genetic betterment of potato.},
	language = {en},
	number = {6},
	urldate = {2023-06-30},
	journal = {Genes},
	publisher = {Multidisciplinary Digital Publishing Institute},
	author = {Ortiz, Rodomiro and Reslow, Fredrik and Vetukuri, Ramesh and García-Gil, M. Rosario and Pérez-Rodríguez, Paulino and Crossa, José},
	month = jun,
	year = {2023},
	note = {Number: 6},
	keywords = {\textit{Solanum tuberosum} L., Fennoscandia, GEBV, QTL, Scandinavia, accuracy, genetic gains, germplasm enhancement, hybrid, inbred},
	pages = {1302},
}

Inbreeding depression (ID) is caused by increased homozygosity in the offspring after selfing. Although the self-compatible, highly heterozygous, tetrasomic polyploid potato (Solanum tuberosum L.) suffers from ID, some argue that the potential genetic gains from using inbred lines in a sexual propagation system of potato are too large to be ignored. The aim of this research was to assess the effects of inbreeding on potato offspring performance under a high latitude and the accuracy of the genomic prediction of breeding values (GEBVs) for further use in selection. Four inbred (S1) and two hybrid (F1) offspring and their parents (S0) were used in the experiment, with a field layout of an augmented design with the four S0 replicated in nine incomplete blocks comprising 100, four-plant plots at Umeå (63°49′30″ N 20°15′50″ E), Sweden. S0 was significantly (p \textless 0.01) better than both S1 and F1 offspring for tuber weight (total and according to five grading sizes), tuber shape and size uniformity, tuber eye depth and reducing sugars in the tuber flesh, while F1 was significantly (p \textless 0.01) better than S1 for all tuber weight and uniformity traits. Some F1 hybrid offspring (15–19%) had better total tuber yield than the best-performing parent. The GEBV accuracy ranged from −0.3928 to 0.4436. Overall, tuber shape uniformity had the highest GEBV accuracy, while tuber weight traits exhibited the lowest accuracy. The F1 full sib’s GEBV accuracy was higher, on average, than that of S1. Genomic prediction may facilitate eliminating undesired inbred or hybrid offspring for further use in the genetic betterment of potato.

@article{gil-munoz_qtl_2023,
	title = {{QTL} mapping of the narrow-branch “{Pendula}” phenotype in {Norway} spruce ({Picea} abies {L}. {Karst}.)},
	volume = {19},
	issn = {1614-2950},
	url = {https://doi.org/10.1007/s11295-023-01599-6},
	doi = {10.1007/s11295-023-01599-6},
	abstract = {Pendula-phenotyped Norway spruce has a potential forestry interest for high-density plantations. This phenotype is believed to be caused by a dominant single mutation. Despite the availability of RAPD markers linked to the trait, the nature of the mutation is yet unknown. We performed a quantitative trait loci (QTL) mapping based on two different progenies of F1 crosses between pendula and normal crowned trees using NGS technologies. Approximately 25\% of all gene bearing scaffolds of Picea abies genome assembly v1.0 were mapped to 12 linkage groups and a single QTL, positioned near the center of LG VI, was found in both crosses. The closest probe markers placed on the maps were positioned 0.82 cm and 0.48 cm away from the Pendula marker in two independent pendula-crowned × normal-crowned wild-type crosses, respectively. We have identified genes close to the QTL region with differential mutations on coding regions and discussed their potential role in changing branch architecture.},
	language = {en},
	number = {3},
	urldate = {2023-05-08},
	journal = {Tree Genetics \& Genomes},
	author = {Gil-Muñoz, Francisco and Bernhardsson, Carolina and Ranade, Sonali Sachin and Scofield, Douglas G. and Pulkkinen, Pertti O. and Ingvarsson, Pär K. and García-Gil, M. Rosario},
	month = may,
	year = {2023},
	keywords = {Forest breeding, Genetic map, Pendula, Picea, QTL, Spruce},
	pages = {28},
}

Pendula-phenotyped Norway spruce has a potential forestry interest for high-density plantations. This phenotype is believed to be caused by a dominant single mutation. Despite the availability of RAPD markers linked to the trait, the nature of the mutation is yet unknown. We performed a quantitative trait loci (QTL) mapping based on two different progenies of F1 crosses between pendula and normal crowned trees using NGS technologies. Approximately 25% of all gene bearing scaffolds of Picea abies genome assembly v1.0 were mapped to 12 linkage groups and a single QTL, positioned near the center of LG VI, was found in both crosses. The closest probe markers placed on the maps were positioned 0.82 cm and 0.48 cm away from the Pendula marker in two independent pendula-crowned × normal-crowned wild-type crosses, respectively. We have identified genes close to the QTL region with differential mutations on coding regions and discussed their potential role in changing branch architecture.

@article{ranade_adaptive_2022,
	title = {Adaptive strategies of {Scots} pine under shade: increase in lignin synthesis and ecotypic variation in defence-related gene expression},
	volume = {2022-10},
	issn = {1399-3054},
	shorttitle = {Adaptive strategies of {Scots} pine under shade},
	url = {https://onlinelibrary.wiley.com/doi/abs/10.1111/ppl.13792},
	doi = {10.1111/ppl.13792},
	abstract = {Shade is a stressful condition for plants characterized by low Red:Far-Red (R:FR) ratio. The northern latitudes in Sweden daily receive more hours of FR-enriched light (twilight) or shade-like conditions compared to southern forests during the growth season. Scots pine (Pinus sylvestris L.) is a shade-intolerant species. Yet, it is well adapted to this latitudinal variation in light, which is evident by a northward increase in FR requirement to maintain growth. Shade adversely affects plant growth; it makes the plant weak and, therefore, susceptible to pathogen attack. Lignin is involved in plant protection against pathogen invasion mainly by forming a physical barrier. We studied lignin synthesis and expression of defence-related genes (growth-defence trade-offs) under a low R:FR (shade) ratio in Scots pine. A higher number of immunity/defence-related genes were up-regulated in response to shade in northern populations compared to southern ones, which can be viewed as a local adaptation to light quality for optimal growth and survival. Light quality regulates lignin metabolism; light stimulates lignin synthesis, while shade causes a decrease in lignin synthesis in most angiosperms. In contrast, Scots pine shows an increase in lignin synthesis supported by the higher expression of a few key genes in the lignin biosynthetic pathway, a novel finding reported by our study. These findings can be applied to future breeding strategies in forestry to produce disease-resilient trees.},
	language = {en},
	urldate = {2022-10-06},
	journal = {Physiologia Plantarum},
	author = {Ranade, Sonali Sachin and Seipel, George and Gorzsás, András and García-Gil, María Rosario},
	month = sep,
	year = {2022},
	pages = {e13792},
}

Shade is a stressful condition for plants characterized by low Red:Far-Red (R:FR) ratio. The northern latitudes in Sweden daily receive more hours of FR-enriched light (twilight) or shade-like conditions compared to southern forests during the growth season. Scots pine (Pinus sylvestris L.) is a shade-intolerant species. Yet, it is well adapted to this latitudinal variation in light, which is evident by a northward increase in FR requirement to maintain growth. Shade adversely affects plant growth; it makes the plant weak and, therefore, susceptible to pathogen attack. Lignin is involved in plant protection against pathogen invasion mainly by forming a physical barrier. We studied lignin synthesis and expression of defence-related genes (growth-defence trade-offs) under a low R:FR (shade) ratio in Scots pine. A higher number of immunity/defence-related genes were up-regulated in response to shade in northern populations compared to southern ones, which can be viewed as a local adaptation to light quality for optimal growth and survival. Light quality regulates lignin metabolism; light stimulates lignin synthesis, while shade causes a decrease in lignin synthesis in most angiosperms. In contrast, Scots pine shows an increase in lignin synthesis supported by the higher expression of a few key genes in the lignin biosynthetic pathway, a novel finding reported by our study. These findings can be applied to future breeding strategies in forestry to produce disease-resilient trees.

@article{ranade_enhanced_2022,
	title = {Enhanced lignin synthesis and ecotypic variation in defense-related gene expression in response to shade in {Norway} spruce},
	volume = {45},
	issn = {1365-3040},
	url = {https://onlinelibrary.wiley.com/doi/abs/10.1111/pce.14387},
	doi = {10.1111/pce.14387},
	abstract = {During the growth season, northern forests in Sweden daily receive more hours of far-red (FR)-enriched light or twilight (shade) as compared to southern forests. Norway spruce (shade-tolerant) are adapted to latitudinal variation in twilight characterized by a northward increase in FR requirement to maintain growth. Shade is a stressful condition that affects plant growth and increases plant's susceptibility to pathogen attack. Lignin plays a central role in plant defense and its metabolism is regulated by light wavelength composition (light quality). In the current work, we studied regulation of lignin synthesis and defense-related genes (growth-defense trade-offs) in response to shade in Norway spruce. In most angiosperms, light promotes lignin synthesis, whereas shade decreases lignin production leading to weaker stem, which may make plants more disease susceptible. In contrast, enhanced lignin synthesis was detected in response to shade in Norway spruce. We detected a higher number of immunity/defense-related genes up-regulated in northern populations as compared to south ones in response to shade. Enhanced lignin synthesis coupled with higher defense-related gene expression can be interpreted as an adaptive strategy for better survival in northern populations. Findings will contribute to ensuring deployment of well-adapted genetic material and identifying tree families with enhanced disease resistance.},
	language = {en},
	number = {9},
	urldate = {2022-08-19},
	journal = {Plant, Cell \& Environment},
	author = {Ranade, Sonali Sachin and Seipel, George and Gorzsás, András and García-Gil, María Rosario},
	year = {2022},
	note = {\_eprint: https://onlinelibrary.wiley.com/doi/pdf/10.1111/pce.14387},
	keywords = {Conifer, Defense, Ecotypic variation, Immunity, Light quality, Lignin, Local adaptation, Norway spruce, R:FR ratio, RNA sequencing, Response to shade, conifer, disease resistance, far-red light, immunity, latitudinal cline, light quality, local adaptation, red light},
	pages = {2671--2681},
}

During the growth season, northern forests in Sweden daily receive more hours of far-red (FR)-enriched light or twilight (shade) as compared to southern forests. Norway spruce (shade-tolerant) are adapted to latitudinal variation in twilight characterized by a northward increase in FR requirement to maintain growth. Shade is a stressful condition that affects plant growth and increases plant's susceptibility to pathogen attack. Lignin plays a central role in plant defense and its metabolism is regulated by light wavelength composition (light quality). In the current work, we studied regulation of lignin synthesis and defense-related genes (growth-defense trade-offs) in response to shade in Norway spruce. In most angiosperms, light promotes lignin synthesis, whereas shade decreases lignin production leading to weaker stem, which may make plants more disease susceptible. In contrast, enhanced lignin synthesis was detected in response to shade in Norway spruce. We detected a higher number of immunity/defense-related genes up-regulated in northern populations as compared to south ones in response to shade. Enhanced lignin synthesis coupled with higher defense-related gene expression can be interpreted as an adaptive strategy for better survival in northern populations. Findings will contribute to ensuring deployment of well-adapted genetic material and identifying tree families with enhanced disease resistance.

@article{chen_genetic_2022,
	title = {Genetic architecture behind developmental and seasonal control of tree growth and wood properties in {Norway} spruce},
	volume = {13},
	issn = {1664-462X},
	url = {https://www.frontiersin.org/articles/10.3389/fpls.2022.927673},
	abstract = {Genetic control of tree growth and wood formation varies depending on the age of the tree and the time of the year. Single-locus, multi-locus, and multi-trait genome-wide association studies (GWAS) were conducted on 34 growth and wood property traits in 1,303 Norway spruce individuals using exome capture to cover {\textasciitilde}130K single-nucleotide polymorphisms (SNPs). GWAS identified associations to the different wood traits in a total of 85 gene models, and several of these were validated in a progenitor population. A multi-locus GWAS model identified more SNPs associated with the studied traits than single-locus or multivariate models. Changes in tree age and annual season influenced the genetic architecture of growth and wood properties in unique ways, manifested by non-overlapping SNP loci. In addition to completely novel candidate genes, SNPs were located in genes previously associated with wood formation, such as cellulose synthases and a NAC transcription factor, but that have not been earlier linked to seasonal or age-dependent regulation of wood properties. Interestingly, SNPs associated with the width of the year rings were identified in homologs of Arabidopsis thaliana BARELY ANY MERISTEM 1 and rice BIG GRAIN 1, which have been previously shown to control cell division and biomass production. The results provide tools for future Norway spruce breeding and functional studies.},
	urldate = {2022-09-01},
	journal = {Frontiers in Plant Science},
	author = {Chen, Zhi-Qiang and Zan, Yanjun and Zhou, Linghua and Karlsson, Bo and Tuominen, Hannele and García-Gil, Maria Rosario and Wu, Harry X.},
	month = aug,
	year = {2022},
	keywords = {⛔ No DOI found},
}

Genetic control of tree growth and wood formation varies depending on the age of the tree and the time of the year. Single-locus, multi-locus, and multi-trait genome-wide association studies (GWAS) were conducted on 34 growth and wood property traits in 1,303 Norway spruce individuals using exome capture to cover ~130K single-nucleotide polymorphisms (SNPs). GWAS identified associations to the different wood traits in a total of 85 gene models, and several of these were validated in a progenitor population. A multi-locus GWAS model identified more SNPs associated with the studied traits than single-locus or multivariate models. Changes in tree age and annual season influenced the genetic architecture of growth and wood properties in unique ways, manifested by non-overlapping SNP loci. In addition to completely novel candidate genes, SNPs were located in genes previously associated with wood formation, such as cellulose synthases and a NAC transcription factor, but that have not been earlier linked to seasonal or age-dependent regulation of wood properties. Interestingly, SNPs associated with the width of the year rings were identified in homologs of Arabidopsis thaliana BARELY ANY MERISTEM 1 and rice BIG GRAIN 1, which have been previously shown to control cell division and biomass production. The results provide tools for future Norway spruce breeding and functional studies.

@incollection{calleja-rodriguez_genomic_2022,
	address = {Cham},
	title = {Genomic {Selection} in {Scots} ({Pinus} {Sylvestris}) and {Radiata} ({Pinus} {Radiata}) {Pines}},
	isbn = {978-3-030-93390-6},
	url = {https://doi.org/10.1007/978-3-030-93390-6_11},
	doi = {10.1007/978-3-030-93390-6_11},
	abstract = {Pines are economically important species widely planted across the globe. Therefore, the industry is interested in increasing the efficacy of their breeding programs, which explains the urge to implement new technological solutions to increase breeding efficiency for traditional and novel breeding objectives. Recently, the development of genotyping platforms accessible even for non-model organisms such as Scots and radiata pines has made it possible to evaluate genomic selection for their breeding programs. Genomic studies in both species are limited by the size and complexity of their genomes; therefore, genotyping platforms based on reduced genome representation have been implemented. Genomic selection studies performed within their breeding programs show viability and potential to increase the intensity of genetic progress compared to conventional (i.e., pedigree-based) strategies. Additionally, genomic prediction of traits with challenging or costly phenotyping, such as forest diseases or wood quality and cell wall chemistry, might allow for large-scale screening and selection of individuals with superior traits. This chapter presents a review of the recent research on genomic selection for Scots pine in Sweden, and radiata pine in New Zealand, as well as future perspectives for the implementation of this methodology in their breeding programs.},
	language = {en},
	urldate = {2024-10-16},
	booktitle = {The {Pine} {Genomes}},
	publisher = {Springer International Publishing},
	author = {Calleja-Rodríguez, Ainhoa and Klápště, Jaroslav and Dungey, Heidi and Graham, Natalie and Ismael, Ahmed and García-Gil, Maria Rosario and Abrahamsson, Sara and Suontama, Mari},
	editor = {De La Torre, Amanda R.},
	year = {2022},
	pages = {233--250},
}

Pines are economically important species widely planted across the globe. Therefore, the industry is interested in increasing the efficacy of their breeding programs, which explains the urge to implement new technological solutions to increase breeding efficiency for traditional and novel breeding objectives. Recently, the development of genotyping platforms accessible even for non-model organisms such as Scots and radiata pines has made it possible to evaluate genomic selection for their breeding programs. Genomic studies in both species are limited by the size and complexity of their genomes; therefore, genotyping platforms based on reduced genome representation have been implemented. Genomic selection studies performed within their breeding programs show viability and potential to increase the intensity of genetic progress compared to conventional (i.e., pedigree-based) strategies. Additionally, genomic prediction of traits with challenging or costly phenotyping, such as forest diseases or wood quality and cell wall chemistry, might allow for large-scale screening and selection of individuals with superior traits. This chapter presents a review of the recent research on genomic selection for Scots pine in Sweden, and radiata pine in New Zealand, as well as future perspectives for the implementation of this methodology in their breeding programs.

@article{gauchan_annulohypoxylon_2021,
	title = {Annulohypoxylon sp. strain {MUS1}, an endophytic fungus isolated from {Taxus} wallichiana {Zucc}., produces taxol and other bioactive metabolites},
	volume = {11},
	issn = {2190-572X, 2190-5738},
	url = {http://link.springer.com/10.1007/s13205-021-02693-z},
	doi = {10/gkcr8j},
	language = {en},
	number = {3},
	urldate = {2021-06-03},
	journal = {3 Biotech},
	author = {Gauchan, Dhurva Prasad and Vélëz, Heriberto and Acharya, Ashesh and Östman, Johnny R. and Lundén, Karl and Elfstrand, Malin and García-Gil, M. Rosario},
	month = mar,
	year = {2021},
	pages = {152},
}

@article{chen_leveraging_2021,
	title = {Leveraging breeding programs and genomic data in {Norway} spruce ({Picea} abies {L}. {Karst}) for {GWAS} analysis},
	volume = {22},
	issn = {1474-760X},
	url = {https://doi.org/10.1186/s13059-021-02392-1},
	doi = {10.1186/s13059-021-02392-1},
	abstract = {Genome-wide association studies (GWAS) identify loci underlying the variation of complex traits. One of the main limitations of GWAS is the availability of reliable phenotypic data, particularly for long-lived tree species. Although an extensive amount of phenotypic data already exists in breeding programs, accounting for its high heterogeneity is a great challenge. We combine spatial and factor-analytics analyses to standardize the heterogeneous data from 120 field experiments of 483,424 progenies of Norway spruce to implement the largest reported GWAS for trees using 134 605 SNPs from exome sequencing of 5056 parental trees.},
	number = {1},
	urldate = {2021-10-14},
	journal = {Genome Biology},
	author = {Chen, Zhi-Qiang and Zan, Yanjun and Milesi, Pascal and Zhou, Linghua and Chen, Jun and Li, Lili and Cui, BinBin and Niu, Shihui and Westin, Johan and Karlsson, Bo and García-Gil, Maria Rosario and Lascoux, Martin and Wu, Harry X.},
	month = jun,
	year = {2021},
	keywords = {Budburst stage, Frost damage, Genome-wide association study, MAP3K gene, Norway spruce, Wood quality},
	pages = {179},
}

Genome-wide association studies (GWAS) identify loci underlying the variation of complex traits. One of the main limitations of GWAS is the availability of reliable phenotypic data, particularly for long-lived tree species. Although an extensive amount of phenotypic data already exists in breeding programs, accounting for its high heterogeneity is a great challenge. We combine spatial and factor-analytics analyses to standardize the heterogeneous data from 120 field experiments of 483,424 progenies of Norway spruce to implement the largest reported GWAS for trees using 134 605 SNPs from exome sequencing of 5056 parental trees.

@article{ahlinder_life_2021,
	title = {Life stage-specific inbreeding depression in long-lived {Pinaceae} species depends on population connectivity},
	volume = {11},
	issn = {2045-2322},
	url = {http://www.nature.com/articles/s41598-021-88128-4},
	doi = {10.1038/s41598-021-88128-4},
	abstract = {Inbreeding depression (ID) is a fundamental selective pressure that shapes mating systems and population genetic structures in plants. Although it has been shown that ID varies over the life stages of shorter-lived plants, less is known about how the fitness effects of inbreeding vary across life stages in long-lived species. We conducted a literature survey in the Pinaceae, a tree family known to harbour some of the highest mutational loads ever reported. Using a meta-regression model, we investigated distributions of inbreeding depression over life stages, adjusting for effects of inbreeding levels and the genetic differentiation of populations within species. The final dataset contained 147 estimates of ID across life stages from 41 studies. 44 Fst estimates were collected from 40 peer-reviewed studies for the 18 species to aid genetic differentiation modelling. Partitioning species into fragmented and well-connected groups using Fst resulted in the best way (i.e. trade-off between high goodness-of-fit of the model to the data and reduced model complexity) to incorporate genetic connectivity in the meta-regression analysis. Inclusion of a life stage term and its interaction with the inbreeding coefficient (F) dramatically increased model precision. We observed that the correlation between ID and F was significant at the earliest life stage. Although partitioning of species populations into fragmented and well-connected groups explained little of the between-study heterogeneity, the inclusion of an interaction between life stage and population differentiation revealed that populations with fragmented distributions suffered lower inbreeding depression at early embryonic stages than species with well-connected populations. There was no evidence for increased ID in late life stages in well-connected populations, although ID tended to increase across life stages in the fragmented group. These findings suggest that life stage data should be included in inbreeding depression studies and that inbreeding needs to be managed over life stages in commercial populations of long-lived plants.},
	language = {en},
	number = {1},
	urldate = {2021-06-03},
	journal = {Scientific Reports},
	author = {Ahlinder, Jon and Giles, Barbara E. and García-Gil, M. Rosario},
	month = apr,
	year = {2021},
	pages = {8834},
}

Inbreeding depression (ID) is a fundamental selective pressure that shapes mating systems and population genetic structures in plants. Although it has been shown that ID varies over the life stages of shorter-lived plants, less is known about how the fitness effects of inbreeding vary across life stages in long-lived species. We conducted a literature survey in the Pinaceae, a tree family known to harbour some of the highest mutational loads ever reported. Using a meta-regression model, we investigated distributions of inbreeding depression over life stages, adjusting for effects of inbreeding levels and the genetic differentiation of populations within species. The final dataset contained 147 estimates of ID across life stages from 41 studies. 44 Fst estimates were collected from 40 peer-reviewed studies for the 18 species to aid genetic differentiation modelling. Partitioning species into fragmented and well-connected groups using Fst resulted in the best way (i.e. trade-off between high goodness-of-fit of the model to the data and reduced model complexity) to incorporate genetic connectivity in the meta-regression analysis. Inclusion of a life stage term and its interaction with the inbreeding coefficient (F) dramatically increased model precision. We observed that the correlation between ID and F was significant at the earliest life stage. Although partitioning of species populations into fragmented and well-connected groups explained little of the between-study heterogeneity, the inclusion of an interaction between life stage and population differentiation revealed that populations with fragmented distributions suffered lower inbreeding depression at early embryonic stages than species with well-connected populations. There was no evidence for increased ID in late life stages in well-connected populations, although ID tended to increase across life stages in the fragmented group. These findings suggest that life stage data should be included in inbreeding depression studies and that inbreeding needs to be managed over life stages in commercial populations of long-lived plants.

@article{ranade_molecular_2021,
	title = {Molecular signatures of local adaptation to light in {Norway} spruce},
	volume = {253},
	issn = {0032-0935, 1432-2048},
	url = {http://link.springer.com/10.1007/s00425-020-03517-9},
	doi = {10/gjd69n},
	abstract = {Abstract
            
              Main conclusion
              Transcriptomic and exome capture analysis reveal an adaptive cline for shade tolerance in Norway spruce. Genes involved in the lignin pathway and immunity seem to play a potential role in contributing towards local adaptation to light.
            
            
              Abstract
              The study of natural variation is an efficient method to elucidate how plants adapt to local climatic conditions, a key process for the evolution of a species. Norway spruce is a shade-tolerant conifer in which the requirement of far-red light for growth increases latitudinally northwards. The objective of the study is to characterize the genetic control of local adaptation to light enriched in far-red in Norway spruce, motivated by a latitudinal gradient for the Red:Far-red (R:FR) ratio to which Norway spruce has been proven to be genetically adapted. We have established the genomic signatures of local adaptation by conducting transcriptomic (total RNA-sequencing) and genomic analyses (exome capture), for the identification of genes differentially regulated along the cline. RNA-sequencing revealed 274 differentially expressed genes in response to SHADE (low R:FR light), between the southern and northern natural populations in Sweden. Exome capture included analysis of a uniquely large data set (1654 trees) that revealed missense variations in coding regions of nine differentially expressed candidate genes, which followed a latitudinal cline in allele and genotype frequencies. These genes included five transcription factors involved in vital processes like bud-set/bud-flush, lignin pathway, and cold acclimation and other genes that take part in cell-wall remodeling, secondary cell-wall thickening, response to starvation, and immunity. Based on these results, we suggest that the northern populations might not only be able to adjust their growing season in response to low R:FR light, but they may also be better adapted towards disease resistance by up-regulation of the lignin pathway that is linked to immunity. This forms a concrete basis for local adaptation to light quality in Norway spruce, one of the most economically important conifer tree species in Sweden.},
	language = {en},
	number = {2},
	urldate = {2021-06-03},
	journal = {Planta},
	author = {Ranade, Sonali Sachin and García-Gil, María Rosario},
	month = feb,
	year = {2021},
	pages = {53},
}

Abstract Main conclusion Transcriptomic and exome capture analysis reveal an adaptive cline for shade tolerance in Norway spruce. Genes involved in the lignin pathway and immunity seem to play a potential role in contributing towards local adaptation to light. Abstract The study of natural variation is an efficient method to elucidate how plants adapt to local climatic conditions, a key process for the evolution of a species. Norway spruce is a shade-tolerant conifer in which the requirement of far-red light for growth increases latitudinally northwards. The objective of the study is to characterize the genetic control of local adaptation to light enriched in far-red in Norway spruce, motivated by a latitudinal gradient for the Red:Far-red (R:FR) ratio to which Norway spruce has been proven to be genetically adapted. We have established the genomic signatures of local adaptation by conducting transcriptomic (total RNA-sequencing) and genomic analyses (exome capture), for the identification of genes differentially regulated along the cline. RNA-sequencing revealed 274 differentially expressed genes in response to SHADE (low R:FR light), between the southern and northern natural populations in Sweden. Exome capture included analysis of a uniquely large data set (1654 trees) that revealed missense variations in coding regions of nine differentially expressed candidate genes, which followed a latitudinal cline in allele and genotype frequencies. These genes included five transcription factors involved in vital processes like bud-set/bud-flush, lignin pathway, and cold acclimation and other genes that take part in cell-wall remodeling, secondary cell-wall thickening, response to starvation, and immunity. Based on these results, we suggest that the northern populations might not only be able to adjust their growing season in response to low R:FR light, but they may also be better adapted towards disease resistance by up-regulation of the lignin pathway that is linked to immunity. This forms a concrete basis for local adaptation to light quality in Norway spruce, one of the most economically important conifer tree species in Sweden.

@article{zhou_effect_2020,
	title = {Effect of number of annual rings and tree ages on genomic predictive ability for solid wood properties of {Norway} spruce},
	volume = {21},
	issn = {1471-2164},
	url = {https://bmcgenomics.biomedcentral.com/articles/10.1186/s12864-020-6737-3},
	doi = {10.1186/s12864-020-6737-3},
	abstract = {Abstract
            
              Background
              
                Genomic selection (GS) or genomic prediction is considered as a promising approach to accelerate tree breeding and increase genetic gain by shortening breeding cycle, but the efforts to develop routines for operational breeding are so far limited. We investigated the predictive ability (PA) of GS based on 484 progeny trees from 62 half-sib families in Norway spruce (
                Picea abies
                (L.) Karst.) for wood density, modulus of elasticity (MOE) and microfibril angle (MFA) measured with SilviScan, as well as for measurements on standing trees by Pilodyn and Hitman instruments.
              
            
            
              Results
              GS predictive abilities were comparable with those based on pedigree-based prediction. Marker-based PAs were generally 25–30\% higher for traits density, MFA and MOE measured with SilviScan than for their respective standing tree-based method which measured with Pilodyn and Hitman. Prediction accuracy (PC) of the standing tree-based methods were similar or even higher than increment core-based method. 78–95\% of the maximal PAs of density, MFA and MOE obtained from coring to the pith at high age were reached by using data possible to obtain by drilling 3–5 rings towards the pith at tree age 10–12.
            
            
              Conclusions
              This study indicates standing tree-based measurements is a cost-effective alternative method for GS. PA of GS methods were comparable with those pedigree-based prediction. The highest PAs were reached with at least 80–90\% of the dataset used as training set. Selection for trait density could be conducted at an earlier age than for MFA and MOE. Operational breeding can also be optimized by training the model at an earlier age or using 3 to 5 outermost rings at tree age 10 to 12 years, thereby shortening the cycle and reducing the impact on the tree.},
	language = {en},
	number = {1},
	urldate = {2021-06-07},
	journal = {BMC Genomics},
	author = {Zhou, Linghua and Chen, Zhiqiang and Olsson, Lars and Grahn, Thomas and Karlsson, Bo and Wu, Harry X. and Lundqvist, Sven-Olof and García-Gil, María Rosario},
	month = dec,
	year = {2020},
	pages = {323},
}

Abstract Background Genomic selection (GS) or genomic prediction is considered as a promising approach to accelerate tree breeding and increase genetic gain by shortening breeding cycle, but the efforts to develop routines for operational breeding are so far limited. We investigated the predictive ability (PA) of GS based on 484 progeny trees from 62 half-sib families in Norway spruce ( Picea abies (L.) Karst.) for wood density, modulus of elasticity (MOE) and microfibril angle (MFA) measured with SilviScan, as well as for measurements on standing trees by Pilodyn and Hitman instruments. Results GS predictive abilities were comparable with those based on pedigree-based prediction. Marker-based PAs were generally 25–30% higher for traits density, MFA and MOE measured with SilviScan than for their respective standing tree-based method which measured with Pilodyn and Hitman. Prediction accuracy (PC) of the standing tree-based methods were similar or even higher than increment core-based method. 78–95% of the maximal PAs of density, MFA and MOE obtained from coring to the pith at high age were reached by using data possible to obtain by drilling 3–5 rings towards the pith at tree age 10–12. Conclusions This study indicates standing tree-based measurements is a cost-effective alternative method for GS. PA of GS methods were comparable with those pedigree-based prediction. The highest PAs were reached with at least 80–90% of the dataset used as training set. Selection for trait density could be conducted at an earlier age than for MFA and MOE. Operational breeding can also be optimized by training the model at an earlier age or using 3 to 5 outermost rings at tree age 10 to 12 years, thereby shortening the cycle and reducing the impact on the tree.

@article{gauchan_evaluation_2020,
	title = {Evaluation of antimicrobial, antioxidant and cytotoxic properties of bioactive compounds produced from endophytic fungi of {Himalayan} yew ({Taxus} wallichiana) in {Nepal}},
	volume = {9},
	issn = {2046-1402},
	url = {https://f1000research.com/articles/9-379/v2},
	doi = {10.12688/f1000research.23250.2},
	abstract = {Background:
              Endophytic fungi are largely underexplored in the discovery of natural bioactive products though being rich sources of novel compounds with promising pharmaceutical potential. In this study,
              Taxus wallichiana,
              which has huge medicinal value, was investigated for its endophytic diversity and capability to produce bioactive secondary metabolites by analyzing antioxidant, antimicrobial and cytotoxic properties.
            
            
              Methods:
              The endophytes were identified by ITS-PCR using genomic DNA samples. The secondary metabolites were extracted by solvent extraction method using ethyl acetate. The antioxidant activity was analyzed by Thin Layer Chromatography, Total Phenol Content (TPC), Total Flavonoid Content (TFC) and DPPH assay, and the antimicrobial activity was analyzed by agar-well diffusion method. Brine shrimp lethality assay was used to analyze the cytotoxicity of the fungal extracts.
            
            
              Results:
              Out of 16 different
              Taxus
              trees sampled from different locations of Dhorpatan, 13 distinctive endophytic fungi were isolated and grouped into 9 different genera:
              Bjerkandera, Trichoderma, Preussia, Botrytis, Arthrinium, Alternaria, Cladosporium, Sporormiella
              and
              Daldinia
              . The ethyl acetate extracts isolated from three endophytic fungi:
              Alternaria alternata
              ,
              Cladosporium cladosporioides
              and
              Alternaria brassicae
              showed significant TPC values of 204±6.144, 312.3±2.147 and 152.7±4.958µg GAE/mg of dry extract, respectively, and TFC values of 177.9±2.911, 644.1±4.202 and 96.38±3.851µg RE/mg of dry extract, respectively. Furthermore, these three extracts showed a dose dependent radical scavenging activity with IC
              50
              concentration of 22.85, 22.15 and 23.001 µg/ml, respectively. The extracts of
              C. cladosporioides
              and
              A. brassicae
              also showed promising antimicrobial activity against
              Escherichia coli
              ,
              Staphylococcus aureus
              and
              Bacillus subtilis
              with a minimum inhibitory concentration of 250μg/ml for all bacteria. Both the samples showed cytotoxic property against shrimp nauplii with LC
              50
              of 104.2 and 125.9µg/ml, respectively.
            
            
              Conclusions:
              The crude fungal extracts obtained from endophytes:
              A. alternata
              ,
              C. cladosporioides
              and
              A. brassicae
              upon purification and further identification of the bioactive compounds can be a fascinating source for novel pharmaceutical agents.},
	language = {en},
	urldate = {2021-06-07},
	journal = {F1000Research},
	author = {Gauchan, Dhurva Prasad and Kandel, Pratistha and Tuladhar, Astha and Acharya, Ashesh and Kadel, Upendra and Baral, Aayush and Shahi, Arjan Bir and García-Gil, María Rosario},
	month = oct,
	year = {2020},
	pages = {379},
}

Background: Endophytic fungi are largely underexplored in the discovery of natural bioactive products though being rich sources of novel compounds with promising pharmaceutical potential. In this study, Taxus wallichiana, which has huge medicinal value, was investigated for its endophytic diversity and capability to produce bioactive secondary metabolites by analyzing antioxidant, antimicrobial and cytotoxic properties. Methods: The endophytes were identified by ITS-PCR using genomic DNA samples. The secondary metabolites were extracted by solvent extraction method using ethyl acetate. The antioxidant activity was analyzed by Thin Layer Chromatography, Total Phenol Content (TPC), Total Flavonoid Content (TFC) and DPPH assay, and the antimicrobial activity was analyzed by agar-well diffusion method. Brine shrimp lethality assay was used to analyze the cytotoxicity of the fungal extracts. Results: Out of 16 different Taxus trees sampled from different locations of Dhorpatan, 13 distinctive endophytic fungi were isolated and grouped into 9 different genera: Bjerkandera, Trichoderma, Preussia, Botrytis, Arthrinium, Alternaria, Cladosporium, Sporormiella and Daldinia . The ethyl acetate extracts isolated from three endophytic fungi: Alternaria alternata , Cladosporium cladosporioides and Alternaria brassicae showed significant TPC values of 204±6.144, 312.3±2.147 and 152.7±4.958µg GAE/mg of dry extract, respectively, and TFC values of 177.9±2.911, 644.1±4.202 and 96.38±3.851µg RE/mg of dry extract, respectively. Furthermore, these three extracts showed a dose dependent radical scavenging activity with IC 50 concentration of 22.85, 22.15 and 23.001 µg/ml, respectively. The extracts of C. cladosporioides and A. brassicae also showed promising antimicrobial activity against Escherichia coli , Staphylococcus aureus and Bacillus subtilis with a minimum inhibitory concentration of 250μg/ml for all bacteria. Both the samples showed cytotoxic property against shrimp nauplii with LC 50 of 104.2 and 125.9µg/ml, respectively. Conclusions: The crude fungal extracts obtained from endophytes: A. alternata , C. cladosporioides and A. brassicae upon purification and further identification of the bioactive compounds can be a fascinating source for novel pharmaceutical agents.

@article{baison_genetic_2020,
	title = {Genetic control of tracheid properties in {Norway} spruce wood},
	volume = {10},
	issn = {2045-2322},
	url = {http://www.nature.com/articles/s41598-020-72586-3},
	doi = {10.1038/s41598-020-72586-3},
	abstract = {Abstract
            
              Through the use of genome-wide association studies (GWAS) mapping it is possible to establish the genetic basis of phenotypic trait variation. Our GWAS study presents the first such effort in Norway spruce (
              Picea abies
              (L). Karst.) for the traits related to wood tracheid characteristics. The study employed an exome capture genotyping approach that generated 178 101 Single Nucleotide Polymorphisms (SNPs) from 40 018 probes within a population of 517 Norway spruce mother trees. We applied a least absolute shrinkage and selection operator (LASSO) based association mapping method using a functional multi-locus mapping approach, with a stability selection probability method as the hypothesis testing approach to determine significant Quantitative Trait Loci (QTLs). The analysis has provided 30 significant associations, the majority of which show specific expression in wood-forming tissues or high ubiquitous expression, potentially controlling tracheids dimensions, their cell wall thickness and microfibril angle. Among the most promising candidates based on our results and prior information for other species are:
              Picea abies BIG GRAIN 2
              (
              PabBG2)
              with a predicted function in auxin transport and sensitivity, and
              MA\_373300g0010
              encoding a protein similar to wall-associated receptor kinases, which were both associated with cell wall thickness. The results demonstrate feasibility of GWAS to identify novel candidate genes controlling industrially-relevant tracheid traits in Norway spruce.},
	language = {en},
	number = {1},
	urldate = {2021-06-07},
	journal = {Scientific Reports},
	author = {Baison, J. and Zhou, Linghua and Forsberg, Nils and Mörling, Tommy and Grahn, Thomas and Olsson, Lars and Karlsson, Bo and Wu, Harry X. and Mellerowicz, Ewa J. and Lundqvist, Sven-Olof and García-Gil, María Rosario},
	month = dec,
	year = {2020},
	pages = {18089},
}

Abstract Through the use of genome-wide association studies (GWAS) mapping it is possible to establish the genetic basis of phenotypic trait variation. Our GWAS study presents the first such effort in Norway spruce ( Picea abies (L). Karst.) for the traits related to wood tracheid characteristics. The study employed an exome capture genotyping approach that generated 178 101 Single Nucleotide Polymorphisms (SNPs) from 40 018 probes within a population of 517 Norway spruce mother trees. We applied a least absolute shrinkage and selection operator (LASSO) based association mapping method using a functional multi-locus mapping approach, with a stability selection probability method as the hypothesis testing approach to determine significant Quantitative Trait Loci (QTLs). The analysis has provided 30 significant associations, the majority of which show specific expression in wood-forming tissues or high ubiquitous expression, potentially controlling tracheids dimensions, their cell wall thickness and microfibril angle. Among the most promising candidates based on our results and prior information for other species are: Picea abies BIG GRAIN 2 ( PabBG2) with a predicted function in auxin transport and sensitivity, and MA_373300g0010 encoding a protein similar to wall-associated receptor kinases, which were both associated with cell wall thickness. The results demonstrate feasibility of GWAS to identify novel candidate genes controlling industrially-relevant tracheid traits in Norway spruce.

@article{gil-munoz_transcriptomic_2020,
	title = {Transcriptomic {Analysis} {Reveals} {Salt} {Tolerance} {Mechanisms} {Present} in {Date}-{Plum} {Persimmon} {Rootstock} ({Diospyros} lotus {L}.)},
	volume = {10},
	issn = {2073-4395},
	url = {https://www.mdpi.com/2073-4395/10/11/1703},
	doi = {10/gjd6kb},
	abstract = {Agriculture needs solutions for adapting crops to increasing salinity globally. Research on physiological and molecular responses activated by salinity is needed to elucidate mechanisms of salinity tolerance. Transcriptome profiling (RNA-Seq) is a powerful tool to study the transcriptomic profile of genotypes under stress conditions. Persimmon species have different levels of tolerance to salinity, this variability may provide knowledge on persimmon species and development of salt--tolerant rootstocks. In this study, we conducted a physiological and transcriptomic profiling of roots and leaves in tolerant and sensitive plants of persimmon rootstock grown under saline and control conditions. Characterization of physiological responses along with gene expression changes in roots and leaves allowed the identification of several salt tolerance mechanisms related to ion transport and thermospermine synthesis. Differences were observed in putative H+/ATPases that allow transmembrane ionic transport and chloride channel protein-like genes. Furthermore, an overexpression of thermospermine synthase found in the roots of tolerant plants may indicate that alterations in root architecture could act as an additional mechanism of response to salt stress. These results indicate that Diospyros lotus L. exhibits genetically-controlled variability for salt tolerance traits which opens potential opportunities for breeding salt-tolerant persimmon rootstocks in a Mediterranean environment challenged by drought and salinity.},
	language = {en},
	number = {11},
	urldate = {2021-06-07},
	journal = {Agronomy},
	author = {Gil-Muñoz, Francisco and Delhomme, Nicolas and Quiñones, Ana and Naval, Maria del Mar and Badenes, Maria Luisa and García-Gil, M. Rosario},
	month = nov,
	year = {2020},
	pages = {1703},
}

Agriculture needs solutions for adapting crops to increasing salinity globally. Research on physiological and molecular responses activated by salinity is needed to elucidate mechanisms of salinity tolerance. Transcriptome profiling (RNA-Seq) is a powerful tool to study the transcriptomic profile of genotypes under stress conditions. Persimmon species have different levels of tolerance to salinity, this variability may provide knowledge on persimmon species and development of salt–tolerant rootstocks. In this study, we conducted a physiological and transcriptomic profiling of roots and leaves in tolerant and sensitive plants of persimmon rootstock grown under saline and control conditions. Characterization of physiological responses along with gene expression changes in roots and leaves allowed the identification of several salt tolerance mechanisms related to ion transport and thermospermine synthesis. Differences were observed in putative H+/ATPases that allow transmembrane ionic transport and chloride channel protein-like genes. Furthermore, an overexpression of thermospermine synthase found in the roots of tolerant plants may indicate that alterations in root architecture could act as an additional mechanism of response to salt stress. These results indicate that Diospyros lotus L. exhibits genetically-controlled variability for salt tolerance traits which opens potential opportunities for breeding salt-tolerant persimmon rootstocks in a Mediterranean environment challenged by drought and salinity.

@article{bernhardsson_ultra-dense_2019,
	title = {An {Ultra}-{Dense} {Haploid} {Genetic} {Map} for {Evaluating} the {Highly} {Fragmented} {Genome} {Assembly} of {Norway} {Spruce} ({Picea} abies )},
	volume = {9},
	issn = {2160-1836},
	url = {https://academic.oup.com/g3journal/article/9/5/1623/6026441},
	doi = {10/gjcr63},
	abstract = {Abstract
            Norway spruce (Picea abies (L.) Karst.) is a conifer species of substanital economic and ecological importance. In common with most conifers, the P. abies genome is very large (∼20 Gbp) and contains a high fraction of repetitive DNA. The current P. abies genome assembly (v1.0) covers approximately 60\% of the total genome size but is highly fragmented, consisting of \>10 million scaffolds. The genome annotation contains 66,632 gene models that are at least partially validated (www.congenie.org), however, the fragmented nature of the assembly means that there is currently little information available on how these genes are physically distributed over the 12 P. abies chromosomes. By creating an ultra-dense genetic linkage map, we anchored and ordered scaffolds into linkage groups, which complements the fine-scale information available in assembly contigs. Our ultra-dense haploid consensus genetic map consists of 21,056 markers derived from 14,336 scaffolds that contain 17,079 gene models (25.6\% of the validated gene models) that we have anchored to the 12 linkage groups. We used data from three independent component maps, as well as comparisons with previously published Picea maps to evaluate the accuracy and marker ordering of the linkage groups. We demonstrate that approximately 3.8\% of the anchored scaffolds and 1.6\% of the gene models covered by the consensus map have likely assembly errors as they contain genetic markers that map to different regions within or between linkage groups. We further evaluate the utility of the genetic map for the conifer research community by using an independent data set of unrelated individuals to assess genome-wide variation in genetic diversity using the genomic regions anchored to linkage groups. The results show that our map is sufficiently dense to enable detailed evolutionary analyses across the P. abies genome.},
	language = {en},
	number = {5},
	urldate = {2021-06-07},
	journal = {G3 Genes{\textbar}Genomes{\textbar}Genetics},
	author = {Bernhardsson, Carolina and Vidalis, Amaryllis and Wang, Xi and Scofield, Douglas G and Schiffthaler, Bastian and Baison, John and Street, Nathaniel R and García-Gil, M Rosario and Ingvarsson, Pär K},
	month = may,
	year = {2019},
	pages = {1623--1632},
}

Abstract Norway spruce (Picea abies (L.) Karst.) is a conifer species of substanital economic and ecological importance. In common with most conifers, the P. abies genome is very large (∼20 Gbp) and contains a high fraction of repetitive DNA. The current P. abies genome assembly (v1.0) covers approximately 60% of the total genome size but is highly fragmented, consisting of >10 million scaffolds. The genome annotation contains 66,632 gene models that are at least partially validated (www.congenie.org), however, the fragmented nature of the assembly means that there is currently little information available on how these genes are physically distributed over the 12 P. abies chromosomes. By creating an ultra-dense genetic linkage map, we anchored and ordered scaffolds into linkage groups, which complements the fine-scale information available in assembly contigs. Our ultra-dense haploid consensus genetic map consists of 21,056 markers derived from 14,336 scaffolds that contain 17,079 gene models (25.6% of the validated gene models) that we have anchored to the 12 linkage groups. We used data from three independent component maps, as well as comparisons with previously published Picea maps to evaluate the accuracy and marker ordering of the linkage groups. We demonstrate that approximately 3.8% of the anchored scaffolds and 1.6% of the gene models covered by the consensus map have likely assembly errors as they contain genetic markers that map to different regions within or between linkage groups. We further evaluate the utility of the genetic map for the conifer research community by using an independent data set of unrelated individuals to assess genome-wide variation in genetic diversity using the genomic regions anchored to linkage groups. The results show that our map is sufficiently dense to enable detailed evolutionary analyses across the P. abies genome.

@article{calleja-rodriguez_analysis_2019,
	title = {Analysis of phenotypic- and {Estimated} {Breeding} {Values} ({EBV}) to dissect the genetic architecture of complex traits in a {Scots} pine three-generation pedigree design},
	volume = {462},
	issn = {00225193},
	url = {https://linkinghub.elsevier.com/retrieve/pii/S002251931830554X},
	doi = {10.1016/j.jtbi.2018.11.007},
	language = {en},
	urldate = {2021-06-07},
	journal = {Journal of Theoretical Biology},
	author = {Calleja-Rodriguez, Ainhoa and Li, Zitong and Hallingbäck, Henrik R. and Sillanpää, Mikko J. and Wu, Harry X. and Abrahamsson, Sara and García-Gil, Maria Rosario},
	month = feb,
	year = {2019},
	pages = {283--292},
}

@article{zhou_genetic_2019,
	title = {Genetic analysis of wood quality traits in {Norway} spruce open-pollinated progenies and their parent plus trees at clonal archives and the evaluation of phenotypic selection of plus trees},
	volume = {49},
	issn = {0045-5067, 1208-6037},
	url = {http://www.nrcresearchpress.com/doi/10.1139/cjfr-2018-0117},
	doi = {10/gjcjw5},
	abstract = {A two-generation pedigree involving 519 Norway spruce (Picea abies (L.) Karst.) plus trees (at clonal archives) and their open-pollinated (OP) progenies was studied with the aim to evaluate the potential of plus-tree selection based on phenotype data scored on the plus trees. Two wood properties (wood density and modulus of elasticity, MOE) and one fiber property (microfibril angle, MFA) were measured with a SilviScan instrument on samples from one ramet per plus tree and 12 OP progenies per plus tree (total of 6288 trees). Three ramets per plus tree and their OP progenies were also assessed for Pilodyn penetration depth and Hitman acoustic velocity, which were used to estimate MOE. The narrow-sense heritability (h
              2
              ) estimates based on parent–offspring regression were marginally higher than those based on half-sib correlation when three ramets per plus tree were included. For SilviScan data, estimates of the correlation between half-sib, progeny-based breeding values (BVs) and plus-tree phenotypes, as well as repeatability estimates, were highest for wood density, followed by MOE and MFA. Considering that the repeatability estimates from the clonal archive trees were higher than any h
              2
              estimate, selection of the best clones from clonal archives would be an effective alternative.},
	language = {en},
	number = {7},
	urldate = {2021-06-07},
	journal = {Canadian Journal of Forest Research},
	author = {Zhou, Linghua and Chen, Zhiqiang and Lundqvist, Sven-Olof and Olsson, Lars and Grahn, Thomas and Karlsson, Bo and Wu, Harry X. and García-Gil, María Rosario},
	month = jul,
	year = {2019},
	pages = {810--818},
}

A two-generation pedigree involving 519 Norway spruce (Picea abies (L.) Karst.) plus trees (at clonal archives) and their open-pollinated (OP) progenies was studied with the aim to evaluate the potential of plus-tree selection based on phenotype data scored on the plus trees. Two wood properties (wood density and modulus of elasticity, MOE) and one fiber property (microfibril angle, MFA) were measured with a SilviScan instrument on samples from one ramet per plus tree and 12 OP progenies per plus tree (total of 6288 trees). Three ramets per plus tree and their OP progenies were also assessed for Pilodyn penetration depth and Hitman acoustic velocity, which were used to estimate MOE. The narrow-sense heritability (h 2 ) estimates based on parent–offspring regression were marginally higher than those based on half-sib correlation when three ramets per plus tree were included. For SilviScan data, estimates of the correlation between half-sib, progeny-based breeding values (BVs) and plus-tree phenotypes, as well as repeatability estimates, were highest for wood density, followed by MOE and MFA. Considering that the repeatability estimates from the clonal archive trees were higher than any h 2 estimate, selection of the best clones from clonal archives would be an effective alternative.

@article{baison_genomewide_2019,
	title = {Genome‐wide association study identified novel candidate loci affecting wood formation in {Norway} spruce},
	volume = {100},
	issn = {0960-7412, 1365-313X},
	url = {https://onlinelibrary.wiley.com/doi/abs/10.1111/tpj.14429},
	doi = {10/gjcj3d},
	language = {en},
	number = {1},
	urldate = {2021-06-07},
	journal = {The Plant Journal},
	author = {Baison, John and Vidalis, Amaryllis and Zhou, Linghua and Chen, Zhi‐Qiang and Li, Zitong and Sillanpää, Mikko J. and Bernhardsson, Carolina and Scofield, Douglas and Forsberg, Nils and Grahn, Thomas and Olsson, Lars and Karlsson, Bo and Wu, Harry and Ingvarsson, Pär K. and Lundqvist, Sven‐Olof and Niittylä, Totte and García‐Gil, M Rosario},
	month = oct,
	year = {2019},
	pages = {83--100},
}

@article{ranade_global_2019,
	title = {Global gene expression analysis in etiolated and de-etiolated seedlings in conifers},
	volume = {14},
	issn = {1932-6203},
	url = {https://dx.plos.org/10.1371/journal.pone.0219272},
	doi = {10/gjcsvr},
	language = {en},
	number = {7},
	urldate = {2021-06-07},
	journal = {PLOS ONE},
	author = {Ranade, Sonali Sachin and Delhomme, Nicolas and García-Gil, M. Rosario},
	editor = {Zhang, Jin-Song},
	month = jul,
	year = {2019},
	pages = {e0219272},
}

@article{ranade_transcriptome_2019,
	title = {Transcriptome analysis of shade avoidance and shade tolerance in conifers},
	volume = {250},
	issn = {0032-0935, 1432-2048},
	url = {http://link.springer.com/10.1007/s00425-019-03160-z},
	doi = {10/gjcr99},
	language = {en},
	number = {1},
	urldate = {2021-06-07},
	journal = {Planta},
	author = {Ranade, Sonali Sachin and Delhomme, Nicolas and García-Gil, María Rosario},
	month = jul,
	year = {2019},
	pages = {299--318},
}

@article{chen_accuracy_2018,
	title = {Accuracy of genomic selection for growth and wood quality traits in two control-pollinated progeny trials using exome capture as the genotyping platform in {Norway} spruce},
	volume = {19},
	issn = {1471-2164},
	url = {https://bmcgenomics.biomedcentral.com/articles/10.1186/s12864-018-5256-y},
	doi = {10/ghk9pc},
	language = {en},
	number = {1},
	urldate = {2021-06-07},
	journal = {BMC Genomics},
	author = {Chen, Zhi-Qiang and Baison, John and Pan, Jin and Karlsson, Bo and Andersson, Bengt and Westin, Johan and García-Gil, María Rosario and Wu, Harry X.},
	month = dec,
	year = {2018},
	pages = {946},
}

@article{lundqvist_age_2018,
	title = {Age and weather effects on between and within ring variations of number, width and coarseness of tracheids and radial growth of young {Norway} spruce},
	volume = {137},
	issn = {1612-4669, 1612-4677},
	url = {http://link.springer.com/10.1007/s10342-018-1136-x},
	doi = {10.1007/s10342-018-1136-x},
	language = {en},
	number = {5},
	urldate = {2021-06-07},
	journal = {European Journal of Forest Research},
	author = {Lundqvist, Sven-Olof and Seifert, Stefan and Grahn, Thomas and Olsson, Lars and García-Gil, Maria Rosario and Karlsson, Bo and Seifert, Thomas},
	month = oct,
	year = {2018},
	pages = {719--743},
}

@article{hayatgheibi_genetic_2018,
	title = {Genetic control of transition from juvenile to mature wood with respect to microfibril angle in {Norway} spruce ( \textit{{Picea} abies} ) and lodgepole pine ( \textit{{Pinus} contorta} )},
	volume = {48},
	issn = {0045-5067, 1208-6037},
	url = {http://www.nrcresearchpress.com/doi/10.1139/cjfr-2018-0140},
	doi = {10.1139/cjfr-2018-0140},
	abstract = {Genetic control of microfibril angle (MFA) transition from juvenile wood to mature wood was evaluated in Norway spruce (Picea abies (L.) Karst) and lodgepole pine (Pinus contorta Douglas ex Loudon). Increment cores were collected at breast height (1.3 m) from 5664 trees in two 21-year-old Norway spruce progeny trials in southern Sweden and from 823 trees in two lodgepole pine progeny trials, aged 34–35 years, in northern Sweden. Radial variations in MFA from pith to bark were measured for each core using SilviScan. To estimate MFA transition from juvenile wood to mature wood, a threshold level of MFA 20° was considered, and six different regression functions were fitted to the MFA profile of each tree after exclusion of outliers, following three steps. The narrow-sense heritability estimates (h
              2
              ) obtained for MFA transition were highest based on the slope function, ranging from 0.21 to 0.23 for Norway spruce and from 0.34 to 0.53 for lodgepole pine, while h
              2
              were mostly non-significant based on the logistic function, under all exclusion methods. Results of this study indicate that it is possible to select for an earlier MFA transition from juvenile wood to mature wood in Norway spruce and lodgepole pine selective breeding programs, as the genetic gains (ΔG) obtained in direct selection of this trait were very high in both species.},
	language = {en},
	number = {11},
	urldate = {2021-06-07},
	journal = {Canadian Journal of Forest Research},
	author = {Hayatgheibi, Haleh and Forsberg, Nils Erik Gustaf and Lundqvist, Sven-Olof and Mörling, Tommy and Mellerowicz, Ewa J. and Karlsson, Bo and Wu, Harry X. and García-Gil, M. Rosario},
	month = nov,
	year = {2018},
	pages = {1358--1365},
}

Genetic control of microfibril angle (MFA) transition from juvenile wood to mature wood was evaluated in Norway spruce (Picea abies (L.) Karst) and lodgepole pine (Pinus contorta Douglas ex Loudon). Increment cores were collected at breast height (1.3 m) from 5664 trees in two 21-year-old Norway spruce progeny trials in southern Sweden and from 823 trees in two lodgepole pine progeny trials, aged 34–35 years, in northern Sweden. Radial variations in MFA from pith to bark were measured for each core using SilviScan. To estimate MFA transition from juvenile wood to mature wood, a threshold level of MFA 20° was considered, and six different regression functions were fitted to the MFA profile of each tree after exclusion of outliers, following three steps. The narrow-sense heritability estimates (h 2 ) obtained for MFA transition were highest based on the slope function, ranging from 0.21 to 0.23 for Norway spruce and from 0.34 to 0.53 for lodgepole pine, while h 2 were mostly non-significant based on the logistic function, under all exclusion methods. Results of this study indicate that it is possible to select for an earlier MFA transition from juvenile wood to mature wood in Norway spruce and lodgepole pine selective breeding programs, as the genetic gains (ΔG) obtained in direct selection of this trait were very high in both species.

@article{razzak_differential_2017,
	title = {Differential response of {Scots} pine seedlings to variable intensity and ratio of red and far-red light: {Scots} pine response to light intensity and shade},
	volume = {40},
	issn = {01407791},
	shorttitle = {Differential response of {Scots} pine seedlings to variable intensity and ratio of red and far-red light},
	url = {http://doi.wiley.com/10.1111/pce.12921},
	doi = {10.1111/pce.12921},
	language = {en},
	number = {8},
	urldate = {2021-06-07},
	journal = {Plant, Cell \& Environment},
	author = {Razzak, Abdur and Ranade, Sonali Sachin and Strand, Åsa and García-Gil, M. R.},
	month = aug,
	year = {2017},
	pages = {1332--1340},
}

@article{ranade_application_2016,
	title = {Application of monochromatic blue light during germination and hypocotyl development improves outplanted {Scots} pine ({Pinus} sylvestris {L}.) trees performance},
	volume = {361},
	issn = {03781127},
	url = {https://linkinghub.elsevier.com/retrieve/pii/S037811271500657X},
	doi = {10.1016/j.foreco.2015.11.034},
	language = {en},
	urldate = {2021-06-07},
	journal = {Forest Ecology and Management},
	author = {Ranade, Sonali Sachin and García Gil, M.R.},
	month = feb,
	year = {2016},
	pages = {368--374},
}

@article{ranade_non-functional_2016,
	title = {Non-functional plastid ndh gene fragments are present in the nuclear genome of {Norway} spruce ({Picea} abies {L}. {Karsch}): insights from in silico analysis of nuclear and organellar genomes},
	volume = {291},
	issn = {1617-4615, 1617-4623},
	shorttitle = {Non-functional plastid ndh gene fragments are present in the nuclear genome of {Norway} spruce ({Picea} abies {L}. {Karsch})},
	url = {http://link.springer.com/10.1007/s00438-015-1159-7},
	doi = {10.1007/s00438-015-1159-7},
	language = {en},
	number = {2},
	urldate = {2021-06-07},
	journal = {Molecular Genetics and Genomics},
	author = {Ranade, Sonali Sachin and García-Gil, María Rosario and Rosselló, Josep A.},
	month = apr,
	year = {2016},
	pages = {935--941},
}

@article{bernhardsson_present_2016,
	title = {Present genetic structure is congruent with the common origin of distant {Scots} pine populations in its {Romanian} distribution},
	volume = {361},
	issn = {03781127},
	url = {https://linkinghub.elsevier.com/retrieve/pii/S0378112715006052},
	doi = {10.1016/j.foreco.2015.10.047},
	language = {en},
	urldate = {2021-06-07},
	journal = {Forest Ecology and Management},
	author = {Bernhardsson, C. and Floran, V. and Ganea, S.L. and García-Gil, M.R.},
	month = feb,
	year = {2016},
	pages = {131--143},
}

@article{ranade_fungal_2015,
	title = {Fungal {Infection} {Increases} the {Rate} of {Somatic} {Mutation} in {Scots} {Pine} ({Pinus} sylvestris {L}.)},
	volume = {106},
	issn = {1465-7333 (Electronic) 0022-1503 (Linking)},
	url = {https://www.ncbi.nlm.nih.gov/pubmed/25890976},
	doi = {10.1093/jhered/esv017},
	abstract = {Somatic mutations are transmitted during mitosis in developing somatic tissue. Somatic cells bearing the mutations can develop into reproductive (germ) cells and the somatic mutations are then passed on to the next generation of plants. Somatic mutations are a source of variation essential to evolve new defense strategies and adapt to the environment. Stem rust disease in Scots pine has a negative effect on wood quality, and thus adversely affects the economy. It is caused by the 2 most destructive fungal species in Scandinavia: Peridermium pini and Cronartium flaccidum. We studied nuclear genome stability in Scots pine under biotic stress (fungus-infected, 22 trees) compared to a control population (plantation, 20 trees). Stability was assessed as accumulation of new somatic mutations in 10 microsatellite loci selected for genotyping. Microsatellites are widely used as molecular markers in population genetics studies of plants, and are particularly used for detection of somatic mutations as their rate of mutation is of a much higher magnitude when compared with other DNA markers. We report double the rate of somatic mutation per locus in the fungus-infected trees (4.8x10(-3) mutations per locus), as compared to the controls (2.0x10(-3) mutations per locus) when individual samples were analyzed at 10 different microsatellite markers. Pearson's chi-squared test indicated a significant effect of the fungal infection which increased the number of mutations in the fungus-infected trees (chi(2) = 12.9883, df = 1, P = 0.0003134).},
	language = {en},
	number = {4},
	urldate = {2021-06-07},
	journal = {J Hered},
	author = {Ranade, S. S. and Ganea, L. S. and Razzak, A. M. and Garcia Gil, M. R.},
	month = jul,
	year = {2015},
	note = {Edition: 2015/04/22},
	keywords = {*Mutation Rate, Basidiomycota/*pathogenicity, DNA, Plant/genetics, Genetic Markers, Genetics, Population, Genome, Plant, Genomic Instability, Genotype, Host-Pathogen Interactions/*genetics, Microsatellite Repeats, Mutation, Pinus sylvestris/*genetics/microbiology, Plant Diseases/genetics/*microbiology, Scots pine, Sequence Analysis, DNA, Somatic mutation., Sweden, abiotic stress, microsatellite, simple sequence repeats},
	pages = {386--94},
}

Somatic mutations are transmitted during mitosis in developing somatic tissue. Somatic cells bearing the mutations can develop into reproductive (germ) cells and the somatic mutations are then passed on to the next generation of plants. Somatic mutations are a source of variation essential to evolve new defense strategies and adapt to the environment. Stem rust disease in Scots pine has a negative effect on wood quality, and thus adversely affects the economy. It is caused by the 2 most destructive fungal species in Scandinavia: Peridermium pini and Cronartium flaccidum. We studied nuclear genome stability in Scots pine under biotic stress (fungus-infected, 22 trees) compared to a control population (plantation, 20 trees). Stability was assessed as accumulation of new somatic mutations in 10 microsatellite loci selected for genotyping. Microsatellites are widely used as molecular markers in population genetics studies of plants, and are particularly used for detection of somatic mutations as their rate of mutation is of a much higher magnitude when compared with other DNA markers. We report double the rate of somatic mutation per locus in the fungus-infected trees (4.8x10(-3) mutations per locus), as compared to the controls (2.0x10(-3) mutations per locus) when individual samples were analyzed at 10 different microsatellite markers. Pearson's chi-squared test indicated a significant effect of the fungal infection which increased the number of mutations in the fungus-infected trees (chi(2) = 12.9883, df = 1, P = 0.0003134).

@article{li_functional_2014,
	title = {Functional {Multi}-{Locus} {QTL} {Mapping} of {Temporal} {Trends} in {Scots} {Pine} {Wood} {Traits}},
	volume = {4},
	issn = {2160-1836},
	url = {https://academic.oup.com/g3journal/article/4/12/2365/6025852},
	doi = {10/f3p5gx},
	abstract = {Abstract
            Quantitative trait loci (QTL) mapping of wood properties in conifer species has focused on single time point measurements or on trait means based on heterogeneous wood samples (e.g., increment cores), thus ignoring systematic within-tree trends. In this study, functional QTL mapping was performed for a set of important wood properties in increment cores from a 17-yr-old Scots pine (Pinus sylvestris L.) full-sib family with the aim of detecting wood trait QTL for general intercepts (means) and for linear slopes by increasing cambial age. Two multi-locus functional QTL analysis approaches were proposed and their performances were compared on trait datasets comprising 2 to 9 time points, 91 to 455 individual tree measurements and genotype datasets of amplified length polymorphisms (AFLP), and single nucleotide polymorphism (SNP) markers. The first method was a multilevel LASSO analysis whereby trend parameter estimation and QTL mapping were conducted consecutively; the second method was our Bayesian linear mixed model whereby trends and underlying genetic effects were estimated simultaneously. We also compared several different hypothesis testing methods under either the LASSO or the Bayesian framework to perform QTL inference. In total, five and four significant QTL were observed for the intercepts and slopes, respectively, across wood traits such as earlywood percentage, wood density, radial fiberwidth, and spiral grain angle. Four of these QTL were represented by candidate gene SNPs, thus providing promising targets for future research in QTL mapping and molecular function. Bayesian and LASSO methods both detected similar sets of QTL given datasets that comprised large numbers of individuals.},
	language = {en},
	number = {12},
	urldate = {2021-06-08},
	journal = {G3 Genes{\textbar}Genomes{\textbar}Genetics},
	author = {Li, Zitong and Hallingbäck, Henrik R and Abrahamsson, Sara and Fries, Anders and Gull, Bengt Andersson and Sillanpää, Mikko J and García-Gil, M Rosario},
	month = dec,
	year = {2014},
	pages = {2365--2379},
}

Abstract Quantitative trait loci (QTL) mapping of wood properties in conifer species has focused on single time point measurements or on trait means based on heterogeneous wood samples (e.g., increment cores), thus ignoring systematic within-tree trends. In this study, functional QTL mapping was performed for a set of important wood properties in increment cores from a 17-yr-old Scots pine (Pinus sylvestris L.) full-sib family with the aim of detecting wood trait QTL for general intercepts (means) and for linear slopes by increasing cambial age. Two multi-locus functional QTL analysis approaches were proposed and their performances were compared on trait datasets comprising 2 to 9 time points, 91 to 455 individual tree measurements and genotype datasets of amplified length polymorphisms (AFLP), and single nucleotide polymorphism (SNP) markers. The first method was a multilevel LASSO analysis whereby trend parameter estimation and QTL mapping were conducted consecutively; the second method was our Bayesian linear mixed model whereby trends and underlying genetic effects were estimated simultaneously. We also compared several different hypothesis testing methods under either the LASSO or the Bayesian framework to perform QTL inference. In total, five and four significant QTL were observed for the intercepts and slopes, respectively, across wood traits such as earlywood percentage, wood density, radial fiberwidth, and spiral grain angle. Four of these QTL were represented by candidate gene SNPs, thus providing promising targets for future research in QTL mapping and molecular function. Bayesian and LASSO methods both detected similar sets of QTL given datasets that comprised large numbers of individuals.

@article{abrahamsson_maternal_2013,
	title = {Maternal heterozygosity and progeny fitness association in an inbred {Scots} pine population},
	volume = {141},
	issn = {0016-6707, 1573-6857},
	url = {http://link.springer.com/10.1007/s10709-013-9704-y},
	doi = {10/f2242n},
	language = {en},
	number = {1-3},
	urldate = {2021-06-08},
	journal = {Genetica},
	author = {Abrahamsson, S. and Ahlinder, J. and Waldmann, P. and García-Gil, M. R.},
	month = mar,
	year = {2013},
	pages = {41--50},
}

@article{ranade_pinus_2013,
	title = {Pinus taeda {cDNA} {Microarray} as a {Tool} for {Candidate} {Gene} {Identification} for {Local} {Red}/{Far}-{Red} {Light} {Adaptive} {Response} in {Pinus} sylvestris},
	volume = {4},
	copyright = {http://creativecommons.org/licenses/by/4.0/},
	url = {http://www.scirp.org/Journal/Paperabs.aspx?paperid=28683},
	doi = {10/gjcmm4},
	abstract = {Light quality response is a vital environmental cue regulating plant development. Conifers, like angiosperms, respond to the changes in light quality including the level of red (R) and far-red (FR) light, which follows a latitudinal cline. R and FR wavelengths form a significant component of the entire plant life cycle, including the initial developmental stages such as seed germination, cotyledon expansion and hypocotyl elongation. With an aim to identify differentially expressed candidate genes, which would provide a clue regarding genes involved in the local adaptive response in Scots pine (Pinus sylvestris) with reference to red/far-red light; we performed a global expression analysis of Scots pine hypocotyls grown under two light treatments, continuous R (cR) and continuous FR (cFR) light; using Pinus taeda cDNA microarrays on bulked hypocotyl tissues from different individuals, which represented different genotypes. This experiment was performed with the seeds collected from northern part of Sweden (Ylinen, 68?N). Interestingly, gene expression pattern with reference to cryptochrome1, a blue light photoreceptor, was relatively high under cFR as compared to cR light treatment. Additionally, the microarray data analysis also revealed expression of 405 genes which was enhanced under cR light treatment; while the expression of 239 genes was enhanced under the cFR light treatment. Differentially expressed genes were re-annotated using Blast2GO tool. These results indicated that cR light acts as promoting factor whereas cFR antagonises the effect in most of the processes like C/N metabolism, photosynthesis and cell wall metabolism which is in accordance with former findings in Arabidopsis. We propose cryptochrome1 as a strong candidate gene to study the adaptive cline response under R and FR light in Scots pine as it shows a differential expression under the two light conditions.},
	language = {en},
	number = {3},
	urldate = {2021-06-21},
	journal = {American Journal of Plant Sciences},
	publisher = {Scientific Research Publishing},
	author = {Ranade, Sonali S. and Abrahamsson, Sara and Niemi, Juha and García-Gil, María Rosario},
	month = mar,
	year = {2013},
	note = {Number: 3},
	pages = {479--493},
}

Light quality response is a vital environmental cue regulating plant development. Conifers, like angiosperms, respond to the changes in light quality including the level of red (R) and far-red (FR) light, which follows a latitudinal cline. R and FR wavelengths form a significant component of the entire plant life cycle, including the initial developmental stages such as seed germination, cotyledon expansion and hypocotyl elongation. With an aim to identify differentially expressed candidate genes, which would provide a clue regarding genes involved in the local adaptive response in Scots pine (Pinus sylvestris) with reference to red/far-red light; we performed a global expression analysis of Scots pine hypocotyls grown under two light treatments, continuous R (cR) and continuous FR (cFR) light; using Pinus taeda cDNA microarrays on bulked hypocotyl tissues from different individuals, which represented different genotypes. This experiment was performed with the seeds collected from northern part of Sweden (Ylinen, 68?N). Interestingly, gene expression pattern with reference to cryptochrome1, a blue light photoreceptor, was relatively high under cFR as compared to cR light treatment. Additionally, the microarray data analysis also revealed expression of 405 genes which was enhanced under cR light treatment; while the expression of 239 genes was enhanced under the cFR light treatment. Differentially expressed genes were re-annotated using Blast2GO tool. These results indicated that cR light acts as promoting factor whereas cFR antagonises the effect in most of the processes like C/N metabolism, photosynthesis and cell wall metabolism which is in accordance with former findings in Arabidopsis. We propose cryptochrome1 as a strong candidate gene to study the adaptive cline response under R and FR light in Scots pine as it shows a differential expression under the two light conditions.

@article{nystedt_norway_2013,
	title = {The {Norway} spruce genome sequence and conifer genome evolution},
	volume = {497},
	issn = {0028-0836, 1476-4687},
	url = {http://www.nature.com/articles/nature12211},
	doi = {10/f2zsx6},
	language = {en},
	number = {7451},
	urldate = {2021-06-08},
	journal = {Nature},
	author = {Nystedt, Björn and Street, Nathaniel R. and Wetterbom, Anna and Zuccolo, Andrea and Lin, Yao-Cheng and Scofield, Douglas G. and Vezzi, Francesco and Delhomme, Nicolas and Giacomello, Stefania and Alexeyenko, Andrey and Vicedomini, Riccardo and Sahlin, Kristoffer and Sherwood, Ellen and Elfstrand, Malin and Gramzow, Lydia and Holmberg, Kristina and Hällman, Jimmie and Keech, Olivier and Klasson, Lisa and Koriabine, Maxim and Kucukoglu, Melis and Käller, Max and Luthman, Johannes and Lysholm, Fredrik and Niittylä, Totte and Olson, Åke and Rilakovic, Nemanja and Ritland, Carol and Rosselló, Josep A. and Sena, Juliana and Svensson, Thomas and Talavera-López, Carlos and Theißen, Günter and Tuominen, Hannele and Vanneste, Kevin and Wu, Zhi-Qiang and Zhang, Bo and Zerbe, Philipp and Arvestad, Lars and Bhalerao, Rishikesh P. and Bohlmann, Joerg and Bousquet, Jean and Garcia Gil, Rosario and Hvidsten, Torgeir R. and de Jong, Pieter and MacKay, John and Morgante, Michele and Ritland, Kermit and Sundberg, Björn and Lee Thompson, Stacey and Van de Peer, Yves and Andersson, Björn and Nilsson, Ove and Ingvarsson, Pär K. and Lundeberg, Joakim and Jansson, Stefan},
	month = may,
	year = {2013},
	pages = {579--584},
}

@article{floran_organelle_2011,
	title = {Organelle {Genetic} {Diversity} and {Phylogeography} of {Scots} {Pine} ({Pinus} sylvestris {L}.)},
	volume = {39},
	doi = {10/gg32mz},
	abstract = {The paper reviews the present knowledge of Scots pine (Pinus sylvestris L.) diversity, historical and geographical distribution, based on mitochondrial and chloroplast DNA data. The observed differences in the estimates of genetic differentiation between different types of genomes suggest that both pollen and seed contribute significantly to gene flow within species. Organelles' diversity represents an important criterion which could be later applied in planning for future forest management and breeding through a better understanding of adaptation strategies of different Scots pine haplotypes. This analysis would provide valuable references when facing current day problems with climate change, species adaptation, and loss of forest with negative effects on biodiversity. Research on organelles' diversity could lead to important practical applications in areas such as traceability and eco-certification of forest products, and the identification of plant populations for conservation. Based on the results from earlier investigations, Scots pine in Europe can be divided into at least three evolutionary units (Spain, northern/central Europe and northern Fennoscandia), each with a different origin after glaciations. However, it must be emphasized that these interpretations are preliminary and further mitochondrial and chloroplast DNA data need to be analyzed in conjunction with evidence from pollen and fossil analysis.},
	journal = {Notulae Botanicae Horti Agrobotanici Cluj-Napoca},
	author = {Floran, Valentina and Sestras, Radu and Garcia Gil, Rosario},
	month = may,
	year = {2011},
	pages = {317--322},
}

The paper reviews the present knowledge of Scots pine (Pinus sylvestris L.) diversity, historical and geographical distribution, based on mitochondrial and chloroplast DNA data. The observed differences in the estimates of genetic differentiation between different types of genomes suggest that both pollen and seed contribute significantly to gene flow within species. Organelles' diversity represents an important criterion which could be later applied in planning for future forest management and breeding through a better understanding of adaptation strategies of different Scots pine haplotypes. This analysis would provide valuable references when facing current day problems with climate change, species adaptation, and loss of forest with negative effects on biodiversity. Research on organelles' diversity could lead to important practical applications in areas such as traceability and eco-certification of forest products, and the identification of plant populations for conservation. Based on the results from earlier investigations, Scots pine in Europe can be divided into at least three evolutionary units (Spain, northern/central Europe and northern Fennoscandia), each with a different origin after glaciations. However, it must be emphasized that these interpretations are preliminary and further mitochondrial and chloroplast DNA data need to be analyzed in conjunction with evidence from pollen and fossil analysis.

@incollection{gonzalez-martinez_patterns_2011,
	title = {Patterns of {Nucleotide} {Diversity} and {Association} {Mapping}},
	isbn = {978-0-429-06593-4},
	abstract = {Understanding the molecular basis of adaptive traits is a major interest in conservation and population genetics. In commercial species, such as several conifers, it is also interesting for operational breeding. In this chapter, we provide a state-of-the-art view on candidate gene research, from general estimates of nucleotide diversity and recombination to new-generation neutrality tests and association genetics methodologies. Levels of nucleotide diversity in conifers are substantial, although lower than expected given their life-history traits. In addition, linkage disequilibrium seems to decay rapidly in this group of species, at least within genes that are not submitted to natural selection. These two facts makes genetic association studies appealing in conifers, as significant associations may correspond to the actual causal polymorphisms. Population genomic methods also seem appropriate in conifers, in particular for those species with accused population genetic structure and strong response to environmental gradients. New-generation neutrality tests, outlier loci detection methods and genotype/phenotype association studies have revealed various candidate genes and single nucleotide polymorphisms underlying different adaptive phenotypes, despite potential confounding effects of demographical and historical processes. Finally, perspectives about future genomic research in conifers are provided, including its application for conservation and breeding.},
	booktitle = {Genetics, {Genomics} and {Breeding} of {Conifers}},
	publisher = {CRC Press},
	author = {González-Martínez, S. C. and Dillon, S. and Garnier-Géré, P. H. and Krutovsky, K. V. and Alía, R. and Burgarella, C. and Eckert, A. J. and García-Gil, M. R. and Grivet, D. and Heuertz, M.},
	year = {2011},
	note = {Num Pages: 36},
}

Understanding the molecular basis of adaptive traits is a major interest in conservation and population genetics. In commercial species, such as several conifers, it is also interesting for operational breeding. In this chapter, we provide a state-of-the-art view on candidate gene research, from general estimates of nucleotide diversity and recombination to new-generation neutrality tests and association genetics methodologies. Levels of nucleotide diversity in conifers are substantial, although lower than expected given their life-history traits. In addition, linkage disequilibrium seems to decay rapidly in this group of species, at least within genes that are not submitted to natural selection. These two facts makes genetic association studies appealing in conifers, as significant associations may correspond to the actual causal polymorphisms. Population genomic methods also seem appropriate in conifers, in particular for those species with accused population genetic structure and strong response to environmental gradients. New-generation neutrality tests, outlier loci detection methods and genotype/phenotype association studies have revealed various candidate genes and single nucleotide polymorphisms underlying different adaptive phenotypes, despite potential confounding effects of demographical and historical processes. Finally, perspectives about future genomic research in conifers are provided, including its application for conservation and breeding.

@article{garcia-gil_evolutionary_2008,
	title = {Evolutionary {Aspects} of {Functional} and {Pseudogene} {Members} of the {Phytochrome} {Gene} {Family} in {Scots} {Pine}},
	volume = {67},
	issn = {0022-2844, 1432-1432},
	url = {http://link.springer.com/10.1007/s00239-008-9135-z},
	doi = {10/dmzkqj},
	language = {en},
	number = {2},
	urldate = {2021-06-10},
	journal = {Journal of Molecular Evolution},
	author = {García-Gil, Maria Rosario},
	month = aug,
	year = {2008},
	pages = {222--232},
}

@article{pyhajarvi_demographic_2007,
	title = {Demographic {History} {Has} {Influenced} {Nucleotide} {Diversity} in {European} \textit{{Pinus} sylvestris} {Populations}},
	volume = {177},
	issn = {1943-2631},
	url = {https://academic.oup.com/genetics/article/177/3/1713/6064487},
	doi = {10/cmrqmt},
	abstract = {Abstract
            To infer the role of natural selection in shaping standing genetic diversity, it is necessary to assess the genomewide impact of demographic history on nucleotide diversity. In this study we analyzed sequence diversity of 16 nuclear loci in eight Pinus sylvestris populations. Populations were divided into four geographical groups on the basis of their current location and the geographical history of the region: northern Europe, central Europe, Spain, and Turkey. There were no among-group differences in the level of silent nucleotide diversity, which was ∼0.005/bp in all groups. There was some evidence that linkage disequilibrium extended further in northern Europe than in central Europe: the estimates of the population recombination rate parameter, ρ, were 0.0064 and 0.0294, respectively. The summary statistics of nucleotide diversity in central and northern European populations were compatible with an ancient bottleneck rather than the standard neutral model.},
	language = {en},
	number = {3},
	urldate = {2021-06-10},
	journal = {Genetics},
	author = {Pyhäjärvi, Tanja and García-Gil, M Rosario and Knürr, Timo and Mikkonen, Merja and Wachowiak, Witold and Savolainen, Outi},
	month = nov,
	year = {2007},
	pages = {1713--1724},
}

Abstract To infer the role of natural selection in shaping standing genetic diversity, it is necessary to assess the genomewide impact of demographic history on nucleotide diversity. In this study we analyzed sequence diversity of 16 nuclear loci in eight Pinus sylvestris populations. Populations were divided into four geographical groups on the basis of their current location and the geographical history of the region: northern Europe, central Europe, Spain, and Turkey. There were no among-group differences in the level of silent nucleotide diversity, which was ∼0.005/bp in all groups. There was some evidence that linkage disequilibrium extended further in northern Europe than in central Europe: the estimates of the population recombination rate parameter, ρ, were 0.0064 and 0.0294, respectively. The summary statistics of nucleotide diversity in central and northern European populations were compatible with an ancient bottleneck rather than the standard neutral model.

@article{notivol_genetic_2007,
	title = {Genetic variation of growth rhythm traits in the limits of a latitudinal cline in {Scots} pine},
	volume = {37},
	issn = {0045-5067, 1208-6037},
	url = {http://www.nrcresearchpress.com/doi/10.1139/X06-243},
	doi = {10/bjtx48},
	abstract = {Scots pine ( Pinus sylvestris L.) has the widest distribution of pine species and the populations are locally adapted to very different environmental conditions. Adaptive traits such as those related to growth are optimal for understanding adaptation of populations to local conditions in widely distributed forest species. A study of the timing of growth during the first growing period of families in four populations from the latitudinal limits of the distribution range was conducted. Individual growth curves were fitted, and a set of variables related to growth rhythm and timing of budset was obtained for genetic analyses. Pooled heritabilities across populations were very high for most of the traits (0.43–1.09), and population differentiation for growth variables showed high values as well (Q
              ST
              = 0.19–0.71). Phenotypic correlations were higher than genetic ones, and most of them were positives. Even no general patterns of additive variances were found, the high additive genetic variance obtained (14\% ± 8\%, mean ± SE) suggests that additive genetic variance is not the limiting factor for adaptation to a new optimum within much of the range for these traits. Changes in means, additive genetic variances, and additive genetic coefficient of variation by population are also discussed.},
	language = {en},
	number = {3},
	urldate = {2021-06-10},
	journal = {Canadian Journal of Forest Research},
	author = {Notivol, E. and García-Gil, M. R. and Alía, R. and Savolainen, O.},
	month = mar,
	year = {2007},
	pages = {540--551},
}

Scots pine ( Pinus sylvestris L.) has the widest distribution of pine species and the populations are locally adapted to very different environmental conditions. Adaptive traits such as those related to growth are optimal for understanding adaptation of populations to local conditions in widely distributed forest species. A study of the timing of growth during the first growing period of families in four populations from the latitudinal limits of the distribution range was conducted. Individual growth curves were fitted, and a set of variables related to growth rhythm and timing of budset was obtained for genetic analyses. Pooled heritabilities across populations were very high for most of the traits (0.43–1.09), and population differentiation for growth variables showed high values as well (Q ST = 0.19–0.71). Phenotypic correlations were higher than genetic ones, and most of them were positives. Even no general patterns of additive variances were found, the high additive genetic variance obtained (14% ± 8%, mean ± SE) suggests that additive genetic variance is not the limiting factor for adaptation to a new optimum within much of the range for these traits. Changes in means, additive genetic variances, and additive genetic coefficient of variation by population are also discussed.

@article{waldmann_comparing_2005,
	title = {Comparing {Bayesian} estimates of genetic differentiation of molecular markers and quantitative traits: an application to {Pinus} sylvestris},
	volume = {94},
	copyright = {2005 The Genetics Society},
	issn = {1365-2540},
	shorttitle = {Comparing {Bayesian} estimates of genetic differentiation of molecular markers and quantitative traits},
	url = {https://www.nature.com/articles/6800672},
	doi = {10.1038/sj.hdy.6800672},
	abstract = {Comparison of the level of differentiation at neutral molecular markers (estimated as FST or GST) with the level of differentiation at quantitative traits (estimated as QST) has become a standard tool for inferring that there is differential selection between populations. We estimated QST of timing of bud set from a latitudinal cline of Pinus sylvestris with a Bayesian hierarchical variance component method utilizing the information on the pre-estimated population structure from neutral molecular markers. Unfortunately, the between-family variances differed substantially between populations that resulted in a bimodal posterior of QST that could not be compared in any sensible way with the unimodal posterior of the microsatellite FST. In order to avoid publishing studies with flawed QST estimates, we recommend that future studies should present heritability estimates for each trait and population. Moreover, to detect variance heterogeneity in frequentist methods (ANOVA and REML), it is of essential importance to check also that the residuals are normally distributed and do not follow any systematically deviating trends.},
	language = {en},
	number = {6},
	urldate = {2021-06-11},
	journal = {Heredity},
	publisher = {Nature Publishing Group},
	author = {Waldmann, P. and García-Gil, M. R. and Sillanpää, M. J.},
	month = jun,
	year = {2005},
	note = {Number: 6},
	pages = {623--629},
}

Comparison of the level of differentiation at neutral molecular markers (estimated as FST or GST) with the level of differentiation at quantitative traits (estimated as QST) has become a standard tool for inferring that there is differential selection between populations. We estimated QST of timing of bud set from a latitudinal cline of Pinus sylvestris with a Bayesian hierarchical variance component method utilizing the information on the pre-estimated population structure from neutral molecular markers. Unfortunately, the between-family variances differed substantially between populations that resulted in a bimodal posterior of QST that could not be compared in any sensible way with the unimodal posterior of the microsatellite FST. In order to avoid publishing studies with flawed QST estimates, we recommend that future studies should present heritability estimates for each trait and population. Moreover, to detect variance heterogeneity in frequentist methods (ANOVA and REML), it is of essential importance to check also that the residuals are normally distributed and do not follow any systematically deviating trends.

@article{savolainen_genetic_2004,
	title = {Genetic variation in cessation of growth and frost hardiness and consequences for adaptation of {Pinus} sylvestris to climatic changes},
	volume = {197},
	issn = {0378-1127},
	doi = {10/dvn6cp},
	abstract = {Responses to climate change will include changes in species composition, but adaptation through genetic change may also be possible. The response to selection depends on the availability of additive genetic variation and the strength of selection. We found that Finnish populations of Scots pine have much genetic variation within the populations with respect to two traits related to climatic adaptation. Heritabilities (standard deviations) were 0.67 (0.16) and 0.33 (0.17) for the timing of bud set of 1-year-old seedlings and for frost hardiness 0.36 (0.14) and 0.20 (0.13) (not significantly different from zero) in the northern and southern populations, respectively. The additive genetic correlation between the traits was 0.57 (0.07). The proportion of additive genetic variation between the populations (Q(ST)) was 0.86 (0.11). Assuming that the new phenotypic optimum can be deduced based on the current match of temperature sums and phenotypic means, we test whether Scots pine in northern Finland can change to the new predicted optimum through migration and local selection during the next 100 years. The simulation model was based on monitoring 10 populations of 100 individuals. Five independent loci with two alleles were used to model the phenotypic trait of growth period. The results showed that genetic change will be slow and lag behind the moving optimum. Part of the slowness was due to the survival of current trees, which makes establishment of new trees with more suitable genotypes slower. Adaptation in species with fragmented populations and little migration could be even slower. Artificial regeneration with suitable seed sources can increase the proportion of adapted genotypes in cultivated species. (C) 2004 Published by Elsevier B.V.},
	language = {English},
	number = {1-3},
	journal = {Forest Ecology and Management},
	publisher = {Elsevier Science Bv},
	author = {Savolainen, O. and Bokma, F. and Garcia-Gil, R. and Komulainen, P. and Repo, T.},
	month = aug,
	year = {2004},
	note = {Place: Amsterdam
WOS:000223382700007},
	keywords = {abies l karst, adaptation, boreal forests, climate change, cold-hardiness, contorta, f-st, frost hardiness, nucleotide diversity, pollen migration, populations, responses, scots pine, timing of growth, traits},
	pages = {79--89},
}

Responses to climate change will include changes in species composition, but adaptation through genetic change may also be possible. The response to selection depends on the availability of additive genetic variation and the strength of selection. We found that Finnish populations of Scots pine have much genetic variation within the populations with respect to two traits related to climatic adaptation. Heritabilities (standard deviations) were 0.67 (0.16) and 0.33 (0.17) for the timing of bud set of 1-year-old seedlings and for frost hardiness 0.36 (0.14) and 0.20 (0.13) (not significantly different from zero) in the northern and southern populations, respectively. The additive genetic correlation between the traits was 0.57 (0.07). The proportion of additive genetic variation between the populations (Q(ST)) was 0.86 (0.11). Assuming that the new phenotypic optimum can be deduced based on the current match of temperature sums and phenotypic means, we test whether Scots pine in northern Finland can change to the new predicted optimum through migration and local selection during the next 100 years. The simulation model was based on monitoring 10 populations of 100 individuals. Five independent loci with two alleles were used to model the phenotypic trait of growth period. The results showed that genetic change will be slow and lag behind the moving optimum. Part of the slowness was due to the survival of current trees, which makes establishment of new trees with more suitable genotypes slower. Adaptation in species with fragmented populations and little migration could be even slower. Artificial regeneration with suitable seed sources can increase the proportion of adapted genotypes in cultivated species. (C) 2004 Published by Elsevier B.V.

@article{komulainen_comparing_2003,
	title = {Comparing {EST}-based genetic maps between {Pinus} sylvestris and {Pinus} taeda},
	volume = {107},
	issn = {1432-2242},
	url = {https://doi.org/10.1007/s00122-003-1312-2},
	doi = {10/fvc7mz},
	abstract = {A genetic map of Pinus sylvestris was constructed using ESTP (expressed sequence tag polymorphism) markers and other gene-based markers, AFLP markers and microsatellites. Part of the ESTP markers (40) were developed and mapped earlier in Pinus taeda, and additional markers were generated based on P. sylvestris sequences or sequences from other pine species. The mapping in P. sylvestris was based on 94 F1 progeny from a cross between plus-tree parents E635C and E1101. AFLP framework maps for the parent trees were first constructed. The ESTP and other gene sequence-based markers were added to the framework maps, as well as five published microsatellite loci. The separate maps were then integrated with the aid of AFLPs segregating in both trees (dominant segregation ratios 3:1) as well as gene markers and microsatellites segregating in both parent trees (segregation ratios 1:1:1:1 or 1:2:1). The integrated map consisted of 12 groups corresponding to the P. taeda linkage groups, and additionally three and six smaller groups for E1101 and E635C, respectively. The number of framework AFLP markers in the integrated map is altogether 194 and the number of gene markers 61. The total length of the integrated map was 1,314 cM. The set of markers developed for P. sylvestris was also added to existing maps of two P. taeda pedigrees. Starting with a mapped marker from one pedigree in the source species resulted in a mapped marker in a pedigree of the other species in more than 40\% of the cases, with about equal success in both directions. The maps of the two species are largely colinear, even if the species have diverged more than 70 MYA. Most cases of different locations were probably due to problems in identifying the orthologous members of gene families. These data provide a first ESTP-containing map of P. sylvestris, which can also be used for comparing this species to additional species mapped with the same markers.},
	language = {en},
	number = {4},
	urldate = {2021-07-05},
	journal = {Theoretical and Applied Genetics},
	author = {Komulainen, P. and Brown, G. R. and Mikkonen, M. and Karhu, A. and García-Gil, M. R. and O'Malley, D. and Lee, B. and Neale, D. B. and Savolainen, O.},
	month = aug,
	year = {2003},
	pages = {667--678},
}

A genetic map of Pinus sylvestris was constructed using ESTP (expressed sequence tag polymorphism) markers and other gene-based markers, AFLP markers and microsatellites. Part of the ESTP markers (40) were developed and mapped earlier in Pinus taeda, and additional markers were generated based on P. sylvestris sequences or sequences from other pine species. The mapping in P. sylvestris was based on 94 F1 progeny from a cross between plus-tree parents E635C and E1101. AFLP framework maps for the parent trees were first constructed. The ESTP and other gene sequence-based markers were added to the framework maps, as well as five published microsatellite loci. The separate maps were then integrated with the aid of AFLPs segregating in both trees (dominant segregation ratios 3:1) as well as gene markers and microsatellites segregating in both parent trees (segregation ratios 1:1:1:1 or 1:2:1). The integrated map consisted of 12 groups corresponding to the P. taeda linkage groups, and additionally three and six smaller groups for E1101 and E635C, respectively. The number of framework AFLP markers in the integrated map is altogether 194 and the number of gene markers 61. The total length of the integrated map was 1,314 cM. The set of markers developed for P. sylvestris was also added to existing maps of two P. taeda pedigrees. Starting with a mapped marker from one pedigree in the source species resulted in a mapped marker in a pedigree of the other species in more than 40% of the cases, with about equal success in both directions. The maps of the two species are largely colinear, even if the species have diverged more than 70 MYA. Most cases of different locations were probably due to problems in identifying the orthologous members of gene families. These data provide a first ESTP-containing map of P. sylvestris, which can also be used for comparing this species to additional species mapped with the same markers.

@article{garcia-gil_nucleotide_2003,
	title = {Nucleotide diversity at two phytochrome loci along a latitudinal cline in {Pinus} sylvestris},
	volume = {12},
	issn = {1365-294X},
	url = {https://onlinelibrary.wiley.com/doi/abs/10.1046/j.1365-294X.2003.01826.x},
	doi = {10.1046/j.1365-294X.2003.01826.x},
	abstract = {Forest tree species provide many examples of well-studied adaptive differentiation, where the search for the underlying genes might be possible. In earlier studies and in our common conditions in a greenhouse, northern populations set bud earlier than southern ones. A difference in latitude of origin of one degree corresponded to a change of 1.4 days in number of days to terminal bud set of seedlings. Earlier physiological and ecological genetics work in conifers and other plants have suggested that such variation could be governed by phytochromes. Nucleotide variation was examined at two phytochrome loci (PHYP and PHYO, homologues of the Arabidopsis thaliana PHYB and PHYA, respectively) in three populations: northern Finland, southern Finland and northern Spain. In our samples of 12–15 sequences (2980 and 1156 base pairs at the two loci) we found very low nonsynonymous variation; π was 0.0003 and 0.0002 at PHYP and PHYO loci, respectively. There was no functional differentiation between populations at the photosensory domains of either locus. The overall silent variation was also low, only 0.0024 for the PHYP locus. The low estimates of silent variation are consistent with the estimated low synonymous substitution rates between Pinus sylvestris and Picea abies at the PHYO locus. Despite the low level of nucleotide variation, haplotypic diversity was relatively high (0.42 and 0.41 for fragments of 1156 nucleotides) at the two loci.},
	language = {en},
	number = {5},
	urldate = {2024-10-02},
	journal = {Molecular Ecology},
	author = {García-Gil, M. R. and Mikkonen, M. and Savolainen, O.},
	year = {2003},
	note = {\_eprint: https://onlinelibrary.wiley.com/doi/pdf/10.1046/j.1365-294X.2003.01826.x},
	keywords = {Pinus sylvestris, bud set date, latitudinal cline, nucleotide diversity, photoperiod, phytochrome},
	pages = {1195--1206},
}

Forest tree species provide many examples of well-studied adaptive differentiation, where the search for the underlying genes might be possible. In earlier studies and in our common conditions in a greenhouse, northern populations set bud earlier than southern ones. A difference in latitude of origin of one degree corresponded to a change of 1.4 days in number of days to terminal bud set of seedlings. Earlier physiological and ecological genetics work in conifers and other plants have suggested that such variation could be governed by phytochromes. Nucleotide variation was examined at two phytochrome loci (PHYP and PHYO, homologues of the Arabidopsis thaliana PHYB and PHYA, respectively) in three populations: northern Finland, southern Finland and northern Spain. In our samples of 12–15 sequences (2980 and 1156 base pairs at the two loci) we found very low nonsynonymous variation; π was 0.0003 and 0.0002 at PHYP and PHYO loci, respectively. There was no functional differentiation between populations at the photosensory domains of either locus. The overall silent variation was also low, only 0.0024 for the PHYP locus. The low estimates of silent variation are consistent with the estimated low synonymous substitution rates between Pinus sylvestris and Picea abies at the PHYO locus. Despite the low level of nucleotide variation, haplotypic diversity was relatively high (0.42 and 0.41 for fragments of 1156 nucleotides) at the two loci.

@article{wahl_plant_2026,
	title = {The plant energy management machinery: an essential hub for stress resilience and developmental dynamics with great potential for crop improvement},
	volume = {77},
	issn = {0022-0957},
	shorttitle = {The plant energy management machinery},
	url = {https://doi.org/10.1093/jxb/erag032},
	doi = {10.1093/jxb/erag032},
	abstract = {Plants coordinate resource uptake, developmental pace, and morphological efficiency. This ensures that energy use is balanced across time and tissues, enabling resilience and stable growth under fluctuating environmental conditions. The plant energy management machinery encompasses the interconnected signalling and metabolic networks that coordinate energy acquisition, storage, mobilization, and utilization to support growth, development, and environmental adaptation. In contrast to animals, where dedicated organs such as fat bodies in Drosophila and the liver in mammals, play crucial roles in energy metabolism and sensing (Chatterjee and Perrimon, 2021), plants exhibit a more integrative concept of nutrient and energy regulation. Here, the term ‘nutrients’ extends beyond simple energy carriers to include a broad spectrum of organic and inorganic compounds, such as sugars, amino acids, nitrate, phosphate, and lipids, that function both as metabolic substrates and as signalling molecules, influencing gene expression, enzyme activity, developmental transitions, and growth.},
	number = {5},
	urldate = {2026-03-10},
	journal = {Journal of Experimental Botany},
	author = {Wahl, Vanessa and Hanson, Johannes and Menand, Benoît},
	month = mar,
	year = {2026},
	pages = {1357--1361},
}

Plants coordinate resource uptake, developmental pace, and morphological efficiency. This ensures that energy use is balanced across time and tissues, enabling resilience and stable growth under fluctuating environmental conditions. The plant energy management machinery encompasses the interconnected signalling and metabolic networks that coordinate energy acquisition, storage, mobilization, and utilization to support growth, development, and environmental adaptation. In contrast to animals, where dedicated organs such as fat bodies in Drosophila and the liver in mammals, play crucial roles in energy metabolism and sensing (Chatterjee and Perrimon, 2021), plants exhibit a more integrative concept of nutrient and energy regulation. Here, the term ‘nutrients’ extends beyond simple energy carriers to include a broad spectrum of organic and inorganic compounds, such as sugars, amino acids, nitrate, phosphate, and lipids, that function both as metabolic substrates and as signalling molecules, influencing gene expression, enzyme activity, developmental transitions, and growth.

@article{wang_ribosome_2025,
	title = {Ribosome biogenesis in plants requires the nuclear envelope and mitochondria localized {OPENER} complex},
	volume = {16},
	copyright = {2025 The Author(s)},
	issn = {2041-1723},
	url = {https://www.nature.com/articles/s41467-025-62652-7},
	doi = {10.1038/s41467-025-62652-7},
	abstract = {Eukaryotic ribosome biogenesis proceeds from nucleolus to cytosol assisted by various assembly factors. The process is evolutionarily conserved across eukaryotes but differences between the kingdoms are emerging. Here, we describe how the OPENER (OPNR) protein complex is required for 60S ribosome assembly in the model plant Arabidopsis thaliana. The complex is observed on both nuclear envelope and mitochondria, and contains OPNR, OPENER ASSOCIATED PROTEIN 1 (OAP1), OAP2, Cell Division Cycle 48 D (CDC48D) and Calmodulin-interacting protein 111 (CIP111). Depletion of the OPNR complex components results in reproductive lethality and cytoplasmic retention of assembly factors on 60S ribosomes. Subsequent biochemical analyses and structural modelling suggest that OPNR, OAP1 and OAP2 form a claw-like trimer which grabs the ribosome assembly factor RIBOSOMAL PROTEIN L24C (RPL24C) on the pre-60S ribosome. Our results reveal previously unrecognised subcellular complexity of ribosome biogenesis in plants, and point to mitochondria association as a feature to ensure sufficient translational capacity.},
	language = {en},
	number = {1},
	urldate = {2025-08-12},
	journal = {Nature Communications},
	publisher = {Nature Publishing Group},
	author = {Wang, Wei and Mahboubi, Amir and Zhu, Shaochun and Hanson, Johannes and Mateus, André and Niittylä, Totte},
	month = aug,
	year = {2025},
	keywords = {Plant cell biology, Plant molecular biology, Ribosome},
	pages = {7301},
}

Eukaryotic ribosome biogenesis proceeds from nucleolus to cytosol assisted by various assembly factors. The process is evolutionarily conserved across eukaryotes but differences between the kingdoms are emerging. Here, we describe how the OPENER (OPNR) protein complex is required for 60S ribosome assembly in the model plant Arabidopsis thaliana. The complex is observed on both nuclear envelope and mitochondria, and contains OPNR, OPENER ASSOCIATED PROTEIN 1 (OAP1), OAP2, Cell Division Cycle 48 D (CDC48D) and Calmodulin-interacting protein 111 (CIP111). Depletion of the OPNR complex components results in reproductive lethality and cytoplasmic retention of assembly factors on 60S ribosomes. Subsequent biochemical analyses and structural modelling suggest that OPNR, OAP1 and OAP2 form a claw-like trimer which grabs the ribosome assembly factor RIBOSOMAL PROTEIN L24C (RPL24C) on the pre-60S ribosome. Our results reveal previously unrecognised subcellular complexity of ribosome biogenesis in plants, and point to mitochondria association as a feature to ensure sufficient translational capacity.

@article{kreisz_s1_2024,
	title = {S1 basic leucine zipper transcription factors shape plant architecture by controlling {C}/{N} partitioning to apical and lateral organs},
	volume = {121},
	url = {https://www.pnas.org/doi/10.1073/pnas.2313343121},
	doi = {10.1073/pnas.2313343121},
	abstract = {Plants tightly control growth of their lateral organs, which led to the concept of apical dominance. However, outgrowth of the dormant lateral primordia is sensitive to the plant’s nutritional status, resulting in an immense plasticity in plant architecture. While the impact of hormonal regulation on apical dominance is well characterized, the prime importance of sugar signaling to unleash lateral organ formation has just recently emerged. Here, we aimed to identify transcriptional regulators, which control the trade-off between growth of apical versus lateral organs. Making use of locally inducible gain-of-function as well as single and higher-order loss-of-function approaches of the sugar-responsive S1-basic-leucine-zipper (S1-bZIP) transcription factors, we disclosed their largely redundant function in establishing apical growth dominance. Consistently, comprehensive phenotypical and analytical studies of S1-bZIP mutants show a clear shift of sugar and organic nitrogen (N) allocation from apical to lateral organs, coinciding with strong lateral organ outgrowth. Tissue-specific transcriptomics reveal specific clade III SWEET sugar transporters, crucial for long-distance sugar transport to apical sinks and the glutaminase GLUTAMINE AMIDO-TRANSFERASE 1\_2.1, involved in N homeostasis, as direct S1-bZIP targets, linking the architectural and metabolic mutant phenotypes to downstream gene regulation. Based on these results, we propose that S1-bZIPs control carbohydrate (C) partitioning from source leaves to apical organs and tune systemic N supply to restrict lateral organ formation by C/N depletion. Knowledge of the underlying mechanisms controlling plant C/N partitioning is of pivotal importance for breeding strategies to generate plants with desired architectural and nutritional characteristics.},
	number = {7},
	urldate = {2024-02-09},
	journal = {Proceedings of the National Academy of Sciences},
	publisher = {Proceedings of the National Academy of Sciences},
	author = {Kreisz, Philipp and Hellens, Alicia M. and Fröschel, Christian and Krischke, Markus and Maag, Daniel and Feil, Regina and Wildenhain, Theresa and Draken, Jan and Braune, Gabriel and Erdelitsch, Leon and Cecchino, Laura and Wagner, Tobias C. and Ache, Peter and Mueller, Martin J. and Becker, Dirk and Lunn, John E. and Hanson, Johannes and Beveridge, Christine A. and Fichtner, Franziska and Barbier, Francois F. and Weiste, Christoph},
	month = feb,
	year = {2024},
	pages = {e2313343121},
}

Plants tightly control growth of their lateral organs, which led to the concept of apical dominance. However, outgrowth of the dormant lateral primordia is sensitive to the plant’s nutritional status, resulting in an immense plasticity in plant architecture. While the impact of hormonal regulation on apical dominance is well characterized, the prime importance of sugar signaling to unleash lateral organ formation has just recently emerged. Here, we aimed to identify transcriptional regulators, which control the trade-off between growth of apical versus lateral organs. Making use of locally inducible gain-of-function as well as single and higher-order loss-of-function approaches of the sugar-responsive S1-basic-leucine-zipper (S1-bZIP) transcription factors, we disclosed their largely redundant function in establishing apical growth dominance. Consistently, comprehensive phenotypical and analytical studies of S1-bZIP mutants show a clear shift of sugar and organic nitrogen (N) allocation from apical to lateral organs, coinciding with strong lateral organ outgrowth. Tissue-specific transcriptomics reveal specific clade III SWEET sugar transporters, crucial for long-distance sugar transport to apical sinks and the glutaminase GLUTAMINE AMIDO-TRANSFERASE 1_2.1, involved in N homeostasis, as direct S1-bZIP targets, linking the architectural and metabolic mutant phenotypes to downstream gene regulation. Based on these results, we propose that S1-bZIPs control carbohydrate (C) partitioning from source leaves to apical organs and tune systemic N supply to restrict lateral organ formation by C/N depletion. Knowledge of the underlying mechanisms controlling plant C/N partitioning is of pivotal importance for breeding strategies to generate plants with desired architectural and nutritional characteristics.

@article{hoffmann_cauliflower_2023,
	title = {Cauliflower mosaic virus protein {P6} is a multivalent node for {RNA} granule proteins and interferes with stress granule responses during plant infection},
	volume = {35},
	issn = {1040-4651},
	url = {https://doi.org/10.1093/plcell/koad101},
	doi = {10.1093/plcell/koad101},
	abstract = {Biomolecular condensation is a multipurpose cellular process that viruses use ubiquitously during their multiplication. Cauliflower mosaic virus replication complexes are condensates that differ from those of most viruses, as they are nonmembranous assemblies that consist of RNA and protein, mainly the viral protein P6. Although these viral factories (VFs) were described half a century ago, with many observations that followed since, functional details of the condensation process and the properties and relevance of VFs have remained enigmatic. Here, we studied these issues in Arabidopsis thaliana and Nicotiana benthamiana. We observed a large dynamic mobility range of host proteins within VFs, while the viral matrix protein P6 is immobile, as it represents the central node of these condensates. We identified the stress granule (SG) nucleating factors G3BP7 and UBP1 family members as components of VFs. Similarly, as SG components localize to VFs during infection, ectopic P6 localizes to SGs and reduces their assembly after stress. Intriguingly, it appears that soluble rather than condensed P6 suppresses SG formation and mediates other essential P6 functions, suggesting that the increased condensation over the infection time-course may accompany a progressive shift in selected P6 functions. Together, this study highlights VFs as dynamic condensates and P6 as a complex modulator of SG responses.},
	number = {9},
	urldate = {2023-09-07},
	journal = {The Plant Cell},
	author = {Hoffmann, Gesa and López-González, Silvia and Mahboubi, Amir and Hanson, Johannes and Hafrén, Anders},
	month = sep,
	year = {2023},
	pages = {3363--3382},
}

Biomolecular condensation is a multipurpose cellular process that viruses use ubiquitously during their multiplication. Cauliflower mosaic virus replication complexes are condensates that differ from those of most viruses, as they are nonmembranous assemblies that consist of RNA and protein, mainly the viral protein P6. Although these viral factories (VFs) were described half a century ago, with many observations that followed since, functional details of the condensation process and the properties and relevance of VFs have remained enigmatic. Here, we studied these issues in Arabidopsis thaliana and Nicotiana benthamiana. We observed a large dynamic mobility range of host proteins within VFs, while the viral matrix protein P6 is immobile, as it represents the central node of these condensates. We identified the stress granule (SG) nucleating factors G3BP7 and UBP1 family members as components of VFs. Similarly, as SG components localize to VFs during infection, ectopic P6 localizes to SGs and reduces their assembly after stress. Intriguingly, it appears that soluble rather than condensed P6 suppresses SG formation and mediates other essential P6 functions, suggesting that the increased condensation over the infection time-course may accompany a progressive shift in selected P6 functions. Together, this study highlights VFs as dynamic condensates and P6 as a complex modulator of SG responses.

@article{bai_seedtransnet_2023,
	title = {{SeedTransNet}: a directional translational network revealing regulatory patterns during seed maturation and germination},
	volume = {74},
	issn = {0022-0957},
	shorttitle = {{SeedTransNet}},
	url = {https://doi.org/10.1093/jxb/erac394},
	doi = {10.1093/jxb/erac394},
	abstract = {Seed maturation is the developmental process that prepares the embryo for the desiccated waiting period before germination. It is associated with a series of physiological changes leading to the establishment of seed dormancy, seed longevity, and desiccation tolerance. We studied translational changes during seed maturation and observed a gradual reduction in global translation during seed maturation. Transcriptome and translatome profiling revealed specific reduction in the translation of thousands of genes. By including previously published data on germination and seedling establishment, a regulatory network based on polysome occupancy data was constructed: SeedTransNet. Network analysis predicted translational regulatory pathways involving hundreds of genes with distinct functions. The network identified specific transcript sequence features suggesting separate translational regulatory circuits. The network revealed several seed maturation-associated genes as central nodes, and this was confirmed by specific seed phenotypes of the respective mutants. One of the regulators identified, an AWPM19 family protein, PM19-Like1 (PM19L1), was shown to regulate seed dormancy and longevity. This putative RNA-binding protein also affects the translational regulation of its target mRNA, as identified by SeedTransNet. Our data show the usefulness of SeedTransNet in identifying regulatory pathways during seed phase transitions.},
	number = {7},
	urldate = {2023-04-14},
	journal = {Journal of Experimental Botany},
	author = {Bai, Bing and Schiffthaler, Bastian and van der Horst, Sjors and Willems, Leo and Vergara, Alexander and Karlström, Jacob and Mähler, Niklas and Delhomme, Nicolas and Bentsink, Leónie and Hanson, Johannes},
	month = apr,
	year = {2023},
	pages = {2416--2432},
}

Seed maturation is the developmental process that prepares the embryo for the desiccated waiting period before germination. It is associated with a series of physiological changes leading to the establishment of seed dormancy, seed longevity, and desiccation tolerance. We studied translational changes during seed maturation and observed a gradual reduction in global translation during seed maturation. Transcriptome and translatome profiling revealed specific reduction in the translation of thousands of genes. By including previously published data on germination and seedling establishment, a regulatory network based on polysome occupancy data was constructed: SeedTransNet. Network analysis predicted translational regulatory pathways involving hundreds of genes with distinct functions. The network identified specific transcript sequence features suggesting separate translational regulatory circuits. The network revealed several seed maturation-associated genes as central nodes, and this was confirmed by specific seed phenotypes of the respective mutants. One of the regulators identified, an AWPM19 family protein, PM19-Like1 (PM19L1), was shown to regulate seed dormancy and longevity. This putative RNA-binding protein also affects the translational regulation of its target mRNA, as identified by SeedTransNet. Our data show the usefulness of SeedTransNet in identifying regulatory pathways during seed phase transitions.

@article{hoffmann_arabidopsis_2022,
	title = {Arabidopsis {RNA} processing body components {LSM1} and {DCP5} aid in the evasion of translational repression during {Cauliflower} mosaic virus infection},
	issn = {1532-298X},
	doi = {10.1093/plcell/koac132},
	abstract = {Viral infections impose extraordinary RNA stress, triggering cellular RNA surveillance pathways such as RNA decapping, nonsense-mediated decay, and RNA silencing. Viruses need to maneuver among these pathways to establish infection and succeed in producing high amounts of viral proteins. Processing bodies (PBs) are integral to RNA triage in eukaryotic cells, with several distinct RNA quality control pathways converging for selective RNA regulation. In this study, we investigated the role of Arabidopsis thaliana PBs during Cauliflower mosaic virus (CaMV) infection. We found that several PB components are co-opted into viral factories that support virus multiplication. This pro-viral role was not associated with RNA decay pathways but instead, we established that PB components are helpers in viral RNA translation. While CaMV is normally resilient to RNA silencing, dysfunctions in PB components expose the virus to this pathway, which is similar to previous observations for transgenes. Transgenes, however, undergo RNA quality control-dependent RNA degradation and transcriptional silencing, whereas CaMV RNA remains stable but becomes translationally repressed through decreased ribosome association, revealing a unique dependence among PBs, RNA silencing, and translational repression. Together, our study shows that PB components are co-opted by the virus to maintain efficient translation, a mechanism not associated with canonical PB functions.},
	language = {eng},
	journal = {The Plant Cell},
	author = {Hoffmann, Gesa and Mahboubi, Amir and Bente, Heinrich and Garcia, Damien and Hanson, Johannes and Hafrén, Anders},
	month = may,
	year = {2022},
	pages = {koac132},
}

Viral infections impose extraordinary RNA stress, triggering cellular RNA surveillance pathways such as RNA decapping, nonsense-mediated decay, and RNA silencing. Viruses need to maneuver among these pathways to establish infection and succeed in producing high amounts of viral proteins. Processing bodies (PBs) are integral to RNA triage in eukaryotic cells, with several distinct RNA quality control pathways converging for selective RNA regulation. In this study, we investigated the role of Arabidopsis thaliana PBs during Cauliflower mosaic virus (CaMV) infection. We found that several PB components are co-opted into viral factories that support virus multiplication. This pro-viral role was not associated with RNA decay pathways but instead, we established that PB components are helpers in viral RNA translation. While CaMV is normally resilient to RNA silencing, dysfunctions in PB components expose the virus to this pathway, which is similar to previous observations for transgenes. Transgenes, however, undergo RNA quality control-dependent RNA degradation and transcriptional silencing, whereas CaMV RNA remains stable but becomes translationally repressed through decreased ribosome association, revealing a unique dependence among PBs, RNA silencing, and translational repression. Together, our study shows that PB components are co-opted by the virus to maintain efficient translation, a mechanism not associated with canonical PB functions.

@article{prior_arabidopsis_2021,
	title = {Arabidopsis {bZIP11} {Is} a {Susceptibility} {Factor} {During} {Pseudomonas} syringae {Infection}},
	volume = {34},
	issn = {0894-0282},
	url = {https://apsjournals.apsnet.org/doi/10.1094/MPMI-11-20-0310-R},
	doi = {10/gj6p4s},
	abstract = {The induction of plant nutrient secretion systems is critical for successful pathogen infection. Some bacterial pathogens (e.g., Xanthomonas spp.) use transcription activator-like (TAL) effectors to induce transcription of SWEET sucrose efflux transporters. Pseudomonas syringae pv. tomato strain DC3000 lacks TAL effectors yet is able to induce multiple SWEETs in Arabidopsis thaliana by unknown mechanisms. Because bacteria require other nutrients in addition to sugars for efficient reproduction, we hypothesized that Pseudomonas spp. may depend on host transcription factors involved in secretory programs to increase access to essential nutrients. Bioinformatic analyses identified the Arabidopsis basic-leucine zipper transcription factor bZIP11 as a potential regulator of nutrient transporters, including SWEETs and UmamiT amino acid transporters. Inducible downregulation of bZIP11 expression in Arabidopsis resulted in reduced growth of P. syringae pv. tomato strain DC3000, whereas inducible overexpression of bZIP11 resulted in increased bacterial growth, supporting the hypothesis that bZIP11-regulated transcription programs are essential for maximal pathogen titer in leaves. Our data are consistent with a model in which a pathogen alters host transcription factor expression upstream of secretory transcription networks to promote nutrient efflux from host cells. Copyright © 2021 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license.},
	number = {4},
	urldate = {2021-06-21},
	journal = {Molecular Plant-Microbe Interactions®},
	author = {Prior, Matthew J. and Selvanayagam, Jebasingh and Kim, Jung-Gun and Tomar, Monika and Jonikas, Martin and Mudgett, Mary Beth and Smeekens, Sjef and Hanson, Johannes and Frommer, Wolf B.},
	month = apr,
	year = {2021},
	pages = {439--447},
}

The induction of plant nutrient secretion systems is critical for successful pathogen infection. Some bacterial pathogens (e.g., Xanthomonas spp.) use transcription activator-like (TAL) effectors to induce transcription of SWEET sucrose efflux transporters. Pseudomonas syringae pv. tomato strain DC3000 lacks TAL effectors yet is able to induce multiple SWEETs in Arabidopsis thaliana by unknown mechanisms. Because bacteria require other nutrients in addition to sugars for efficient reproduction, we hypothesized that Pseudomonas spp. may depend on host transcription factors involved in secretory programs to increase access to essential nutrients. Bioinformatic analyses identified the Arabidopsis basic-leucine zipper transcription factor bZIP11 as a potential regulator of nutrient transporters, including SWEETs and UmamiT amino acid transporters. Inducible downregulation of bZIP11 expression in Arabidopsis resulted in reduced growth of P. syringae pv. tomato strain DC3000, whereas inducible overexpression of bZIP11 resulted in increased bacterial growth, supporting the hypothesis that bZIP11-regulated transcription programs are essential for maximal pathogen titer in leaves. Our data are consistent with a model in which a pathogen alters host transcription factor expression upstream of secretory transcription networks to promote nutrient efflux from host cells. Copyright © 2021 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license.

@article{muralidhara_perturbations_2021,
	title = {Perturbations in plant energy homeostasis prime lateral root initiation via {SnRK1}-{bZIP63}-{ARF19} signaling},
	volume = {118},
	copyright = {© 2021 . https://www.pnas.org/site/aboutpnas/licenses.xhtmlPublished under the PNAS license.},
	issn = {0027-8424, 1091-6490},
	url = {https://www.pnas.org/content/118/37/e2106961118},
	doi = {10/gmvnsg},
	abstract = {Plants adjust their energy metabolism to continuous environmental fluctuations, resulting in a tremendous plasticity in their architecture. The regulatory circuits involved, however, remain largely unresolved. In Arabidopsis, moderate perturbations in photosynthetic activity, administered by short-term low light exposure or unexpected darkness, lead to increased lateral root (LR) initiation. Consistent with expression of low-energy markers, these treatments alter energy homeostasis and reduce sugar availability in roots. Here, we demonstrate that the LR response requires the metabolic stress sensor kinase Snf1-RELATED-KINASE1 (SnRK1), which phosphorylates the transcription factor BASIC LEUCINE ZIPPER63 (bZIP63) that directly binds and activates the promoter of AUXIN RESPONSE FACTOR19 (ARF19), a key regulator of LR initiation. Consistently, starvation-induced ARF19 transcription is impaired in bzip63 mutants. This study highlights a positive developmental function of SnRK1. During energy limitation, LRs are initiated and primed for outgrowth upon recovery. Hence, this study provides mechanistic insights into how energy shapes the agronomically important root system.},
	language = {en},
	number = {37},
	urldate = {2021-11-12},
	journal = {Proceedings of the National Academy of Sciences},
	author = {Muralidhara, Prathibha and Weiste, Christoph and Collani, Silvio and Krischke, Markus and Kreisz, Philipp and Draken, Jan and Feil, Regina and Mair, Andrea and Teige, Markus and Müller, Martin J. and Schmid, Markus and Becker, Dirk and Lunn, John E. and Rolland, Filip and Hanson, Johannes and Dröge-Laser, Wolfgang},
	month = sep,
	year = {2021},
	keywords = {ARF19, SnRK1, bZIP63, lateral root, metabolic homeostasis},
}

Plants adjust their energy metabolism to continuous environmental fluctuations, resulting in a tremendous plasticity in their architecture. The regulatory circuits involved, however, remain largely unresolved. In Arabidopsis, moderate perturbations in photosynthetic activity, administered by short-term low light exposure or unexpected darkness, lead to increased lateral root (LR) initiation. Consistent with expression of low-energy markers, these treatments alter energy homeostasis and reduce sugar availability in roots. Here, we demonstrate that the LR response requires the metabolic stress sensor kinase Snf1-RELATED-KINASE1 (SnRK1), which phosphorylates the transcription factor BASIC LEUCINE ZIPPER63 (bZIP63) that directly binds and activates the promoter of AUXIN RESPONSE FACTOR19 (ARF19), a key regulator of LR initiation. Consistently, starvation-induced ARF19 transcription is impaired in bzip63 mutants. This study highlights a positive developmental function of SnRK1. During energy limitation, LRs are initiated and primed for outgrowth upon recovery. Hence, this study provides mechanistic insights into how energy shapes the agronomically important root system.

@article{mahboubi_small-scale_2021,
	title = {Small-scale sequencing enables quality assessment of {Ribo}-{Seq} data: an example from {Arabidopsis} cell culture},
	volume = {17},
	issn = {1746-4811},
	shorttitle = {Small-scale sequencing enables quality assessment of {Ribo}-{Seq} data},
	url = {https://doi.org/10.1186/s13007-021-00791-w},
	doi = {10.1186/s13007-021-00791-w},
	abstract = {Translation is a tightly regulated process, controlling the rate of protein synthesis in cells. Ribosome sequencing (Ribo-Seq) is a recently developed tool for studying actively translated mRNA and can thus directly address translational regulation. Ribo-Seq libraries need to be sequenced to a great depth due to high contamination by rRNA and other contaminating nucleic acid fragments. Deep sequencing is expensive, and it generates large volumes of data, making data analysis complicated and time consuming.},
	number = {1},
	urldate = {2021-10-14},
	journal = {Plant Methods},
	author = {Mahboubi, Amir and Delhomme, Nicolas and Häggström, Sara and Hanson, Johannes},
	month = aug,
	year = {2021},
	keywords = {Evaluation of sequencing library quality, Ribo-Seq, Ribosomal profiling, Translation, Translational profiling},
	pages = {92},
}

Translation is a tightly regulated process, controlling the rate of protein synthesis in cells. Ribosome sequencing (Ribo-Seq) is a recently developed tool for studying actively translated mRNA and can thus directly address translational regulation. Ribo-Seq libraries need to be sequenced to a great depth due to high contamination by rRNA and other contaminating nucleic acid fragments. Deep sequencing is expensive, and it generates large volumes of data, making data analysis complicated and time consuming.

@article{van_der_horst_metabolite_2020,
	title = {Metabolite {Control} of {Translation} by {Conserved} {Peptide} {uORFs}: {The} {Ribosome} as a {Metabolite} {Multisensor}},
	volume = {182},
	issn = {0032-0889, 1532-2548},
	shorttitle = {Metabolite {Control} of {Translation} by {Conserved} {Peptide} {uORFs}},
	url = {https://academic.oup.com/plphys/article/182/1/110-122/6116065},
	doi = {10.1104/pp.19.00940},
	language = {en},
	number = {1},
	urldate = {2021-06-07},
	journal = {Plant Physiology},
	author = {van der Horst, Sjors and Filipovska, Teodora and Hanson, Johannes and Smeekens, Sjef},
	month = jan,
	year = {2020},
	pages = {110--122},
}

@article{bai_seed-stored_2020,
	title = {Seed-{Stored} {mRNAs} that {Are} {Specifically} {Associated} to {Monosomes} {Are} {Translationally} {Regulated} during {Germination1}  [{OPEN}]},
	volume = {182},
	issn = {0032-0889},
	url = {https://doi.org/10.1104/pp.19.00644},
	doi = {10.1104/pp.19.00644},
	abstract = {The life cycle of many organisms includes a quiescent stage, such as bacterial or fungal spores, insect larvae, or plant seeds. Common to these stages is their low water content and high survivability during harsh conditions. Upon rehydration, organisms need to reactivate metabolism and protein synthesis. Plant seeds contain many mRNAs that are transcribed during seed development. Translation of these mRNAs occurs during early seed germination, even before the requirement of transcription. Therefore, stored mRNAs are postulated to be important for germination. How these mRNAs are stored and protected during long-term storage is unknown. The aim of this study was to investigate how mRNAs are stored in dry seeds and whether they are indeed translated during seed germination. We investigated seed polysome profiles and the mRNAs and protein complexes that are associated with these ribosomes in seeds of the model organism Arabidopsis (Arabidopsis thaliana). We showed that most stored mRNAs are associated with monosomes in dry seeds; therefore, we focus on monosomes in this study. Seed ribosome complexes are associated with mRNA-binding proteins, stress granule, and P-body proteins, which suggests regulated packing of seed mRNAs. Interestingly, ∼17\% of the mRNAs that are specifically associated with monosomes are translationally up-regulated during seed germination. These mRNAs are transcribed during seed maturation, suggesting a role for this developmental stage in determining the translational fate of mRNAs during early germination.},
	number = {1},
	urldate = {2021-06-07},
	journal = {Plant Physiology},
	author = {Bai, Bing and van der Horst, Sjors and Cordewener, Jan H.G. and America, Twan A.H.P. and Hanson, Johannes and Bentsink, Leónie},
	month = jan,
	year = {2020},
	pages = {378--392},
}

The life cycle of many organisms includes a quiescent stage, such as bacterial or fungal spores, insect larvae, or plant seeds. Common to these stages is their low water content and high survivability during harsh conditions. Upon rehydration, organisms need to reactivate metabolism and protein synthesis. Plant seeds contain many mRNAs that are transcribed during seed development. Translation of these mRNAs occurs during early seed germination, even before the requirement of transcription. Therefore, stored mRNAs are postulated to be important for germination. How these mRNAs are stored and protected during long-term storage is unknown. The aim of this study was to investigate how mRNAs are stored in dry seeds and whether they are indeed translated during seed germination. We investigated seed polysome profiles and the mRNAs and protein complexes that are associated with these ribosomes in seeds of the model organism Arabidopsis (Arabidopsis thaliana). We showed that most stored mRNAs are associated with monosomes in dry seeds; therefore, we focus on monosomes in this study. Seed ribosome complexes are associated with mRNA-binding proteins, stress granule, and P-body proteins, which suggests regulated packing of seed mRNAs. Interestingly, ∼17% of the mRNAs that are specifically associated with monosomes are translationally up-regulated during seed germination. These mRNAs are transcribed during seed maturation, suggesting a role for this developmental stage in determining the translational fate of mRNAs during early germination.

@article{westman_defence_2019,
	title = {Defence priming in {Arabidopsis} – a {Meta}-{Analysis}},
	volume = {9},
	copyright = {2019 The Author(s)},
	issn = {2045-2322},
	url = {https://www.nature.com/articles/s41598-019-49811-9},
	doi = {10/gh92kh},
	abstract = {Defence priming by organismal and non-organismal stimulants can reduce effects of biotic stress in plants. Thus, it could help efforts to enhance the sustainability of agricultural production by reducing use of agrochemicals in protection of crops from pests and diseases. We have explored effects of applying this approach to both Arabidopsis plants and seeds of various crops in meta-analyses. The results show that its effects on Arabidopsis plants depend on both the priming agent and antagonist. Fungi and vitamins can have strong priming effects, and priming is usually more effective against bacterial pathogens than against herbivores. Moreover, application of bio-stimulants (particularly vitamins and plant defence elicitors) to seeds can have promising defence priming effects. However, the published evidence is scattered, does not include Arabidopsis, and additional studies are required before we can draw general conclusions and understand the molecular mechanisms involved in priming of seeds’ defences. In conclusion, defence priming of plants has clear potential and application of bio-stimulants to seeds may protect plants from an early age, promises to be both labour- and resource-efficient, poses very little environmental risk, and is thus both economically and ecologically promising.},
	language = {en},
	number = {1},
	urldate = {2021-06-07},
	journal = {Scientific Reports},
	publisher = {Nature Publishing Group},
	author = {Westman, Sara M. and Kloth, Karen J. and Hanson, Johannes and Ohlsson, Anna B. and Albrectsen, Benedicte R.},
	month = sep,
	year = {2019},
	note = {Number: 1},
	pages = {13309},
}

Defence priming by organismal and non-organismal stimulants can reduce effects of biotic stress in plants. Thus, it could help efforts to enhance the sustainability of agricultural production by reducing use of agrochemicals in protection of crops from pests and diseases. We have explored effects of applying this approach to both Arabidopsis plants and seeds of various crops in meta-analyses. The results show that its effects on Arabidopsis plants depend on both the priming agent and antagonist. Fungi and vitamins can have strong priming effects, and priming is usually more effective against bacterial pathogens than against herbivores. Moreover, application of bio-stimulants (particularly vitamins and plant defence elicitors) to seeds can have promising defence priming effects. However, the published evidence is scattered, does not include Arabidopsis, and additional studies are required before we can draw general conclusions and understand the molecular mechanisms involved in priming of seeds’ defences. In conclusion, defence priming of plants has clear potential and application of bio-stimulants to seeds may protect plants from an early age, promises to be both labour- and resource-efficient, poses very little environmental risk, and is thus both economically and ecologically promising.

@article{van_der_horst_novel_2019,
	title = {Novel pipeline identifies new upstream {ORFs} and non-{AUG} initiating main {ORFs} with conserved amino acid sequences in the 5′ leader of {mRNAs} in \textit{{Arabidopsis} thaliana}},
	volume = {25},
	issn = {1355-8382, 1469-9001},
	url = {http://rnajournal.cshlp.org/lookup/doi/10.1261/rna.067983.118},
	doi = {10.1261/rna.067983.118},
	language = {en},
	number = {3},
	urldate = {2021-06-07},
	journal = {RNA},
	author = {van der Horst, Sjors and Snel, Berend and Hanson, Johannes and Smeekens, Sjef},
	month = mar,
	year = {2019},
	pages = {292--304},
}

@article{bai_combined_2018,
	title = {Combined transcriptome and translatome analyses reveal a role for tryptophan-dependent auxin biosynthesis in the control of \textit{{DOG1}} -dependent seed dormancy},
	volume = {217},
	issn = {0028646X},
	url = {http://doi.wiley.com/10.1111/nph.14885},
	doi = {10/gcwrgv},
	language = {en},
	number = {3},
	urldate = {2021-06-07},
	journal = {New Phytologist},
	author = {Bai, Bing and Novák, Ondřej and Ljung, Karin and Hanson, Johannes and Bentsink, Leónie},
	month = feb,
	year = {2018},
	pages = {1077--1085},
}

@article{dubreuil_establishment_2018,
	title = {Establishment of {Photosynthesis} through {Chloroplast} {Development} {Is} {Controlled} by {Two} {Distinct} {Regulatory} {Phases}},
	volume = {176},
	issn = {0032-0889, 1532-2548},
	url = {https://academic.oup.com/plphys/article/176/2/1199-1214/6117139},
	doi = {10/gb2hj6},
	language = {en},
	number = {2},
	urldate = {2021-06-07},
	journal = {Plant Physiology},
	author = {Dubreuil, Carole and Jin, Xu and Barajas-López, Juan de Dios and Hewitt, Timothy C. and Tanz, Sandra K. and Dobrenel, Thomas and Schröder, Wolfgang P. and Hanson, Johannes and Pesquet, Edouard and Grönlund, Andreas and Small, Ian and Strand, Åsa},
	month = feb,
	year = {2018},
	pages = {1199--1214},
}

@article{yazdanpanah_differentially_2017,
	title = {Differentially expressed genes during the imbibition of dormant and after-ripened seeds – a reverse genetics approach},
	volume = {17},
	issn = {1471-2229},
	url = {http://bmcplantbiol.biomedcentral.com/articles/10.1186/s12870-017-1098-z},
	doi = {10/gbx65c},
	language = {en},
	number = {1},
	urldate = {2021-06-07},
	journal = {BMC Plant Biology},
	author = {Yazdanpanah, Farzaneh and Hanson, Johannes and Hilhorst, Henk W.M. and Bentsink, Leónie},
	month = dec,
	year = {2017},
	pages = {151},
}

@article{bai_extensive_2017,
	title = {Extensive translational regulation during seed germination revealed by polysomal profiling},
	volume = {214},
	issn = {0028-646X, 1469-8137},
	url = {https://onlinelibrary.wiley.com/doi/10.1111/nph.14355},
	doi = {10.1111/nph.14355},
	language = {en},
	number = {1},
	urldate = {2021-06-07},
	journal = {New Phytologist},
	author = {Bai, Bing and Peviani, Alessia and Horst, Sjors and Gamm, Magdalena and Snel, Berend and Bentsink, Leónie and Hanson, Johannes},
	month = apr,
	year = {2017},
	pages = {233--244},
}

@article{baena-gonzalez_shaping_2017,
	title = {Shaping plant development through the {SnRK1}–{TOR} metabolic regulators},
	volume = {35},
	issn = {13695266},
	url = {https://linkinghub.elsevier.com/retrieve/pii/S1369526616302242},
	doi = {10.1016/j.pbi.2016.12.004},
	language = {en},
	urldate = {2021-06-07},
	journal = {Current Opinion in Plant Biology},
	author = {Baena-González, Elena and Hanson, Johannes},
	month = feb,
	year = {2017},
	pages = {152--157},
}

@article{weiste_arabidopsis_2017,
	title = {The {Arabidopsis} {bZIP11} transcription factor links low-energy signalling to auxin-mediated control of primary root growth},
	volume = {13},
	issn = {1553-7404},
	url = {https://dx.plos.org/10.1371/journal.pgen.1006607},
	doi = {10.1371/journal.pgen.1006607},
	language = {en},
	number = {2},
	urldate = {2021-06-07},
	journal = {PLOS Genetics},
	author = {Weiste, Christoph and Pedrotti, Lorenzo and Selvanayagam, Jebasingh and Muralidhara, Prathibha and Fröschel, Christian and Novák, Ondřej and Ljung, Karin and Hanson, Johannes and Dröge-Laser, Wolfgang},
	editor = {Reed, Jason},
	month = feb,
	year = {2017},
	pages = {e1006607},
}

@article{he_effects_2016,
	title = {Effects of {Parental} {Temperature} and {Nitrate} on {Seed} {Performance} are {Reflected} by {Partly} {Overlapping} {Genetic} and {Metabolic} {Pathways}},
	volume = {57},
	issn = {0032-0781, 1471-9053},
	url = {https://academic.oup.com/pcp/article-lookup/doi/10.1093/pcp/pcv207},
	doi = {10.1093/pcp/pcv207},
	language = {en},
	number = {3},
	urldate = {2021-06-07},
	journal = {Plant and Cell Physiology},
	author = {He, Hanzi and Willems, Leo A. J. and Batushansky, Albert and Fait, Aaron and Hanson, Johannes and Nijveen, Harm and Hilhorst, Henk W.M. and Bentsink, Leónie},
	month = mar,
	year = {2016},
	pages = {473--487},
}

@article{nukarinen_quantitative_2016,
	title = {Quantitative phosphoproteomics reveals the role of the {AMPK} plant ortholog {SnRK1} as a metabolic master regulator under energy deprivation},
	volume = {6},
	issn = {2045-2322},
	url = {http://www.nature.com/articles/srep31697},
	doi = {10/f3rwtq},
	language = {en},
	number = {1},
	urldate = {2021-06-07},
	journal = {Scientific Reports},
	author = {Nukarinen, Ella and Nägele, Thomas and Pedrotti, Lorenzo and Wurzinger, Bernhard and Mair, Andrea and Landgraf, Ramona and Börnke, Frederik and Hanson, Johannes and Teige, Markus and Baena-Gonzalez, Elena and Dröge-Laser, Wolfgang and Weckwerth, Wolfram},
	month = aug,
	year = {2016},
	pages = {31697},
}

@article{dobrenel_tor_2016,
	title = {{TOR} {Signaling} and {Nutrient} {Sensing}},
	volume = {67},
	issn = {1543-5008, 1545-2123},
	url = {http://www.annualreviews.org/doi/10.1146/annurev-arplant-043014-114648},
	doi = {10.1146/annurev-arplant-043014-114648},
	language = {en},
	number = {1},
	urldate = {2021-06-07},
	journal = {Annual Review of Plant Biology},
	author = {Dobrenel, Thomas and Caldana, Camila and Hanson, Johannes and Robaglia, Christophe and Vincentz, Michel and Veit, Bruce and Meyer, Christian},
	month = apr,
	year = {2016},
	pages = {261--285},
}

@article{dekkers_arabidopsis_2016,
	title = {The {Arabidopsis} \textit{{DELAY} {OF} {GERMINATION} 1} gene affects \textit{{ABSCISIC} {ACID} {INSENSITIVE} 5 ({ABI5})} expression and genetically interacts with \textit{{ABI3}} during {Arabidopsis} seed development},
	volume = {85},
	issn = {09607412},
	url = {http://doi.wiley.com/10.1111/tpj.13118},
	doi = {10.1111/tpj.13118},
	language = {en},
	number = {4},
	urldate = {2021-06-07},
	journal = {The Plant Journal},
	author = {Dekkers, Bas J.W. and He, Hanzi and Hanson, Johannes and Willems, Leo A.J. and Jamar, Diaan C.L. and Cueff, Gwendal and Rajjou, Loïc and Hilhorst, Henk W.M. and Bentsink, Leónie},
	month = feb,
	year = {2016},
	pages = {451--465},
}

@article{dobrenel_arabidopsis_2016,
	title = {The {Arabidopsis} {TOR} {Kinase} {Specifically} {Regulates} the {Expression} of {Nuclear} {Genes} {Coding} for {Plastidic} {Ribosomal} {Proteins} and the {Phosphorylation} of the {Cytosolic} {Ribosomal} {Protein} {S6}},
	volume = {7},
	issn = {1664-462X},
	url = {http://journal.frontiersin.org/article/10.3389/fpls.2016.01611/full},
	doi = {10.3389/fpls.2016.01611},
	urldate = {2021-06-07},
	journal = {Frontiers in Plant Science},
	author = {Dobrenel, Thomas and Mancera-Martínez, Eder and Forzani, Céline and Azzopardi, Marianne and Davanture, Marlène and Moreau, Manon and Schepetilnikov, Mikhail and Chicher, Johana and Langella, Olivier and Zivy, Michel and Robaglia, Christophe and Ryabova, Lyubov A. and Hanson, Johannes and Meyer, Christian},
	month = nov,
	year = {2016},
}

@article{peviani_phylogeny_2016,
	title = {The phylogeny of {C}/{S1} {bZIP} transcription factors reveals a shared algal ancestry and the pre-angiosperm translational regulation of {S1} transcripts},
	volume = {6},
	issn = {2045-2322},
	url = {http://www.nature.com/articles/srep30444},
	doi = {10/f3sc79},
	language = {en},
	number = {1},
	urldate = {2021-06-07},
	journal = {Scientific Reports},
	author = {Peviani, Alessia and Lastdrager, Jeroen and Hanson, Johannes and Snel, Berend},
	month = jul,
	year = {2016},
	pages = {30444},
}

@article{hartmann_crosstalk_2015,
	title = {Crosstalk between {Two} {bZIP} {Signaling} {Pathways} {Orchestrates} {Salt}-{Induced} {Metabolic} {Reprogramming} in {Arabidopsis} {Roots}},
	volume = {27},
	issn = {1532-298X (Electronic) 1040-4651 (Linking)},
	url = {https://www.ncbi.nlm.nih.gov/pubmed/26276836},
	doi = {10.1105/tpc.15.00163},
	abstract = {Soil salinity increasingly causes crop losses worldwide. Although roots are the primary targets of salt stress, the signaling networks that facilitate metabolic reprogramming to induce stress tolerance are less understood than those in leaves. Here, a combination of transcriptomic and metabolic approaches was performed in salt-treated Arabidopsis thaliana roots, which revealed that the group S1 basic leucine zipper transcription factors bZIP1 and bZIP53 reprogram primary C- and N-metabolism. In particular, gluconeogenesis and amino acid catabolism are affected by these transcription factors. Importantly, bZIP1 expression reflects cellular stress and energy status in roots. In addition to the well-described abiotic stress response pathway initiated by the hormone abscisic acid (ABA) and executed by SnRK2 (Snf1-RELATED-PROTEIN-KINASE2) and AREB-like bZIP factors, we identify a structurally related ABA-independent signaling module consisting of SnRK1s and S1 bZIPs. Crosstalk between these signaling pathways recruits particular bZIP factor combinations to establish at least four distinct gene expression patterns. Understanding this signaling network provides a framework for securing future crop productivity.},
	language = {en},
	number = {8},
	urldate = {2021-06-07},
	journal = {Plant Cell},
	author = {Hartmann, L. and Pedrotti, L. and Weiste, C. and Fekete, A. and Schierstaedt, J. and Gottler, J. and Kempa, S. and Krischke, M. and Dietrich, K. and Mueller, M. J. and Vicente-Carbajosa, J. and Hanson, J. and Droge-Laser, W.},
	month = aug,
	year = {2015},
	note = {Edition: 2015/08/16},
	keywords = {Abscisic Acid/pharmacology, Amino Acids/metabolism, Arabidopsis Proteins/*genetics/metabolism, Arabidopsis/drug effects/*genetics/metabolism, Basic-Leucine Zipper Transcription Factors/*genetics/metabolism, Calcium/metabolism, Carbohydrate Metabolism/drug effects/genetics, Gene Expression Regulation, Plant/drug effects, Gluconeogenesis/drug effects/genetics, Immunoblotting, Mutation, Plant Growth Regulators/pharmacology, Plant Roots/drug effects/genetics/metabolism, Promoter Regions, Genetic/genetics, Protein Binding/drug effects, Protein-Serine-Threonine Kinases, Reverse Transcriptase Polymerase Chain Reaction, Salt-Tolerant Plants/drug effects/genetics/metabolism, Signal Transduction/drug effects/*genetics, Sodium Chloride/pharmacology, Transcriptome/drug effects/genetics},
	pages = {2244--60},
}

Soil salinity increasingly causes crop losses worldwide. Although roots are the primary targets of salt stress, the signaling networks that facilitate metabolic reprogramming to induce stress tolerance are less understood than those in leaves. Here, a combination of transcriptomic and metabolic approaches was performed in salt-treated Arabidopsis thaliana roots, which revealed that the group S1 basic leucine zipper transcription factors bZIP1 and bZIP53 reprogram primary C- and N-metabolism. In particular, gluconeogenesis and amino acid catabolism are affected by these transcription factors. Importantly, bZIP1 expression reflects cellular stress and energy status in roots. In addition to the well-described abiotic stress response pathway initiated by the hormone abscisic acid (ABA) and executed by SnRK2 (Snf1-RELATED-PROTEIN-KINASE2) and AREB-like bZIP factors, we identify a structurally related ABA-independent signaling module consisting of SnRK1s and S1 bZIPs. Crosstalk between these signaling pathways recruits particular bZIP factor combinations to establish at least four distinct gene expression patterns. Understanding this signaling network provides a framework for securing future crop productivity.

@article{hummel_proteomic_2015,
	title = {Proteomic {LC}-{MS} analysis of {Arabidopsis} cytosolic ribosomes: {Identification} of ribosomal protein paralogs and re-annotation of the ribosomal protein genes},
	volume = {128},
	issn = {1876-7737 (Electronic) 1874-3919 (Linking)},
	shorttitle = {Proteomic {LC}–{MS} analysis of {Arabidopsis} cytosolic ribosomes},
	url = {https://www.ncbi.nlm.nih.gov/pubmed/26232565},
	doi = {10.1016/j.jprot.2015.07.004},
	abstract = {UNLABELLED: Arabidopsis thaliana cytosolic ribosomes are large complexes containing eighty-one distinct ribosomal proteins (r-proteins), four ribosomal RNAs (rRNA) and a plethora of associated (non-ribosomal) proteins. In plants, r-proteins of cytosolic ribosomes are each encoded by two to seven different expressed and similar genes, forming an r-protein family. Distinctions in the r-protein coding sequences of gene family members are a source of variation between ribosomes. We performed proteomic investigation of actively translating cytosolic ribosomes purified using both immunopurification and a classic sucrose cushion centrifugation-based protocol from plants of different developmental stages. Both 1D and 2D LC-MS(E) with data-independent acquisition as well as conventional data-dependent MS/MS procedures were applied. This approach provided detailed identification of 165 r-protein paralogs with high coverage based on proteotypic peptides. The detected r-proteins were the products of the majority (68\%) of the 242 cytosolic r-protein genes encoded by the genome. A total of 70 distinct r-proteins were identified. Based on these results and information from DNA microarray and ribosome footprint profiling studies a re-annotation of Arabidopsis r-proteins and genes is proposed. This compendium of the cytosolic r-protein proteome will serve as a template for future investigations on the dynamic structure and function of plant ribosomes. BIOLOGICAL SIGNIFICANCE: Translation is one of the most energy demanding processes in a living cell and is therefore carefully regulated. Translational activity is tightly linked to growth control and growth regulating mechanism. Recently established translational profiling technologies, including the profiling of mRNAs associated with polysomes and the mapping of ribosome footprints on mRNAs, have revealed that the expression of gene expression is often fine-tuned by differential translation of gene transcripts. The eukaryotic ribosome, the hub of these important processes, consists of close to eighty different proteins (depending on species) and four large RNAs assembled into two highly conserved subunits. In plants and to lesser extent in yeast, the r-proteins are encoded by more than one actively transcribed gene. As r-protein gene paralogs frequently do not encode identical proteins and are regulated by growth conditions and development, in vivo ribosomes are heterogeneous in their protein content. The regulatory and physiological importance of this heterogeneity is unknown. Here, an improved annotation of the more than two hundred r-protein genes of Arabidopsis is presented that combines proteomic and advanced mRNA expression data. This proteomic investigation and re-annotation of Arabidopsis ribosomes establish a base for future investigations of translational control in plants.},
	language = {en},
	urldate = {2021-06-07},
	journal = {J Proteomics},
	author = {Hummel, M. and Dobrenel, T. and Cordewener, J. J. and Davanture, M. and Meyer, C. and Smeekens, S. J. and Bailey-Serres, J. and America, T. A. and Hanson, J.},
	month = oct,
	year = {2015},
	note = {Edition: 2015/08/02},
	keywords = {A. thaliana, Amino Acid Sequence, Arabidopsis Proteins/*metabolism, Arabidopsis/*metabolism, Chromatography, Liquid/*methods, Data-independent acquisition, Dia, Gene Expression Profiling/methods, Lc-ms, Mass Spectrometry/*methods, Molecular Sequence Data, Paralogs, Proteome/chemistry/metabolism, Ribosomal Proteins/*chemistry/*metabolism, Ribosomal protein, Ribosomes},
	pages = {436--49},
}

UNLABELLED: Arabidopsis thaliana cytosolic ribosomes are large complexes containing eighty-one distinct ribosomal proteins (r-proteins), four ribosomal RNAs (rRNA) and a plethora of associated (non-ribosomal) proteins. In plants, r-proteins of cytosolic ribosomes are each encoded by two to seven different expressed and similar genes, forming an r-protein family. Distinctions in the r-protein coding sequences of gene family members are a source of variation between ribosomes. We performed proteomic investigation of actively translating cytosolic ribosomes purified using both immunopurification and a classic sucrose cushion centrifugation-based protocol from plants of different developmental stages. Both 1D and 2D LC-MS(E) with data-independent acquisition as well as conventional data-dependent MS/MS procedures were applied. This approach provided detailed identification of 165 r-protein paralogs with high coverage based on proteotypic peptides. The detected r-proteins were the products of the majority (68%) of the 242 cytosolic r-protein genes encoded by the genome. A total of 70 distinct r-proteins were identified. Based on these results and information from DNA microarray and ribosome footprint profiling studies a re-annotation of Arabidopsis r-proteins and genes is proposed. This compendium of the cytosolic r-protein proteome will serve as a template for future investigations on the dynamic structure and function of plant ribosomes. BIOLOGICAL SIGNIFICANCE: Translation is one of the most energy demanding processes in a living cell and is therefore carefully regulated. Translational activity is tightly linked to growth control and growth regulating mechanism. Recently established translational profiling technologies, including the profiling of mRNAs associated with polysomes and the mapping of ribosome footprints on mRNAs, have revealed that the expression of gene expression is often fine-tuned by differential translation of gene transcripts. The eukaryotic ribosome, the hub of these important processes, consists of close to eighty different proteins (depending on species) and four large RNAs assembled into two highly conserved subunits. In plants and to lesser extent in yeast, the r-proteins are encoded by more than one actively transcribed gene. As r-protein gene paralogs frequently do not encode identical proteins and are regulated by growth conditions and development, in vivo ribosomes are heterogeneous in their protein content. The regulatory and physiological importance of this heterogeneity is unknown. Here, an improved annotation of the more than two hundred r-protein genes of Arabidopsis is presented that combines proteomic and advanced mRNA expression data. This proteomic investigation and re-annotation of Arabidopsis ribosomes establish a base for future investigations of translational control in plants.

@article{zamioudis_rhizobacterial_2015,
	title = {Rhizobacterial volatiles and photosynthesis-related signals coordinate {MYB72} expression in {Arabidopsis} roots during onset of induced systemic resistance and iron-deficiency responses},
	volume = {84},
	issn = {1365-313X (Electronic) 0960-7412 (Linking)},
	shorttitle = {Rhizobacterial volatiles and photosynthesis‐related signals coordinate},
	url = {https://www.ncbi.nlm.nih.gov/pubmed/26307542},
	doi = {10/f3m6j7},
	abstract = {In Arabidopsis roots, the transcription factor MYB72 plays a dual role in the onset of rhizobacteria-induced systemic resistance (ISR) and plant survival under conditions of limited iron availability. Previously, it was shown that MYB72 coordinates the expression of a gene module that promotes synthesis and excretion of iron-mobilizing phenolic compounds in the rhizosphere, a process that is involved in both iron acquisition and ISR signaling. Here, we show that volatile organic compounds (VOCs) from ISR-inducing Pseudomonas bacteria are important elicitors of MYB72. In response to VOC treatment, MYB72 is co-expressed with the iron uptake-related genes FERRIC REDUCTION OXIDASE 2 (FRO2) and IRON-REGULATED TRANSPORTER 1 (IRT1) in a manner that is dependent on FER-LIKE IRON DEFICIENCY TRANSCRIPTION FACTOR (FIT), indicating that MYB72 is an intrinsic part of the plant's iron-acquisition response that is typically activated upon iron starvation. However, VOC-induced MYB72 expression is activated independently of iron availability in the root vicinity. Moreover, rhizobacterial VOC-mediated induction of MYB72 requires photosynthesis-related signals, while iron deficiency in the rhizosphere activates MYB72 in the absence of shoot-derived signals. Together, these results show that the ISR- and iron acquisition-related transcription factor MYB72 in Arabidopsis roots is activated by rhizobacterial volatiles and photosynthesis-related signals, and enhances the iron-acquisition capacity of roots independently of the iron availability in the rhizosphere. This work highlights the role of MYB72 in plant processes by which root microbiota simultaneously stimulate systemic immunity and activate the iron-uptake machinery in their host plants.},
	language = {en},
	number = {2},
	urldate = {2021-06-07},
	journal = {Plant J},
	author = {Zamioudis, C. and Korteland, J. and Van Pelt, J. A. and van Hamersveld, M. and Dombrowski, N. and Bai, Y. and Hanson, J. and Van Verk, M. C. and Ling, H. Q. and Schulze-Lefert, P. and Pieterse, C. M.},
	month = oct,
	year = {2015},
	note = {Edition: 2015/08/27},
	keywords = {Arabidopsis Proteins/genetics/*metabolism, Arabidopsis thaliana, Arabidopsis/drug effects/*metabolism, Gene Expression Regulation, Plant/drug effects/genetics, Iron/*deficiency, MYB transcription factor, Photosynthesis/drug effects, Plant Roots/drug effects/*metabolism, Rhizobium/*chemistry, Volatile Organic Compounds/*pharmacology, induced resistance, iron homeostasis, plant growth-promoting rhizobacteria, volatile organic compounds},
	pages = {309--22},
}

In Arabidopsis roots, the transcription factor MYB72 plays a dual role in the onset of rhizobacteria-induced systemic resistance (ISR) and plant survival under conditions of limited iron availability. Previously, it was shown that MYB72 coordinates the expression of a gene module that promotes synthesis and excretion of iron-mobilizing phenolic compounds in the rhizosphere, a process that is involved in both iron acquisition and ISR signaling. Here, we show that volatile organic compounds (VOCs) from ISR-inducing Pseudomonas bacteria are important elicitors of MYB72. In response to VOC treatment, MYB72 is co-expressed with the iron uptake-related genes FERRIC REDUCTION OXIDASE 2 (FRO2) and IRON-REGULATED TRANSPORTER 1 (IRT1) in a manner that is dependent on FER-LIKE IRON DEFICIENCY TRANSCRIPTION FACTOR (FIT), indicating that MYB72 is an intrinsic part of the plant's iron-acquisition response that is typically activated upon iron starvation. However, VOC-induced MYB72 expression is activated independently of iron availability in the root vicinity. Moreover, rhizobacterial VOC-mediated induction of MYB72 requires photosynthesis-related signals, while iron deficiency in the rhizosphere activates MYB72 in the absence of shoot-derived signals. Together, these results show that the ISR- and iron acquisition-related transcription factor MYB72 in Arabidopsis roots is activated by rhizobacterial volatiles and photosynthesis-related signals, and enhances the iron-acquisition capacity of roots independently of the iron availability in the rhizosphere. This work highlights the role of MYB72 in plant processes by which root microbiota simultaneously stimulate systemic immunity and activate the iron-uptake machinery in their host plants.

@article{mair_snrk1-triggered_2015,
	title = {{SnRK1}-triggered switch of {bZIP63} dimerization mediates the low-energy response in plants},
	volume = {4},
	issn = {2050-084X (Electronic) 2050-084X (Linking)},
	url = {https://www.ncbi.nlm.nih.gov/pubmed/26263501},
	doi = {10.7554/eLife.05828},
	abstract = {Metabolic adjustment to changing environmental conditions, particularly balancing of growth and defense responses, is crucial for all organisms to survive. The evolutionary conserved AMPK/Snf1/SnRK1 kinases are well-known metabolic master regulators in the low-energy response in animals, yeast and plants. They act at two different levels: by modulating the activity of key metabolic enzymes, and by massive transcriptional reprogramming. While the first part is well established, the latter function is only partially understood in animals and not at all in plants. Here we identified the Arabidopsis transcription factor bZIP63 as key regulator of the starvation response and direct target of the SnRK1 kinase. Phosphorylation of bZIP63 by SnRK1 changed its dimerization preference, thereby affecting target gene expression and ultimately primary metabolism. A bzip63 knock-out mutant exhibited starvation-related phenotypes, which could be functionally complemented by wild type bZIP63, but not by a version harboring point mutations in the identified SnRK1 target sites.},
	language = {en},
	urldate = {2021-06-07},
	journal = {Elife},
	author = {Mair, A. and Pedrotti, L. and Wurzinger, B. and Anrather, D. and Simeunovic, A. and Weiste, C. and Valerio, C. and Dietrich, K. and Kirchler, T. and Nagele, T. and Vicente Carbajosa, J. and Hanson, J. and Baena-Gonzalez, E. and Chaban, C. and Weckwerth, W. and Droge-Laser, W. and Teige, M.},
	month = aug,
	year = {2015},
	note = {Edition: 2015/08/12},
	keywords = {*Gene Expression Regulation, Plant, *Protein Multimerization, Adaptation, Physiological, Arabidopsis Proteins/*metabolism, Arabidopsis/*genetics/metabolism, Basic-Leucine Zipper Transcription Factors/deficiency/*metabolism, Gene Knockout Techniques, Genetic Complementation Test, Phosphorylation, Protein Processing, Post-Translational, Protein-Serine-Threonine Kinases/*metabolism, SnRK1 kinase, arabidopsis, bZIP transcription factor, cell biology, metabolic reprogramming, plant biology},
	pages = {e05828},
}

Metabolic adjustment to changing environmental conditions, particularly balancing of growth and defense responses, is crucial for all organisms to survive. The evolutionary conserved AMPK/Snf1/SnRK1 kinases are well-known metabolic master regulators in the low-energy response in animals, yeast and plants. They act at two different levels: by modulating the activity of key metabolic enzymes, and by massive transcriptional reprogramming. While the first part is well established, the latter function is only partially understood in animals and not at all in plants. Here we identified the Arabidopsis transcription factor bZIP63 as key regulator of the starvation response and direct target of the SnRK1 kinase. Phosphorylation of bZIP63 by SnRK1 changed its dimerization preference, thereby affecting target gene expression and ultimately primary metabolism. A bzip63 knock-out mutant exhibited starvation-related phenotypes, which could be functionally complemented by wild type bZIP63, but not by a version harboring point mutations in the identified SnRK1 target sites.

@article{gamm_increased_2014,
	title = {Increased sucrose levels mediate selective {mRNA} translation in {Arabidopsis}},
	volume = {14},
	issn = {1471-2229},
	url = {http://bmcplantbiol.biomedcentral.com/articles/10.1186/s12870-014-0306-3},
	doi = {10/f3nrb4},
	language = {en},
	number = {1},
	urldate = {2021-06-08},
	journal = {BMC Plant Biology},
	author = {Gamm, Magdalena and Peviani, Alessia and Honsel, Anne and Snel, Berend and Smeekens, Sjef and Hanson, Johannes},
	month = dec,
	year = {2014},
	pages = {306},
}

@article{lastdrager_sugar_2014,
	title = {Sugar signals and the control of plant growth and development},
	volume = {65},
	issn = {1460-2431, 0022-0957},
	url = {https://academic.oup.com/jxb/article-lookup/doi/10.1093/jxb/ert474},
	doi = {10/f239qn},
	language = {en},
	number = {3},
	urldate = {2021-06-08},
	journal = {Journal of Experimental Botany},
	author = {Lastdrager, Jeroen and Hanson, Johannes and Smeekens, Sjef},
	month = mar,
	year = {2014},
	pages = {799--807},
}

@article{zamioudis_-glucosidase_2014,
	title = {β-{Glucosidase} {BGLU42} is a {MYB72}-dependent key regulator of rhizobacteria-induced systemic resistance and modulates iron deficiency responses in \textit{{Arabidopsis}} roots},
	volume = {204},
	issn = {0028646X},
	url = {http://doi.wiley.com/10.1111/nph.12980},
	doi = {10/f3nsht},
	language = {en},
	number = {2},
	urldate = {2021-06-08},
	journal = {New Phytologist},
	author = {Zamioudis, Christos and Hanson, Johannes and Pieterse, Corné M. J.},
	month = oct,
	year = {2014},
	pages = {368--379},
}

@article{wind_abi4_2013,
	title = {{ABI4}: versatile activator and repressor},
	volume = {18},
	issn = {13601385},
	shorttitle = {{ABI4}},
	url = {https://linkinghub.elsevier.com/retrieve/pii/S1360138512002312},
	doi = {10/f22p4f},
	language = {en},
	number = {3},
	urldate = {2021-06-08},
	journal = {Trends in Plant Science},
	author = {Wind, Julia J. and Peviani, Alessia and Snel, Berend and Hanson, Johannes and Smeekens, Sjef C.},
	month = mar,
	year = {2013},
	pages = {125--132},
}

@article{hummel_dynamic_2012,
	title = {Dynamic protein composition of {Arabidopsis} thaliana cytosolic ribosomes in response to sucrose feeding as revealed by label free {MSE} proteomics},
	volume = {12},
	issn = {16159853},
	url = {http://doi.wiley.com/10.1002/pmic.201100413},
	doi = {10/f23s9x},
	language = {en},
	number = {7},
	urldate = {2021-06-08},
	journal = {PROTEOMICS},
	author = {Hummel, Maureen and Cordewener, Jan H. G. and de Groot, Joost C. M. and Smeekens, Sjef and America, Antoine H. P. and Hanson, Johannes},
	month = apr,
	year = {2012},
	pages = {1024--1038},
}

@article{li_fructose_2011,
	chapter = {Biological Sciences},
	title = {Fructose sensitivity is suppressed in {Arabidopsis} by the transcription factor {ANAC089} lacking the membrane-bound domain},
	volume = {108},
	issn = {0027-8424, 1091-6490},
	url = {https://www.pnas.org/content/108/8/3436},
	doi = {10/bpszjb},
	abstract = {In living organisms sugars not only provide energy and carbon skeletons but also act as evolutionarily conserved signaling molecules. The three major soluble sugars in plants are sucrose, glucose, and fructose. Information on plant glucose and sucrose signaling is available, but to date no fructose-specific signaling pathway has been reported. In this study, sugar repression of seedling development was used to study fructose sensitivity in the Landsberg erecta (Ler)/Cape Verde Islands (Cvi) recombinant inbred line population, and eight fructose-sensing quantitative trait loci (QTLs) (FSQ1–8) were mapped. Among them, FSQ6 was confirmed to be a fructose-specific QTL by analyzing near-isogenic lines in which Cvi genomic fragments were introgressed in the Ler background. These results indicate the existence of a fructose-specific signaling pathway in Arabidopsis. Further analysis demonstrated that the FSQ6-associated fructose-signaling pathway functions independently of the hexokinase1 (HXK1) glucose sensor. Remarkably, fructose-specific FSQ6 downstream signaling interacts with abscisic acid (ABA)- and ethylene-signaling pathways, similar to HXK1-dependent glucose signaling. The Cvi allele of FSQ6 acts as a suppressor of fructose signaling. The FSQ6 gene was identified using map-based cloning approach, and FSQ6 was shown to encode the transcription factor gene Arabidopsis NAC (petunia No apical meristem and Arabidopsis transcription activation factor 1, 2 and Cup-shaped cotyledon 2) domain containing protein 89 (ANAC089). The Cvi allele of FSQ6/ANAC089 is a gain-of-function allele caused by a premature stop in the third exon of the gene. The truncated Cvi FSQ6/ANAC089 protein lacks a membrane association domain that is present in ANAC089 proteins from other Arabidopsis accessions. As a result, Cvi FSQ6/ANAC089 is constitutively active as a transcription factor in the nucleus.},
	language = {en},
	number = {8},
	urldate = {2021-06-08},
	journal = {Proceedings of the National Academy of Sciences},
	publisher = {National Academy of Sciences},
	author = {Li, Ping and Wind, Julia J. and Shi, Xiaoliang and Zhang, Honglei and Hanson, Johannes and Smeekens, Sjef C. and Teng, Sheng},
	month = feb,
	year = {2011},
	keywords = {fructose quantitative trait locus, map based cloning, natural variation, sugar signaling},
	pages = {3436--3441},
}

In living organisms sugars not only provide energy and carbon skeletons but also act as evolutionarily conserved signaling molecules. The three major soluble sugars in plants are sucrose, glucose, and fructose. Information on plant glucose and sucrose signaling is available, but to date no fructose-specific signaling pathway has been reported. In this study, sugar repression of seedling development was used to study fructose sensitivity in the Landsberg erecta (Ler)/Cape Verde Islands (Cvi) recombinant inbred line population, and eight fructose-sensing quantitative trait loci (QTLs) (FSQ1–8) were mapped. Among them, FSQ6 was confirmed to be a fructose-specific QTL by analyzing near-isogenic lines in which Cvi genomic fragments were introgressed in the Ler background. These results indicate the existence of a fructose-specific signaling pathway in Arabidopsis. Further analysis demonstrated that the FSQ6-associated fructose-signaling pathway functions independently of the hexokinase1 (HXK1) glucose sensor. Remarkably, fructose-specific FSQ6 downstream signaling interacts with abscisic acid (ABA)- and ethylene-signaling pathways, similar to HXK1-dependent glucose signaling. The Cvi allele of FSQ6 acts as a suppressor of fructose signaling. The FSQ6 gene was identified using map-based cloning approach, and FSQ6 was shown to encode the transcription factor gene Arabidopsis NAC (petunia No apical meristem and Arabidopsis transcription activation factor 1, 2 and Cup-shaped cotyledon 2) domain containing protein 89 (ANAC089). The Cvi allele of FSQ6/ANAC089 is a gain-of-function allele caused by a premature stop in the third exon of the gene. The truncated Cvi FSQ6/ANAC089 protein lacks a membrane association domain that is present in ANAC089 proteins from other Arabidopsis accessions. As a result, Cvi FSQ6/ANAC089 is constitutively active as a transcription factor in the nucleus.

@article{ma_sucroseregulated_2011,
	title = {The sucrose‐regulated {Arabidopsis} transcription factor {bZIP11} reprograms metabolism and regulates trehalose metabolism},
	volume = {191},
	issn = {0028-646X, 1469-8137},
	url = {https://onlinelibrary.wiley.com/doi/10.1111/j.1469-8137.2011.03735.x},
	doi = {10/b9vhbj},
	language = {en},
	number = {3},
	urldate = {2021-06-08},
	journal = {New Phytologist},
	author = {Ma, Jingkun and Hanssen, Micha and Lundgren, Krister and Hernández, Lázaro and Delatte, Thierry and Ehlert, Andrea and Liu, Chun‐Ming and Schluepmann, Henriette and Dröge‐Laser, Wolfgang and Moritz, Thomas and Smeekens, Sjef and Hanson, Johannes},
	month = aug,
	year = {2011},
	pages = {733--745},
}

@article{bentsink_natural_2010,
	title = {Natural variation for seed dormancy in {Arabidopsis} is regulated by additive genetic and molecular pathways},
	volume = {107},
	issn = {1091-6490},
	doi = {10/c2gjzz},
	abstract = {Timing of germination is presumably under strong natural selection as it determines the environmental conditions in which a plant germinates and initiates its postembryonic life cycle. To investigate how seed dormancy is controlled, quantitative trait loci (QTL) analyses has been performed in six Arabidopsis thaliana recombinant inbred line populations by analyzing them simultaneously using a mixed model QTL approach. The recombinant inbred line populations were derived from crosses between the reference accession Landsberg erecta (Ler) and accessions from different world regions. In total, 11 delay of germination (DOG) QTL have been identified, and nine of them have been confirmed by near isogenic lines (NILs). The absence of strong epistatic interactions between the different DOG loci suggests that they affect dormancy mainly by distinct genetic pathways. This was confirmed by analyzing the transcriptome of freshly harvested dry seeds of five different DOG NILs. All five DOG NILs showed discernible and different expression patterns compared with the expression of their genetic background Ler. The genes identified in the different DOG NILs represent largely different gene ontology profiles. It is proposed that natural variation for seed dormancy in Arabidopsis is mainly controlled by different additive genetic and molecular pathways rather than epistatic interactions, indicating the involvement of several independent pathways.},
	language = {eng},
	number = {9},
	journal = {Proceedings of the National Academy of Sciences of the United States of America},
	author = {Bentsink, Leónie and Hanson, Johannes and Hanhart, Corrie J. and Blankestijn-de Vries, Hetty and Coltrane, Colin and Keizer, Paul and El-Lithy, Mohamed and Alonso-Blanco, Carlos and de Andrés, M. Teresa and Reymond, Matthieu and van Eeuwijk, Fred and Smeekens, Sjef and Koornneef, Maarten},
	month = mar,
	year = {2010},
	keywords = {Arabidopsis, Arabidopsis Proteins, Gene Expression Profiling, Genetic Variation, Quantitative Trait Loci, Seeds},
	pages = {4264--4269},
}

Timing of germination is presumably under strong natural selection as it determines the environmental conditions in which a plant germinates and initiates its postembryonic life cycle. To investigate how seed dormancy is controlled, quantitative trait loci (QTL) analyses has been performed in six Arabidopsis thaliana recombinant inbred line populations by analyzing them simultaneously using a mixed model QTL approach. The recombinant inbred line populations were derived from crosses between the reference accession Landsberg erecta (Ler) and accessions from different world regions. In total, 11 delay of germination (DOG) QTL have been identified, and nine of them have been confirmed by near isogenic lines (NILs). The absence of strong epistatic interactions between the different DOG loci suggests that they affect dormancy mainly by distinct genetic pathways. This was confirmed by analyzing the transcriptome of freshly harvested dry seeds of five different DOG NILs. All five DOG NILs showed discernible and different expression patterns compared with the expression of their genetic background Ler. The genes identified in the different DOG NILs represent largely different gene ontology profiles. It is proposed that natural variation for seed dormancy in Arabidopsis is mainly controlled by different additive genetic and molecular pathways rather than epistatic interactions, indicating the involvement of several independent pathways.

@article{wind_sucrose_2010,
	title = {Sucrose: metabolite and signaling molecule},
	volume = {71},
	issn = {1873-3700},
	shorttitle = {Sucrose},
	doi = {10/bcnsm2},
	abstract = {Sucrose is a molecule that is synthesized only by oxygenic photosynthetic organisms. In plants, sucrose is synthesized in source tissues and then can be transported to sink tissues, where it is utilized or stored. Interestingly, sucrose is both a metabolite and a signaling molecule. Manipulating the rate of the synthesis, transport or degradation of sucrose affects plant growth, development and physiology. Altered sucrose levels changes the quantity of sucrose derived metabolites and sucrose-specific signaling. In this paper, these changes are summarized. Better understanding of sucrose metabolism and sucrose sensing systems in plants will lead to opportunities to adapt plant metabolism and growth.},
	language = {eng},
	number = {14-15},
	journal = {Phytochemistry},
	author = {Wind, Julia and Smeekens, Sjef and Hanson, Johannes},
	month = oct,
	year = {2010},
	keywords = {Arabidopsis, Molecular Structure, Photosynthesis, Plant Development, Plants, Signal Transduction, Sucrose},
	pages = {1610--1614},
}

Sucrose is a molecule that is synthesized only by oxygenic photosynthetic organisms. In plants, sucrose is synthesized in source tissues and then can be transported to sink tissues, where it is utilized or stored. Interestingly, sucrose is both a metabolite and a signaling molecule. Manipulating the rate of the synthesis, transport or degradation of sucrose affects plant growth, development and physiology. Altered sucrose levels changes the quantity of sucrose derived metabolites and sucrose-specific signaling. In this paper, these changes are summarized. Better understanding of sucrose metabolism and sucrose sensing systems in plants will lead to opportunities to adapt plant metabolism and growth.

@article{smeekens_sugar_2010,
	title = {Sugar signals and molecular networks controlling plant growth},
	volume = {13},
	issn = {1369-5266},
	url = {https://www.sciencedirect.com/science/article/pii/S1369526609001782},
	doi = {10/d9t45g},
	abstract = {In recent years, several regulatory systems that link carbon nutrient status to plant growth and development have emerged. In this paper, we discuss the growth promoting functions of the hexokinase (HXK) glucose sensor, the trehalose 6-phosphate (T6P) signal and the Target of Rapamycin (TOR) kinase pathway, and the growth inhibitory function of the SNF1-related Protein Kinase1 (SnRK1) and the C/S1 bZIP transcription factor network. It is crucial that these systems interact closely in regulating growth and in several cases crosstalk has been demonstrated. Importantly, these nutrient controlled systems must interact with other growth regulatory pathways.},
	language = {en},
	number = {3},
	urldate = {2021-06-08},
	journal = {Current Opinion in Plant Biology},
	author = {Smeekens, Sjef and Ma, Jingkun and Hanson, Johannes and Rolland, Filip},
	month = jun,
	year = {2010},
	pages = {273--278},
}

In recent years, several regulatory systems that link carbon nutrient status to plant growth and development have emerged. In this paper, we discuss the growth promoting functions of the hexokinase (HXK) glucose sensor, the trehalose 6-phosphate (T6P) signal and the Target of Rapamycin (TOR) kinase pathway, and the growth inhibitory function of the SNF1-related Protein Kinase1 (SnRK1) and the C/S1 bZIP transcription factor network. It is crucial that these systems interact closely in regulating growth and in several cases crosstalk has been demonstrated. Importantly, these nutrient controlled systems must interact with other growth regulatory pathways.

@article{weltmeier_expression_2009,
	title = {Expression patterns within the {Arabidopsis} {C}/{S1} {bZIP} transcription factor network: availability of heterodimerization partners controls gene expression during stress response and development},
	volume = {69},
	issn = {0167-4412},
	shorttitle = {Expression patterns within the {Arabidopsis} {C}/{S1} {bZIP} transcription factor network},
	doi = {10/dqff6q},
	abstract = {Members of the Arabidopsis group C/S1 basic leucine zipper (bZIP) transcription factor (TF) network are proposed to implement transcriptional reprogramming of plant growth in response to energy deprivation and environmental stresses. The four group C and five group S1 members form specific heterodimers and are, therefore, considered to cooperate functionally. For example, the interplay of C/S1 bZIP TFs in regulating seed maturation genes was analyzed by expression studies and target gene regulation in both protoplasts and transgenic plants. The abundance of the heterodimerization partners significantly affects target gene transcription. Therefore, a detailed analysis of the developmental and stress related expression patterns was performed by comparing promoter: GUS and transcription data. The idea that the C/S1 network plays a role in the allocation of nutrients is supported by the defined and partially overlapping expression patterns in sink leaves, seeds and anthers. Accordingly, metabolic signals strongly affect bZIP expression on the transcriptional and/or post-transcriptional level. Sucrose induced repression of translation (SIRT) was demonstrated for all group S1 bZIPs. In particular, transcription of group S1 genes strongly responds to various abiotic stresses, such as salt (AtbZIP1) or cold (AtbZIP44). In summary, heterodimerization and expression data provide a basic framework to further determine the functional impact of the C/S1 network in regulating the plant energy balance and nutrient allocation.},
	language = {eng},
	number = {1-2},
	journal = {Plant Molecular Biology},
	author = {Weltmeier, Fridtjof and Rahmani, Fatima and Ehlert, Andrea and Dietrich, Katrin and Schütze, Katia and Wang, Xuan and Chaban, Christina and Hanson, Johannes and Teige, Markus and Harter, Klaus and Vicente-Carbajosa, Jesus and Smeekens, Sjef and Dröge-Laser, Wolfgang},
	month = jan,
	year = {2009},
	keywords = {Arabidopsis, Basic-Leucine Zipper Transcription Factors, Dimerization, Gene Expression Regulation, Plant, Stress, Physiological},
	pages = {107--119},
}

Members of the Arabidopsis group C/S1 basic leucine zipper (bZIP) transcription factor (TF) network are proposed to implement transcriptional reprogramming of plant growth in response to energy deprivation and environmental stresses. The four group C and five group S1 members form specific heterodimers and are, therefore, considered to cooperate functionally. For example, the interplay of C/S1 bZIP TFs in regulating seed maturation genes was analyzed by expression studies and target gene regulation in both protoplasts and transgenic plants. The abundance of the heterodimerization partners significantly affects target gene transcription. Therefore, a detailed analysis of the developmental and stress related expression patterns was performed by comparing promoter: GUS and transcription data. The idea that the C/S1 network plays a role in the allocation of nutrients is supported by the defined and partially overlapping expression patterns in sink leaves, seeds and anthers. Accordingly, metabolic signals strongly affect bZIP expression on the transcriptional and/or post-transcriptional level. Sucrose induced repression of translation (SIRT) was demonstrated for all group S1 bZIPs. In particular, transcription of group S1 genes strongly responds to various abiotic stresses, such as salt (AtbZIP1) or cold (AtbZIP44). In summary, heterodimerization and expression data provide a basic framework to further determine the functional impact of the C/S1 network in regulating the plant energy balance and nutrient allocation.

@article{rahmani_sucrose_2009,
	title = {Sucrose control of translation mediated by an upstream open reading frame-encoded peptide},
	volume = {150},
	issn = {0032-0889},
	doi = {10/dzt95k},
	abstract = {Regulation of gene expression through translational control is common in many organisms. The Arabidopsis (Arabidopsis thaliana) transcription factor bZIP11 is translational repressed in response to sucrose (Suc), resulting in Suc-regulated changes in amino acid metabolism. The 5' leader of the bZIP11 mRNA harbors several upstream open reading frames (uORFs), of which the second uORF is well conserved among bZIP11 homologous genes. The uORF2 element encodes a Suc control peptide (SC-peptide) of 28 residues that is sufficient for imposing Suc-induced repression of translation (SIRT) on a heterologous mRNA. Detailed analysis of the SC-peptide suggests that it functions as an attenuator peptide. Results suggest that the SC-peptide inhibits bZIP11 translation in response to high Suc levels by stalling the ribosome on the mRNA. The conserved noncanonical AUG contexts of bZIP11 uORFs allow inefficient translational initiation of the uORF, resulting in translation initiation of the scanning ribosome at the AUG codon of the bZIP11 main ORF. The results presented show that Suc-dependent signaling mediates differential translation of mRNAs containing SC-peptides encoding uORFs.},
	language = {eng},
	number = {3},
	journal = {Plant Physiology},
	author = {Rahmani, Fatemeh and Hummel, Maureen and Schuurmans, Jolanda and Wiese-Klinkenberg, Anika and Smeekens, Sjef and Hanson, Johannes},
	month = jul,
	year = {2009},
	keywords = {Amino Acid Sequence, Arabidopsis, Arabidopsis Proteins, Base Sequence, Basic-Leucine Zipper Transcription Factors, Conserved Sequence, Gene Expression Regulation, Plant, Molecular Sequence Data, Open Reading Frames, Protein Biosynthesis, RNA, Messenger, Sequence Analysis, RNA, Sucrose},
	pages = {1356--1367},
}

Regulation of gene expression through translational control is common in many organisms. The Arabidopsis (Arabidopsis thaliana) transcription factor bZIP11 is translational repressed in response to sucrose (Suc), resulting in Suc-regulated changes in amino acid metabolism. The 5' leader of the bZIP11 mRNA harbors several upstream open reading frames (uORFs), of which the second uORF is well conserved among bZIP11 homologous genes. The uORF2 element encodes a Suc control peptide (SC-peptide) of 28 residues that is sufficient for imposing Suc-induced repression of translation (SIRT) on a heterologous mRNA. Detailed analysis of the SC-peptide suggests that it functions as an attenuator peptide. Results suggest that the SC-peptide inhibits bZIP11 translation in response to high Suc levels by stalling the ribosome on the mRNA. The conserved noncanonical AUG contexts of bZIP11 uORFs allow inefficient translational initiation of the uORF, resulting in translation initiation of the scanning ribosome at the AUG codon of the bZIP11 main ORF. The results presented show that Suc-dependent signaling mediates differential translation of mRNAs containing SC-peptides encoding uORFs.

@article{hummel_sucrose-mediated_2009,
	title = {Sucrose-mediated translational control},
	volume = {104},
	issn = {1095-8290},
	doi = {10/bwnw47},
	abstract = {BACKGROUND: Environmental factors greatly impact plant gene expression and concentrations of cellular metabolites such as sugars and amino acids. The changed metabolite concentrations affect the expression of many genes both transcriptionally and post-transcriptionally.
RECENT PROGRESS: Sucrose acts as a signalling molecule in the control of translation of the S1 class basic leucine zipper transcription factor (bZIP) genes. In these genes the main bZIP open reading frames (ORFs) are preceded by upstream open reading frames (uORFs). The presence of uORFs generally inhibits translation of the following ORF but can also be instrumental in specific translational control. bZIP11, a member of the S1 class bZIP genes, harbours four uORFs of which uORF2 is required for translational control in response to sucrose concentrations. This uORF encodes the Sucrose Control peptide (SC-peptide), which is evolutionarily conserved among all S1 class bZIP genes in different plant species. Arabidopsis thaliana bZIP11 and related bZIP genes seem to be important regulators of metabolism. These proteins are targets of the Snf1-related protein kinase 1 (SnRK1) KIN10 and KIN11, which are responsive to energy deprivation as well as to various stresses. In response to energy deprivation, ribosomal biogenesis is repressed to preserve cellular function and maintenance. Other key regulators of ribosomal biogenesis such as the protein kinase Target of Rapamycin (TOR) are tightly regulated in response to stress.
CONCLUSIONS: Plants use translational control of gene expression to optimize growth and development in response to stress as well as to energy deprivation. This Botanical Briefing discusses the role of sucrose signalling in the translational control of bZIP11 and the regulation of ribosomal biogenesis in response to metabolic changes and stress conditions.},
	language = {eng},
	number = {1},
	journal = {Annals of Botany},
	author = {Hummel, Maureen and Rahmani, Fatima and Smeekens, Sjef and Hanson, Johannes},
	month = jul,
	year = {2009},
	keywords = {Arabidopsis, Basic-Leucine Zipper Transcription Factors, Gene Expression Regulation, Plant, Open Reading Frames, Plant Proteins, Sucrose},
	pages = {1--7},
}

BACKGROUND: Environmental factors greatly impact plant gene expression and concentrations of cellular metabolites such as sugars and amino acids. The changed metabolite concentrations affect the expression of many genes both transcriptionally and post-transcriptionally. RECENT PROGRESS: Sucrose acts as a signalling molecule in the control of translation of the S1 class basic leucine zipper transcription factor (bZIP) genes. In these genes the main bZIP open reading frames (ORFs) are preceded by upstream open reading frames (uORFs). The presence of uORFs generally inhibits translation of the following ORF but can also be instrumental in specific translational control. bZIP11, a member of the S1 class bZIP genes, harbours four uORFs of which uORF2 is required for translational control in response to sucrose concentrations. This uORF encodes the Sucrose Control peptide (SC-peptide), which is evolutionarily conserved among all S1 class bZIP genes in different plant species. Arabidopsis thaliana bZIP11 and related bZIP genes seem to be important regulators of metabolism. These proteins are targets of the Snf1-related protein kinase 1 (SnRK1) KIN10 and KIN11, which are responsive to energy deprivation as well as to various stresses. In response to energy deprivation, ribosomal biogenesis is repressed to preserve cellular function and maintenance. Other key regulators of ribosomal biogenesis such as the protein kinase Target of Rapamycin (TOR) are tightly regulated in response to stress. CONCLUSIONS: Plants use translational control of gene expression to optimize growth and development in response to stress as well as to energy deprivation. This Botanical Briefing discusses the role of sucrose signalling in the translational control of bZIP11 and the regulation of ribosomal biogenesis in response to metabolic changes and stress conditions.

@article{hanson_sugar_2009,
	title = {Sugar perception and signaling--an update},
	volume = {12},
	issn = {1879-0356},
	doi = {10/b87fkq},
	abstract = {Sugars act as potent signaling molecules in plants. Several sugar sensors, including the highly studied glucose sensor HEXOKINASE1 (HXK1), have been identified or proposed. Many additional sensors likely exist, as plants respond to other sugars and sugar metabolites, such as sucrose and trehalose 6-phosphate. Sugar sensing and signaling is a highly complex process resulting in many changes in physiology and development and is integrated with other signaling pathways in plants such as those for inorganic nutrients, hormones, and different stress factors. Importantly, KIN10 and KIN11 protein kinases are central in coordinating several of the responses to sugars and stress. bZIP transcription factors were found to mediate effects of sugar signaling on gene expression and metabolite content.},
	language = {eng},
	number = {5},
	journal = {Current Opinion in Plant Biology},
	author = {Hanson, Johannes and Smeekens, Sjef},
	month = oct,
	year = {2009},
	keywords = {Basic-Leucine Zipper Transcription Factors, Carbohydrate Metabolism, Gene Expression Regulation, Plant, Hexokinase, Plant Development, Plant Proteins, Plants, Signal Transduction, Sucrose, Sugar Phosphates, Trehalose},
	pages = {562--567},
}

Sugars act as potent signaling molecules in plants. Several sugar sensors, including the highly studied glucose sensor HEXOKINASE1 (HXK1), have been identified or proposed. Many additional sensors likely exist, as plants respond to other sugars and sugar metabolites, such as sucrose and trehalose 6-phosphate. Sugar sensing and signaling is a highly complex process resulting in many changes in physiology and development and is integrated with other signaling pathways in plants such as those for inorganic nutrients, hormones, and different stress factors. Importantly, KIN10 and KIN11 protein kinases are central in coordinating several of the responses to sugars and stress. bZIP transcription factors were found to mediate effects of sugar signaling on gene expression and metabolite content.

@article{hanson_sucrose_2008,
	title = {The sucrose regulated transcription factor {bZIP11} affects amino acid metabolism by regulating the expression of {ASPARAGINE} {SYNTHETASE1} and {PROLINE} {DEHYDROGENASE2}},
	volume = {53},
	copyright = {© 2008 The Authors},
	issn = {1365-313X},
	url = {https://onlinelibrary.wiley.com/doi/abs/10.1111/j.1365-313X.2007.03385.x},
	doi = {10/cqhtc6},
	abstract = {Translation of the transcription factor bZIP11 is repressed by sucrose in a process that involves a highly conserved peptide encoded by the 5′ leaders of bZIP11 and other plant basic region leucine zipper (bZip) genes. It is likely that a specific signaling pathway operating at physiological sucrose concentrations controls metabolism via a feedback mechanism. In this paper bZIP11 target processes are identified using transiently increased nuclear bZIP11 levels and genome-wide expression analysis. bZIP11 affects the expression of hundreds of genes with proposed functions in biochemical pathways and signal transduction. The expression levels of approximately 80\% of the genes tested are not affected by bZIP11 promoter-mediated overexpression of bZIP11. This suggests that {\textless}20\% of the identified genes appear to be physiologically relevant targets of bZIP11. ASPARAGINE SYNTHETASE1 and PROLINE DEHYDROGENASE2 are among the rapidly activated bZIP11 targets, whose induction is independent of protein translation. Transient expression experiments in Arabidopsis protoplasts show that the bZIP11-dependent activation of the ASPARAGINE SYNTHETASE1 gene is dependent on a G-box element present in the promoter. Increased bZIP11 expression leads to decreased proline and increased phenylalanine levels. A model is proposed in which sugar signals control amino acid levels via the bZIP11 transcription factor.},
	language = {en},
	number = {6},
	urldate = {2021-06-10},
	journal = {The Plant Journal},
	author = {Hanson, Johannes and Hanssen, Micha and Wiese, Anika and Hendriks, Margriet M. W. B. and Smeekens, Sjef},
	year = {2008},
	note = {\_eprint: https://onlinelibrary.wiley.com/doi/pdf/10.1111/j.1365-313X.2007.03385.x},
	keywords = {ATB2, nitrogen metabolism, sucrose, sugar signaling, target gene},
	pages = {935--949},
}

Translation of the transcription factor bZIP11 is repressed by sucrose in a process that involves a highly conserved peptide encoded by the 5′ leaders of bZIP11 and other plant basic region leucine zipper (bZip) genes. It is likely that a specific signaling pathway operating at physiological sucrose concentrations controls metabolism via a feedback mechanism. In this paper bZIP11 target processes are identified using transiently increased nuclear bZIP11 levels and genome-wide expression analysis. bZIP11 affects the expression of hundreds of genes with proposed functions in biochemical pathways and signal transduction. The expression levels of approximately 80% of the genes tested are not affected by bZIP11 promoter-mediated overexpression of bZIP11. This suggests that \textless20% of the identified genes appear to be physiologically relevant targets of bZIP11. ASPARAGINE SYNTHETASE1 and PROLINE DEHYDROGENASE2 are among the rapidly activated bZIP11 targets, whose induction is independent of protein translation. Transient expression experiments in Arabidopsis protoplasts show that the bZIP11-dependent activation of the ASPARAGINE SYNTHETASE1 gene is dependent on a G-box element present in the promoter. Increased bZIP11 expression leads to decreased proline and increased phenylalanine levels. A model is proposed in which sugar signals control amino acid levels via the bZIP11 transcription factor.

@article{johannesson_arabidopsis_2003,
	title = {The {Arabidopsis} thaliana homeobox gene {ATHB5} is a potential regulator of abscisic acid responsiveness in developing seedlings},
	volume = {51},
	issn = {0167-4412},
	doi = {10.1023/a:1022567625228},
	abstract = {ATHB5 is a member of the homeodomain-leucine zipper (HDZip) transcription factor gene family of Arabidopsis thaliana. In this report we show that increased expression levels of ATHB5 in transgenic Arabidopsis plants cause an enhanced sensitivity to the inhibitory effect of abscisic acid (ABA) on seed germination and seedling growth. Consistent with this finding we demonstrate in northern blot experiments that the ABA-responsive gene RAB18 is hyperinduced by ABA in transgenic overexpressor lines as compared to the wild type. Northern blot and promoter-GUS fusion analyses show that ATHB5 gene transcription is initiated rapidly after the onset of germination and localized primarily to the hypocotyl of germinating seedlings. Moreover, analysis of ATHB5 gene expression during post-germinative growth in different ABA response mutants shows that ATHB5 gene activity is down-regulated in the abil-1, abi3-1 and abi5-1 mutant lines, but not in abi2-1 or abi4-1. The identification of a T-DNA insertion mutant line of ATHB5 is described and no phenotypic alterations could be discerned, suggesting that ATHB5 may act redundantly with other HDZip genes. Taken together, these data suggest that ATHB5 is a positive regulator of ABA-responsiveness, mediating the inhibitory effect of ABA on growth during seedling establishment.},
	language = {eng},
	number = {5},
	journal = {Plant Molecular Biology},
	author = {Johannesson, Henrik and Wang, Yan and Hanson, Johannes and Engström, Peter},
	month = mar,
	year = {2003},
	keywords = {Abscisic Acid, Arabidopsis, Arabidopsis Proteins, Blotting, Northern, Gene Expression Regulation, Developmental, Gene Expression Regulation, Plant, Germination, Glucuronidase, Homeodomain Proteins, Plants, Genetically Modified, Recombinant Fusion Proteins, Seeds, Signal Transduction, Transcription Factors},
	pages = {719--729},
}

ATHB5 is a member of the homeodomain-leucine zipper (HDZip) transcription factor gene family of Arabidopsis thaliana. In this report we show that increased expression levels of ATHB5 in transgenic Arabidopsis plants cause an enhanced sensitivity to the inhibitory effect of abscisic acid (ABA) on seed germination and seedling growth. Consistent with this finding we demonstrate in northern blot experiments that the ABA-responsive gene RAB18 is hyperinduced by ABA in transgenic overexpressor lines as compared to the wild type. Northern blot and promoter-GUS fusion analyses show that ATHB5 gene transcription is initiated rapidly after the onset of germination and localized primarily to the hypocotyl of germinating seedlings. Moreover, analysis of ATHB5 gene expression during post-germinative growth in different ABA response mutants shows that ATHB5 gene activity is down-regulated in the abil-1, abi3-1 and abi5-1 mutant lines, but not in abi2-1 or abi4-1. The identification of a T-DNA insertion mutant line of ATHB5 is described and no phenotypic alterations could be discerned, suggesting that ATHB5 may act redundantly with other HDZip genes. Taken together, these data suggest that ATHB5 is a positive regulator of ABA-responsiveness, mediating the inhibitory effect of ABA on growth during seedling establishment.

@article{hanson_expression_2002,
	title = {The expression pattern of the homeobox gene {ATHB13} reveals a conservation of transcriptional regulatory mechanisms between {Arabidopsis} and hybrid aspen},
	volume = {21},
	issn = {1432-203X},
	url = {https://doi.org/10.1007/s00299-002-0476-6},
	doi = {10/cvzt76},
	abstract = {ATHB13 belongs to a family of homeodomain leucine zipper (HDZip) transcription factors in Arabidopsis thaliana. To understand the temporal and spatial distribution of ATHB13 gene expression, we examined the ATHB13 promoter activity by means of fusions to the uidA (GUS, β-glucuronidase) reporter gene in transgenic plants. The strongest promoter activity was detected in the vasculature of the basal portion of petioles for both rosette leaves and cotyledons and at the base of cauline leaves. Activity was also detected in the stem at the base of the cauline leaf in an area corresponding to the leaf gap in the vasculature. In flowers, promoter activity was also present in the receptacle and in the stigma. Transformation of the same promoter-GUS construct into hybrid aspen (Populus tremula × P. tremuloides) resulted in an analogous expression pattern in the petioles of leaves. The similarity of these expression patterns indicates that the trans-acting factors responsible for ATHB13 expression are conserved between aspen and Arabidopsis. The conserved expression pattern of the highly specific Arabidopsis ATHB13 promoter in hybrid aspen demonstrates the potential utility of Arabidopsis promoters for tissue-specific expression in angiosperm trees.},
	language = {en},
	number = {1},
	urldate = {2021-08-26},
	journal = {Plant Cell Reports},
	author = {Hanson, J. and Regan, S. and Engström, P.},
	month = jul,
	year = {2002},
	pages = {81--89},
}

ATHB13 belongs to a family of homeodomain leucine zipper (HDZip) transcription factors in Arabidopsis thaliana. To understand the temporal and spatial distribution of ATHB13 gene expression, we examined the ATHB13 promoter activity by means of fusions to the uidA (GUS, β-glucuronidase) reporter gene in transgenic plants. The strongest promoter activity was detected in the vasculature of the basal portion of petioles for both rosette leaves and cotyledons and at the base of cauline leaves. Activity was also detected in the stem at the base of the cauline leaf in an area corresponding to the leaf gap in the vasculature. In flowers, promoter activity was also present in the receptacle and in the stigma. Transformation of the same promoter-GUS construct into hybrid aspen (Populus tremula × P. tremuloides) resulted in an analogous expression pattern in the petioles of leaves. The similarity of these expression patterns indicates that the trans-acting factors responsible for ATHB13 expression are conserved between aspen and Arabidopsis. The conserved expression pattern of the highly specific Arabidopsis ATHB13 promoter in hybrid aspen demonstrates the potential utility of Arabidopsis promoters for tissue-specific expression in angiosperm trees.

@article{hanson_sugar-dependent_2001,
	title = {Sugar-dependent alterations in cotyledon and leaf development in transgenic plants expressing the {HDZhdip} gene {ATHB13}},
	volume = {45},
	issn = {1573-5028},
	url = {https://doi.org/10.1023/A:1006464907710},
	doi = {10.1023/A:1006464907710},
	abstract = {ATHB13 is a new member of the homeodomain leucine zipper (HDZip) transcription factor family of Arabidopsis thaliana. Constitutive high-level expression of the ATHB13 cDNA in transgenic plants results in altered development of cotyledons and leaves, specifically in plants grown on media containing metabolizable sugars. Cotyledons and leaves of sugar-grown transgenic plants are more narrow and the junction between the petiole and the leaf blade less distinct, as compared to the wild type. High-level expression of ATHB13 affects cotyledon shape by inhibiting lateral expansion of epidermal cells in sugar-treated seedlings. Experiments with non-metabolizable sugars indicate that the alteration in leaf shape in the ATHB13 transgenics is mediated by sucrose sensing. ATHB13 further affects a subset of the gene expression responses of the wild-type plant to sugars. The expression of genes encoding β-amylase and vegetative storage protein is induced to higher levels in response to sucrose in the transgenic plants as compared to the wild type. The expression of other sugar-regulated genes examined is unaffected by ATHB13. These data suggest that ATHB13 may be a component of the sucrose-signalling pathway, active close to the targets of the signal transduction.},
	language = {en},
	number = {3},
	urldate = {2021-11-02},
	journal = {Plant Molecular Biology},
	author = {Hanson, Johannes and Johannesson, Henrik and Engström, Peter},
	month = feb,
	year = {2001},
	pages = {247--262},
}

ATHB13 is a new member of the homeodomain leucine zipper (HDZip) transcription factor family of Arabidopsis thaliana. Constitutive high-level expression of the ATHB13 cDNA in transgenic plants results in altered development of cotyledons and leaves, specifically in plants grown on media containing metabolizable sugars. Cotyledons and leaves of sugar-grown transgenic plants are more narrow and the junction between the petiole and the leaf blade less distinct, as compared to the wild type. High-level expression of ATHB13 affects cotyledon shape by inhibiting lateral expansion of epidermal cells in sugar-treated seedlings. Experiments with non-metabolizable sugars indicate that the alteration in leaf shape in the ATHB13 transgenics is mediated by sucrose sensing. ATHB13 further affects a subset of the gene expression responses of the wild-type plant to sugars. The expression of genes encoding β-amylase and vegetative storage protein is induced to higher levels in response to sucrose in the transgenic plants as compared to the wild type. The expression of other sugar-regulated genes examined is unaffected by ATHB13. These data suggest that ATHB13 may be a component of the sucrose-signalling pathway, active close to the targets of the signal transduction.

@article{cainzos_loss_2026,
	title = {Loss of {qE} {Does} {Not} {Necessarily} {Lead} to {Photoinhibition}: {Sustained} {Non}-{Photochemical} {Quenching} in the {Absence} of {PsbS} and {Zeaxanthin}},
	copyright = {© 2026 The Author(s). Plant, Cell \& Environment published by John Wiley \& Sons Ltd.},
	issn = {1365-3040},
	shorttitle = {Loss of {qE} {Does} {Not} {Necessarily} {Lead} to {Photoinhibition}},
	url = {https://onlinelibrary.wiley.com/doi/abs/10.1111/pce.70477},
	doi = {10.1111/pce.70477},
	abstract = {Photosynthetic light-harvesting complexes mediate light absorption and energy dissipation. By modulating the photosystems' absorption cross-section, they affect both photosynthetic activity and non-photochemical quenching (NPQ). These processes are often studied by spectrally integrated chlorophyll fluorescence, masking their associated spectral information. We explore in Aspen and Arabidopsis npq mutants how qE affects the development of NPQ spectra under two contrasting conditions: in the absence and the presence of photoinhibition. We introduce a new parameter, the development of new emitting species (NESD), during time- and spectrally resolved NPQ inductions, and develop a pipeline to resolve PSII energy-partitioning heterogeneity. LHCII, PsbS, and zeaxanthin are required for NESD. Combining gas exchange, P700 oxidation, and spectrally resolved kinetics, we show that under photoinhibitory conditions, NES can develop even without PsbS or zeaxanthin, producing sustained quenching independent of photoinhibition of PSII or PSI. Furthermore, the absence of LHCII and CURVATURE THYLAKOID 1 leads to increased photoinhibition, indicating that long-term photoprotection relies on LHCII and thylakoid plasticity, whereas PsbS and zeaxanthin mainly facilitate LHCII-dependent quenching. Finally, we show the limitations of traditional parameters in discriminating between photoinhibition and photoprotective sustained quenching and propose time-resolved monitoring of CO₂ assimilation and Y(II) for their accurate assessment.},
	language = {en},
	urldate = {2026-03-13},
	journal = {Plant, Cell \& Environment},
	author = {Cainzos, Maximiliano and Hu, Chen and Pissolato, Maria Dolores and Fataftah, Nazeer and Nanda, Sanchali and Jansson, Stefan},
	month = mar,
	year = {2026},
	note = {\_eprint: https://onlinelibrary.wiley.com/doi/pdf/10.1111/pce.70477},
	keywords = {NPQ, high light, new emitting species development, photoinhibition, photosynthesis: carbon reactions, photosynthesis: electron transport, sustained quenching},
}

Photosynthetic light-harvesting complexes mediate light absorption and energy dissipation. By modulating the photosystems' absorption cross-section, they affect both photosynthetic activity and non-photochemical quenching (NPQ). These processes are often studied by spectrally integrated chlorophyll fluorescence, masking their associated spectral information. We explore in Aspen and Arabidopsis npq mutants how qE affects the development of NPQ spectra under two contrasting conditions: in the absence and the presence of photoinhibition. We introduce a new parameter, the development of new emitting species (NESD), during time- and spectrally resolved NPQ inductions, and develop a pipeline to resolve PSII energy-partitioning heterogeneity. LHCII, PsbS, and zeaxanthin are required for NESD. Combining gas exchange, P700 oxidation, and spectrally resolved kinetics, we show that under photoinhibitory conditions, NES can develop even without PsbS or zeaxanthin, producing sustained quenching independent of photoinhibition of PSII or PSI. Furthermore, the absence of LHCII and CURVATURE THYLAKOID 1 leads to increased photoinhibition, indicating that long-term photoprotection relies on LHCII and thylakoid plasticity, whereas PsbS and zeaxanthin mainly facilitate LHCII-dependent quenching. Finally, we show the limitations of traditional parameters in discriminating between photoinhibition and photoprotective sustained quenching and propose time-resolved monitoring of CO₂ assimilation and Y(II) for their accurate assessment.

@article{rydman_metabolomics_2025,
	title = {A {Metabolomics} and {Transcriptomics} {Resource} for {Identifying} {Candidate} {Genes} in the {Biosynthesis} of {Specialised} {Metabolites} in {Populus} tremula},
	volume = {177},
	copyright = {© 2025 The Author(s). Physiologia Plantarum published by John Wiley \& Sons Ltd on behalf of Scandinavian Plant Physiology Society.},
	issn = {1399-3054},
	url = {https://onlinelibrary.wiley.com/doi/abs/10.1111/ppl.70567},
	doi = {10.1111/ppl.70567},
	abstract = {This study aims to identify candidate genes involved in the biosynthesis of salicinoid phenolic glycosides (SPGs), a group of specialised metabolites characteristic of the Salicaceae family. While the integration of multi-omics data represents a powerful approach to link genes encoding enzymes and their regulatory factors to metabolite biosynthesis, suitable multi-omics data resources are scarce. We present a comprehensive dataset comprising untargeted liquid chromatography–mass spectrometry (LC–MS) and mRNA-sequencing data from various organs of European aspen (Populus tremula L.) and from genotypes that produce contrasting sets of SPGs. We present a reproducible pipeline for the analysis of the LC–MS data, including predicted annotation of potential novel SPGs. We demonstrate the utility of the resource by identifying candidate genes involved in the biosynthesis of SPGs with a cinnamoyl moiety. By integrating gene and metabolite differential analyses with a gene co-expression network, we identified two HXXXD-type acyltransferase genes and one UDP-glucosyltransferase gene as candidates for future downstream characterisation. The combined gene expression and metabolomics resource is integrated into PlantGenIE.org to facilitate easy access and data mining. All raw data are available in public databases, and all data and results files are available at an associated Figshare repository.},
	language = {en},
	number = {5},
	urldate = {2025-10-13},
	journal = {Physiologia Plantarum},
	author = {Rydman, Sara M. and Lihavainen, Jenna and Robinson, Kathryn M. and Jansson, Stefan and Albrectsen, Benedicte R. and Street, Nathaniel R.},
	year = {2025},
	note = {\_eprint: https://onlinelibrary.wiley.com/doi/pdf/10.1111/ppl.70567},
	keywords = {Populus tremula, RNA-Seq, aspen, biosynthesis, chemotype, liquid chromatography–mass spectrometry (LC–MS), metabolomics, phenolic glycosides, salicinoid, specialised metabolite},
	pages = {e70567},
}

This study aims to identify candidate genes involved in the biosynthesis of salicinoid phenolic glycosides (SPGs), a group of specialised metabolites characteristic of the Salicaceae family. While the integration of multi-omics data represents a powerful approach to link genes encoding enzymes and their regulatory factors to metabolite biosynthesis, suitable multi-omics data resources are scarce. We present a comprehensive dataset comprising untargeted liquid chromatography–mass spectrometry (LC–MS) and mRNA-sequencing data from various organs of European aspen (Populus tremula L.) and from genotypes that produce contrasting sets of SPGs. We present a reproducible pipeline for the analysis of the LC–MS data, including predicted annotation of potential novel SPGs. We demonstrate the utility of the resource by identifying candidate genes involved in the biosynthesis of SPGs with a cinnamoyl moiety. By integrating gene and metabolite differential analyses with a gene co-expression network, we identified two HXXXD-type acyltransferase genes and one UDP-glucosyltransferase gene as candidates for future downstream characterisation. The combined gene expression and metabolomics resource is integrated into PlantGenIE.org to facilitate easy access and data mining. All raw data are available in public databases, and all data and results files are available at an associated Figshare repository.

@article{marien_natures_2025,
	title = {Nature’s {Master} of {Ceremony}: {The} {Populus} {Circadian} {Clock} as {Orchestrator} of {Tree} {Growth} and {Phenology}},
	volume = {2},
	copyright = {2025 The Author(s)},
	issn = {2948-281X},
	shorttitle = {Nature’s {Master} of {Ceremony}},
	url = {https://www.nature.com/articles/s44323-025-00034-4},
	doi = {10.1038/s44323-025-00034-4},
	abstract = {Understanding the timely regulation of plant growth and phenology is crucial for assessing a terrestrial ecosystem’s productivity and carbon budget. The circadian clock, a system of genetic oscillators, acts as ‘Master of Ceremony’ during plant physiological processes. The mechanism is particularly elusive in trees despite its relevance. The primary and secondary tree growth, leaf senescence, bud set, and bud burst timing were investigated in 68 constructs transformed into Populus hybrids and compared with untransformed or transformed controls grown in natural or controlled conditions. The results were analyzed using generalized additive models with ordered-factor-smooth interaction smoothers. This meta-analysis shows that several genetic components are associated with the clock. Especially core clock-regulated genes affected tree growth and phenology in both controlled and field conditions. Our results highlight the importance of field trials and the potential of using the clock to generate trees with improved characteristics for sustainable silviculture (e.g., reprogrammed to new photoperiodic regimes and increased growth).},
	language = {en},
	number = {1},
	urldate = {2025-04-11},
	journal = {npj Biological Timing and Sleep},
	publisher = {Nature Publishing Group},
	author = {Mariën, Bertold and Robinson, Kathryn M. and Jurca, Manuela and Michelson, Ingrid H. and Takata, Naoki and Kozarewa, Iwanka and Pin, Pierre A. and Ingvarsson, Pär K. and Moritz, Thomas and Ibáñez, Cristian and Nilsson, Ove and Jansson, Stefan and Penfield, Steve and Yu, Jun and Eriksson, Maria E.},
	month = apr,
	year = {2025},
	keywords = {Biological techniques, Plant sciences},
	pages = {1--19},
}

Understanding the timely regulation of plant growth and phenology is crucial for assessing a terrestrial ecosystem’s productivity and carbon budget. The circadian clock, a system of genetic oscillators, acts as ‘Master of Ceremony’ during plant physiological processes. The mechanism is particularly elusive in trees despite its relevance. The primary and secondary tree growth, leaf senescence, bud set, and bud burst timing were investigated in 68 constructs transformed into Populus hybrids and compared with untransformed or transformed controls grown in natural or controlled conditions. The results were analyzed using generalized additive models with ordered-factor-smooth interaction smoothers. This meta-analysis shows that several genetic components are associated with the clock. Especially core clock-regulated genes affected tree growth and phenology in both controlled and field conditions. Our results highlight the importance of field trials and the potential of using the clock to generate trees with improved characteristics for sustainable silviculture (e.g., reprogrammed to new photoperiodic regimes and increased growth).

@article{bag_photosynthetic_2025,
	title = {Photosynthetic advantages of conifers in the boreal forest},
	volume = {30},
	issn = {1360-1385},
	url = {https://www.sciencedirect.com/science/article/pii/S1360138524003005},
	doi = {10.1016/j.tplants.2024.10.018},
	abstract = {Boreal conifers – the ‘Christmas trees’ – maintain their green needles over the winter by retaining their chlorophyll. These conifers face the toughest challenge in February and March, when subzero temperatures coincide with high solar radiation. To balance the light energy they harvest with the light energy they utilise, conifers deploy various mechanisms in parallel. These include, thylakoid destacking, which facilitates direct energy transfer from Photosystem II (PSII) to Photosystem I (PSI), and excess energy dissipation through sustained nonphotochemical quenching (NPQ). Additionally, they upregulate alternative electron transport pathways to safely reroute excess electrons while maintaining ATP production. From an evolutionary and ecological perspective, we consider these mechanisms as part of a comprehensive photosynthetic alteration, which enhances our understanding of winter acclimation in conifers and their dominance in the boreal forests.},
	number = {4},
	urldate = {2025-04-11},
	journal = {Trends in Plant Science},
	author = {Bag, Pushan and Ivanov, Alexander G. and Huner, Norman P. and Jansson, Stefan},
	month = apr,
	year = {2025},
	keywords = {alternative electron transport, conifers, direct energy transfer, flavodiiron proteins, nonphotochemical quenching (NPQ), photosystems},
	pages = {409--423},
}

Boreal conifers – the ‘Christmas trees’ – maintain their green needles over the winter by retaining their chlorophyll. These conifers face the toughest challenge in February and March, when subzero temperatures coincide with high solar radiation. To balance the light energy they harvest with the light energy they utilise, conifers deploy various mechanisms in parallel. These include, thylakoid destacking, which facilitates direct energy transfer from Photosystem II (PSII) to Photosystem I (PSI), and excess energy dissipation through sustained nonphotochemical quenching (NPQ). Additionally, they upregulate alternative electron transport pathways to safely reroute excess electrons while maintaining ATP production. From an evolutionary and ecological perspective, we consider these mechanisms as part of a comprehensive photosynthetic alteration, which enhances our understanding of winter acclimation in conifers and their dominance in the boreal forests.

@article{robinson_improved_2024,
	title = {An {Improved} {Chromosome}-scale {Genome} {Assembly} and {Population} {Genetics} resource for {Populus} tremula.},
	volume = {176},
	copyright = {© 2024 The Author(s). Physiologia Plantarum published by John Wiley \& Sons Ltd on behalf of Scandinavian Plant Physiology Society.},
	issn = {1399-3054},
	url = {https://onlinelibrary.wiley.com/doi/abs/10.1111/ppl.14511},
	doi = {10.1111/ppl.14511},
	abstract = {Aspen (Populus tremula L.) is a keystone species and a model system for forest tree genomics. We present an updated resource comprising a chromosome-scale assembly, population genetics and genomics data. Using the resource, we explore the genetic basis of natural variation in leaf size and shape, traits with complex genetic architecture. We generated the genome assembly using long-read sequencing, optical and high-density genetic maps. We conducted whole-genome resequencing of the Umeå Aspen (UmAsp) collection. Using the assembly and re-sequencing data from the UmAsp, Swedish Aspen (SwAsp) and Scottish Aspen (ScotAsp) collections we performed genome-wide association analyses (GWAS) using Single Nucleotide Polymorphisms (SNPs) for 26 leaf physiognomy phenotypes. We conducted Assay of Transposase Accessible Chromatin sequencing (ATAC-Seq), identified genomic regions of accessible chromatin, and subset SNPs to these regions, improving the GWAS detection rate. We identified candidate long non-coding RNAs in leaf samples, quantified their expression in an updated co-expression network, and used this to explore the functions of candidate genes identified from the GWAS. A GWAS found SNP associations for seven traits. The associated SNPs were in or near genes annotated with developmental functions, which represent candidates for further study. Of particular interest was a 177-kbp region harbouring associations with several leaf phenotypes in ScotAsp. We have incorporated the assembly, population genetics, genomics, and GWAS data into the PlantGenIE.org web resource, including updating existing genomics data to the new genome version, to enable easy exploration and visualisation. We provide all raw and processed data to facilitate reuse in future studies.},
	language = {en},
	number = {5},
	urldate = {2024-09-19},
	journal = {Physiologia Plantarum},
	author = {Robinson, Kathryn M. and Schiffthaler, Bastian and Liu, Hui and Rydman, Sara M. and Rendón-Anaya, Martha and Kalman, Teitur Ahlgren and Kumar, Vikash and Canovi, Camilla and Bernhardsson, Carolina and Delhomme, Nicolas and Jenkins, Jerry and Wang, Jing and Mähler, Niklas and Richau, Kerstin H. and Stokes, Victoria and A'Hara, Stuart and Cottrell, Joan and Coeck, Kizi and Diels, Tim and Vandepoele, Klaas and Mannapperuma, Chanaka and Park, Eung-Jun and Plaisance, Stephane and Jansson, Stefan and Ingvarsson, Pär K. and Street, Nathaniel R.},
	year = {2024},
	note = {\_eprint: https://onlinelibrary.wiley.com/doi/pdf/10.1111/ppl.14511},
	keywords = {ATAC-Seq, GWAS, Populus, aspen, co-expression, genetic architecture, genome assembly, leaf physiognomy, leaf shape, leaf size, lncRNA, natural selection, population genetics},
	pages = {e14511},
}

Aspen (Populus tremula L.) is a keystone species and a model system for forest tree genomics. We present an updated resource comprising a chromosome-scale assembly, population genetics and genomics data. Using the resource, we explore the genetic basis of natural variation in leaf size and shape, traits with complex genetic architecture. We generated the genome assembly using long-read sequencing, optical and high-density genetic maps. We conducted whole-genome resequencing of the Umeå Aspen (UmAsp) collection. Using the assembly and re-sequencing data from the UmAsp, Swedish Aspen (SwAsp) and Scottish Aspen (ScotAsp) collections we performed genome-wide association analyses (GWAS) using Single Nucleotide Polymorphisms (SNPs) for 26 leaf physiognomy phenotypes. We conducted Assay of Transposase Accessible Chromatin sequencing (ATAC-Seq), identified genomic regions of accessible chromatin, and subset SNPs to these regions, improving the GWAS detection rate. We identified candidate long non-coding RNAs in leaf samples, quantified their expression in an updated co-expression network, and used this to explore the functions of candidate genes identified from the GWAS. A GWAS found SNP associations for seven traits. The associated SNPs were in or near genes annotated with developmental functions, which represent candidates for further study. Of particular interest was a 177-kbp region harbouring associations with several leaf phenotypes in ScotAsp. We have incorporated the assembly, population genetics, genomics, and GWAS data into the PlantGenIE.org web resource, including updating existing genomics data to the new genome version, to enable easy exploration and visualisation. We provide all raw and processed data to facilitate reuse in future studies.

@article{nanda_chlorospec_2024,
	title = {{ChloroSpec}: {A} new in vivo chlorophyll fluorescence spectrometer for simultaneous wavelength- and time-resolved detection},
	volume = {176},
	copyright = {© 2024 The Authors. Physiologia Plantarum published by John Wiley \& Sons Ltd on behalf of Scandinavian Plant Physiology Society.},
	issn = {1399-3054},
	url = {https://onlinelibrary.wiley.com/doi/abs/10.1111/ppl.14306},
	doi = {10.1111/ppl.14306},
	abstract = {Chlorophyll fluorescence is a ubiquitous tool in basic and applied plant science research. Various standard commercial instruments are available for characterization of photosynthetic material like leaves or microalgae, most of which integrate the overall fluorescence signals above a certain cut-off wavelength. However, wavelength-resolved (fluorescence signals appearing at different wavelengths having different time dependent decay) signals contain vast information required to decompose complex signals and processes into their underlying components that can untangle the photo-physiological process of photosynthesis. Hence, to address this we describe an advanced chlorophyll fluorescence spectrometer - ChloroSpec - allowing three-dimensional simultaneous detection of fluorescence intensities at different wavelengths in a time-resolved manner. We demonstrate for a variety of typical examples that most of the generally used fluorescence parameters are strongly wavelength dependent. This indicates a pronounced heterogeneity and a highly dynamic nature of the thylakoid and the photosynthetic apparatus under actinic illumination. Furthermore, we provide examples of advanced global analysis procedures integrating this three-dimensional signal and relevant information extracted from them that relate to the physiological properties of the organism. This conveniently obtained broad range of data can make ChloroSpec a new standard tool in photosynthesis research.},
	language = {en},
	number = {2},
	urldate = {2024-09-04},
	journal = {Physiologia Plantarum},
	author = {Nanda, Sanchali and Shutova, Tatyana and Cainzos, Maximiliano and Hu, Chen and Sasbrink, Bart and Bag, Pushan and Blanken, Tristian den and Buijs, Ronald and Gracht, Lex van der and Hendriks, Frans and Lambrev, Petar and Limburg, Rob and Mascoli, Vincenzo and Nawrocki, Wojciech J and Reus, Michael and Parmessar, Ramon and Singerling, Björn and Stokkum, Ivo H M and Jansson, Stefan and Holzwarth, Alfred R.},
	month = aug,
	year = {2024},
	note = {\_eprint: https://onlinelibrary.wiley.com/doi/pdf/10.1111/ppl.14306},
	pages = {e14306},
}

Chlorophyll fluorescence is a ubiquitous tool in basic and applied plant science research. Various standard commercial instruments are available for characterization of photosynthetic material like leaves or microalgae, most of which integrate the overall fluorescence signals above a certain cut-off wavelength. However, wavelength-resolved (fluorescence signals appearing at different wavelengths having different time dependent decay) signals contain vast information required to decompose complex signals and processes into their underlying components that can untangle the photo-physiological process of photosynthesis. Hence, to address this we describe an advanced chlorophyll fluorescence spectrometer - ChloroSpec - allowing three-dimensional simultaneous detection of fluorescence intensities at different wavelengths in a time-resolved manner. We demonstrate for a variety of typical examples that most of the generally used fluorescence parameters are strongly wavelength dependent. This indicates a pronounced heterogeneity and a highly dynamic nature of the thylakoid and the photosynthetic apparatus under actinic illumination. Furthermore, we provide examples of advanced global analysis procedures integrating this three-dimensional signal and relevant information extracted from them that relate to the physiological properties of the organism. This conveniently obtained broad range of data can make ChloroSpec a new standard tool in photosynthesis research.

@article{bag_flavodiiron-mediated_2023,
	title = {Flavodiiron-mediated {O2} photoreduction at photosystem {I} acceptor-side provides photoprotection to conifer thylakoids in early spring},
	volume = {14},
	copyright = {2023 The Author(s)},
	issn = {2041-1723},
	url = {https://www.nature.com/articles/s41467-023-38938-z},
	doi = {10.1038/s41467-023-38938-z},
	abstract = {Green organisms evolve oxygen (O2) via photosynthesis and consume it by respiration. Generally, net O2 consumption only becomes dominant when photosynthesis is suppressed at night. Here, we show that green thylakoid membranes of Scots pine (Pinus sylvestris L) and Norway spruce (Picea abies) needles display strong O2 consumption even in the presence of light when extremely low temperatures coincide with high solar irradiation during early spring (ES). By employing different electron transport chain inhibitors, we show that this unusual light-induced O2 consumption occurs around photosystem (PS) I and correlates with higher abundance of flavodiiron (Flv) A protein in ES thylakoids. With P700 absorption changes, we demonstrate that electron scavenging from the acceptor-side of PSI via O2 photoreduction is a major alternative pathway in ES. This photoprotection mechanism in vascular plants indicates that conifers have developed an adaptative evolution trajectory for growing in harsh environments.},
	language = {en},
	number = {1},
	urldate = {2023-06-09},
	journal = {Nature Communications},
	publisher = {Nature Publishing Group},
	author = {Bag, Pushan and Shutova, Tatyana and Shevela, Dmitry and Lihavainen, Jenna and Nanda, Sanchali and Ivanov, Alexander G. and Messinger, Johannes and Jansson, Stefan},
	month = jun,
	year = {2023},
	note = {Number: 1},
	keywords = {Abiotic, Light responses, Photosystem I},
	pages = {3210},
}

Green organisms evolve oxygen (O2) via photosynthesis and consume it by respiration. Generally, net O2 consumption only becomes dominant when photosynthesis is suppressed at night. Here, we show that green thylakoid membranes of Scots pine (Pinus sylvestris L) and Norway spruce (Picea abies) needles display strong O2 consumption even in the presence of light when extremely low temperatures coincide with high solar irradiation during early spring (ES). By employing different electron transport chain inhibitors, we show that this unusual light-induced O2 consumption occurs around photosystem (PS) I and correlates with higher abundance of flavodiiron (Flv) A protein in ES thylakoids. With P700 absorption changes, we demonstrate that electron scavenging from the acceptor-side of PSI via O2 photoreduction is a major alternative pathway in ES. This photoprotection mechanism in vascular plants indicates that conifers have developed an adaptative evolution trajectory for growing in harsh environments.

@article{escamez_genetic_2023,
	title = {Genetic markers and tree properties predicting wood biorefining potential in aspen ({Populus} tremula) bioenergy feedstock},
	volume = {16},
	issn = {2731-3654},
	url = {https://doi.org/10.1186/s13068-023-02315-1},
	doi = {10.1186/s13068-023-02315-1},
	abstract = {Wood represents the majority of the biomass on land and constitutes a renewable source of biofuels and other bioproducts. However, wood is recalcitrant to bioconversion, raising a need for feedstock improvement in production of, for instance, biofuels. We investigated the properties of wood that affect bioconversion, as well as the underlying genetics, to help identify superior tree feedstocks for biorefining.},
	number = {1},
	urldate = {2023-04-14},
	journal = {Biotechnology for Biofuels and Bioproducts},
	author = {Escamez, Sacha and Robinson, Kathryn M. and Luomaranta, Mikko and Gandla, Madhavi Latha and Mähler, Niklas and Yassin, Zakiya and Grahn, Thomas and Scheepers, Gerhard and Stener, Lars-Göran and Jansson, Stefan and Jönsson, Leif J. and Street, Nathaniel R. and Tuominen, Hannele},
	month = apr,
	year = {2023},
	keywords = {Bioenergy, Biomass, Biorefining, Feedstock recalcitrance, Forest feedstocks, Saccharification},
	pages = {65},
}

Wood represents the majority of the biomass on land and constitutes a renewable source of biofuels and other bioproducts. However, wood is recalcitrant to bioconversion, raising a need for feedstock improvement in production of, for instance, biofuels. We investigated the properties of wood that affect bioconversion, as well as the underlying genetics, to help identify superior tree feedstocks for biorefining.

@article{lihavainen_salicylic_2023,
	title = {Salicylic acid metabolism and signalling coordinate senescence initiation in aspen in nature},
	volume = {14},
	copyright = {2023 The Author(s)},
	issn = {2041-1723},
	url = {https://www.nature.com/articles/s41467-023-39564-5},
	doi = {10.1038/s41467-023-39564-5},
	abstract = {Deciduous trees exhibit a spectacular phenomenon of autumn senescence driven by the seasonality of their growth environment, yet there is no consensus which external or internal cues trigger it. Senescence starts at different times in European aspen (Populus tremula L.) genotypes grown in same location. By integrating omics studies, we demonstrate that aspen genotypes utilize similar transcriptional cascades and metabolic cues to initiate senescence, but at different times during autumn. The timing of autumn senescence initiation appeared to be controlled by two consecutive “switches”; 1) first the environmental variation induced the rewiring of the transcriptional network, stress signalling pathways and metabolic perturbations and 2) the start of senescence process was defined by the ability of the genotype to activate and sustain stress tolerance mechanisms mediated by salicylic acid. We propose that salicylic acid represses the onset of leaf senescence in stressful natural conditions, rather than promoting it as often observed in annual plants.},
	language = {en},
	number = {1},
	urldate = {2023-07-21},
	journal = {Nature Communications},
	publisher = {Nature Publishing Group},
	author = {Lihavainen, Jenna and Šimura, Jan and Bag, Pushan and Fataftah, Nazeer and Robinson, Kathryn Megan and Delhomme, Nicolas and Novák, Ondřej and Ljung, Karin and Jansson, Stefan},
	month = jul,
	year = {2023},
	note = {Number: 1},
	keywords = {Metabolomics, Plant physiology, Regulatory networks, Senescence},
	pages = {4288},
}

Deciduous trees exhibit a spectacular phenomenon of autumn senescence driven by the seasonality of their growth environment, yet there is no consensus which external or internal cues trigger it. Senescence starts at different times in European aspen (Populus tremula L.) genotypes grown in same location. By integrating omics studies, we demonstrate that aspen genotypes utilize similar transcriptional cascades and metabolic cues to initiate senescence, but at different times during autumn. The timing of autumn senescence initiation appeared to be controlled by two consecutive “switches”; 1) first the environmental variation induced the rewiring of the transcriptional network, stress signalling pathways and metabolic perturbations and 2) the start of senescence process was defined by the ability of the genotype to activate and sustain stress tolerance mechanisms mediated by salicylic acid. We propose that salicylic acid represses the onset of leaf senescence in stressful natural conditions, rather than promoting it as often observed in annual plants.

@article{arshad_kaleidoscope_2022,
	title = {A kaleidoscope of photosynthetic antenna proteins and their emerging roles},
	volume = {189},
	issn = {1532-2548},
	doi = {10.1093/plphys/kiac175},
	abstract = {Photosynthetic light-harvesting antennae are pigment-binding proteins that perform one of the most fundamental tasks on Earth, capturing light and transferring energy that enables life in our biosphere. Adaptation to different light environments led to the evolution of an astonishing diversity of light-harvesting systems. At the same time, several strategies have been developed to optimize the light energy input into photosynthetic membranes in response to fluctuating conditions. The basic feature of these prompt responses is the dynamic nature of antenna complexes, whose function readily adapts to the light available. High-resolution microscopy and spectroscopic studies on membrane dynamics demonstrate the crosstalk between antennae and other thylakoid membrane components. With the increased understanding of light-harvesting mechanisms and their regulation, efforts are focusing on the development of sustainable processes for effective conversion of sunlight into functional bio-products. The major challenge in this approach lies in the application of fundamental discoveries in light-harvesting systems for the improvement of plant or algal photosynthesis. Here, we underline some of the latest fundamental discoveries on the molecular mechanisms and regulation of light harvesting that can potentially be exploited for the optimization of photosynthesis.},
	language = {eng},
	number = {3},
	journal = {Plant Physiology},
	author = {Arshad, Rameez and Saccon, Francesco and Bag, Pushan and Biswas, Avratanu and Calvaruso, Claudio and Bhatti, Ahmad Farhan and Grebe, Steffen and Mascoli, Vincenzo and Mahbub, Moontaha and Muzzopappa, Fernando and Polyzois, Alexandros and Schiphorst, Christo and Sorrentino, Mirella and Streckaité, Simona and van Amerongen, Herbert and Aro, Eva-Mari and Bassi, Roberto and Boekema, Egbert J. and Croce, Roberta and Dekker, Jan and van Grondelle, Rienk and Jansson, Stefan and Kirilovsky, Diana and Kouřil, Roman and Michel, Sylvie and Mullineaux, Conrad W. and Panzarová, Klára and Robert, Bruno and Ruban, Alexander V. and van Stokkum, Ivo and Wientjes, Emilie and Büchel, Claudia},
	month = jun,
	year = {2022},
	keywords = {Adaptation, Physiological, Light-Harvesting Protein Complexes, Photosynthesis, Plants, Thylakoids},
	pages = {1204--1219},
}

Photosynthetic light-harvesting antennae are pigment-binding proteins that perform one of the most fundamental tasks on Earth, capturing light and transferring energy that enables life in our biosphere. Adaptation to different light environments led to the evolution of an astonishing diversity of light-harvesting systems. At the same time, several strategies have been developed to optimize the light energy input into photosynthetic membranes in response to fluctuating conditions. The basic feature of these prompt responses is the dynamic nature of antenna complexes, whose function readily adapts to the light available. High-resolution microscopy and spectroscopic studies on membrane dynamics demonstrate the crosstalk between antennae and other thylakoid membrane components. With the increased understanding of light-harvesting mechanisms and their regulation, efforts are focusing on the development of sustainable processes for effective conversion of sunlight into functional bio-products. The major challenge in this approach lies in the application of fundamental discoveries in light-harvesting systems for the improvement of plant or algal photosynthesis. Here, we underline some of the latest fundamental discoveries on the molecular mechanisms and regulation of light harvesting that can potentially be exploited for the optimization of photosynthesis.

@article{fataftah_nitrate_2022,
	title = {Nitrate fertilization may delay autumn leaf senescence, while amino acid treatments do not},
	volume = {174},
	issn = {1399-3054},
	url = {https://onlinelibrary.wiley.com/doi/abs/10.1111/ppl.13690},
	doi = {10.1111/ppl.13690},
	abstract = {Fertilization with nitrogen (N)-rich compounds leads to increased growth but may compromise phenology and winter survival of trees in boreal regions. During autumn, N is remobilized from senescing leaves and stored in other parts of the tree to be used in the next growing season. However, the mechanism behind the N fertilization effect on winter survival is not well understood, and it is unclear how N levels or forms modulate autumn senescence. We performed fertilization experiments and showed that treating Populus saplings with inorganic nitrogen resulted in a delay in senescence. In addition, by using precise delivery of solutes into the xylem stream of Populus trees in their natural environment, we found that delay of autumn senescence was dependent on the form of N administered: inorganic N (NO3−) delayed senescence, but amino acids (Arg, Glu, Gln, and Leu) did not. Metabolite profiling of leaves showed that the levels of tricarboxylic acids, arginine catabolites (ammonium, ornithine), glycine, glycine-serine ratio and overall carbon-to-nitrogen (C/N) ratio were affected differently by the way of applying NO3− and Arg treatments. In addition, the onset of senescence did not coincide with soluble sugar accumulation in control trees or in any of the treatments. We propose that different regulation of C and N status through direct molecular signaling of NO3− and/or different allocation of N between tree parts depending on N forms could account for the contrasting effects of NO3− and tested here amino acids (Arg, Glu, Gln, and Leu) on autumn senescence.},
	language = {en},
	number = {3},
	urldate = {2022-06-30},
	journal = {Physiologia Plantarum},
	author = {Fataftah, Nazeer and Edlund, Erik and Lihavainen, Jenna and Bag, Pushan and Björkén, Lars and Näsholm, Torgny and Jansson, Stefan},
	year = {2022},
	note = {\_eprint: https://onlinelibrary.wiley.com/doi/pdf/10.1111/ppl.13690},
	pages = {e13690},
}

Fertilization with nitrogen (N)-rich compounds leads to increased growth but may compromise phenology and winter survival of trees in boreal regions. During autumn, N is remobilized from senescing leaves and stored in other parts of the tree to be used in the next growing season. However, the mechanism behind the N fertilization effect on winter survival is not well understood, and it is unclear how N levels or forms modulate autumn senescence. We performed fertilization experiments and showed that treating Populus saplings with inorganic nitrogen resulted in a delay in senescence. In addition, by using precise delivery of solutes into the xylem stream of Populus trees in their natural environment, we found that delay of autumn senescence was dependent on the form of N administered: inorganic N (NO3−) delayed senescence, but amino acids (Arg, Glu, Gln, and Leu) did not. Metabolite profiling of leaves showed that the levels of tricarboxylic acids, arginine catabolites (ammonium, ornithine), glycine, glycine-serine ratio and overall carbon-to-nitrogen (C/N) ratio were affected differently by the way of applying NO3− and Arg treatments. In addition, the onset of senescence did not coincide with soluble sugar accumulation in control trees or in any of the treatments. We propose that different regulation of C and N status through direct molecular signaling of NO3− and/or different allocation of N between tree parts depending on N forms could account for the contrasting effects of NO3− and tested here amino acids (Arg, Glu, Gln, and Leu) on autumn senescence.

@article{boussardon_rpn12a_2022,
	title = {The {RPN12a} proteasome subunit is essential for the multiple hormonal homeostasis controlling the progression of leaf senescence},
	volume = {5},
	copyright = {2022 The Author(s)},
	issn = {2399-3642},
	url = {https://www.nature.com/articles/s42003-022-03998-2},
	doi = {10.1038/s42003-022-03998-2},
	abstract = {The 26S proteasome is a conserved multi-subunit machinery in eukaryotes. It selectively degrades ubiquitinated proteins, which in turn provides an efficient molecular mechanism to regulate numerous cellular functions and developmental processes. Here, we studied a new loss-of-function allele of RPN12a, a plant ortholog of the yeast and human structural component of the 19S proteasome RPN12. Combining a set of biochemical and molecular approaches, we confirmed that a rpn12a knock-out had exacerbated 20S and impaired 26S activities. The altered proteasomal activity led to a pleiotropic phenotype affecting both the vegetative growth and reproductive phase of the plant, including a striking repression of leaf senescence associate cell-death. Further investigation demonstrated that RPN12a is involved in the regulation of several conjugates associated with the auxin, cytokinin, ethylene and jasmonic acid homeostasis. Such enhanced aptitude of plant cells for survival in rpn12a contrasts with reports on animals, where 26S proteasome mutants generally show an accelerated cell death phenotype.},
	language = {en},
	number = {1},
	urldate = {2022-10-03},
	journal = {Communications Biology},
	author = {Boussardon, Clément and Bag, Pushan and Juvany, Marta and Šimura, Jan and Ljung, Karin and Jansson, Stefan and Keech, Olivier},
	month = sep,
	year = {2022},
	keywords = {Leaf development, Senescence},
	pages = {1--14},
}

The 26S proteasome is a conserved multi-subunit machinery in eukaryotes. It selectively degrades ubiquitinated proteins, which in turn provides an efficient molecular mechanism to regulate numerous cellular functions and developmental processes. Here, we studied a new loss-of-function allele of RPN12a, a plant ortholog of the yeast and human structural component of the 19S proteasome RPN12. Combining a set of biochemical and molecular approaches, we confirmed that a rpn12a knock-out had exacerbated 20S and impaired 26S activities. The altered proteasomal activity led to a pleiotropic phenotype affecting both the vegetative growth and reproductive phase of the plant, including a striking repression of leaf senescence associate cell-death. Further investigation demonstrated that RPN12a is involved in the regulation of several conjugates associated with the auxin, cytokinin, ethylene and jasmonic acid homeostasis. Such enhanced aptitude of plant cells for survival in rpn12a contrasts with reports on animals, where 26S proteasome mutants generally show an accelerated cell death phenotype.

@article{rendon-anaya_adaptive_2021,
	title = {Adaptive introgression facilitate adaptation to high latitudes in {European} aspen ({Populus} tremula {L}.)},
	volume = {38},
	issn = {1537-1719},
	url = {https://doi.org/10.1093/molbev/msab229},
	doi = {10.1093/molbev/msab229},
	abstract = {Understanding local adaptation has become a key research area given the ongoing climate challenge and the concomitant requirement to conserve genetic resources. Perennial plants, such as forest trees, are good models to study local adaptation given their wide geographic distribution, largely outcrossing mating systems and demographic histories. We evaluated signatures of local adaptation in European aspen (Populus tremula) across Europe by means of whole genome re-sequencing of a collection of 411 individual trees. We dissected admixture patterns between aspen lineages and observed a strong genomic mosaicism in Scandinavian trees, evidencing different colonization trajectories into the peninsula from Russia, Central and Western Europe. As a consequence of the secondary contacts between populations after the last glacial maximum (LGM), we detected an adaptive introgression event in a genome region of ∼500kb in chromosome 10, harboring a large-effect locus that has previously been shown to contribute to adaptation to the short growing seasons characteristic of northern Scandinavia. Demographic simulations and ancestry inference suggest an Eastern origin - probably Russian - of the adaptive Nordic allele which nowadays is present in a homozygous state at the north of Scandinavia. The strength of introgression and positive selection signatures in this region is a unique feature in the genome. Furthermore, we detected signals of balancing selection, shared across regional populations, that highlight the importance of standing variation as a primary source of alleles that facilitate local adaptation. Our results therefore emphasize the importance of migration-selection balance underlying the genetic architecture of key adaptive quantitative traits.},
	language = {eng},
	number = {11},
	journal = {Molecular Biology and Evolution},
	author = {Rendón-Anaya, Martha and Wilson, Jonathan and Sveinsson, Sæmundur and Fedorkov, Aleksey and Cottrell, Joan and Bailey, Mark E. S. and Ruņģis, Dainis and Lexer, Christian and Jansson, Stefan and Robinson, Kathryn M. and Street, Nathaniel R. and Ingvarsson, Pär K.},
	month = jul,
	year = {2021},
	pages = {5034--5050},
}

Understanding local adaptation has become a key research area given the ongoing climate challenge and the concomitant requirement to conserve genetic resources. Perennial plants, such as forest trees, are good models to study local adaptation given their wide geographic distribution, largely outcrossing mating systems and demographic histories. We evaluated signatures of local adaptation in European aspen (Populus tremula) across Europe by means of whole genome re-sequencing of a collection of 411 individual trees. We dissected admixture patterns between aspen lineages and observed a strong genomic mosaicism in Scandinavian trees, evidencing different colonization trajectories into the peninsula from Russia, Central and Western Europe. As a consequence of the secondary contacts between populations after the last glacial maximum (LGM), we detected an adaptive introgression event in a genome region of ∼500kb in chromosome 10, harboring a large-effect locus that has previously been shown to contribute to adaptation to the short growing seasons characteristic of northern Scandinavia. Demographic simulations and ancestry inference suggest an Eastern origin - probably Russian - of the adaptive Nordic allele which nowadays is present in a homozygous state at the north of Scandinavia. The strength of introgression and positive selection signatures in this region is a unique feature in the genome. Furthermore, we detected signals of balancing selection, shared across regional populations, that highlight the importance of standing variation as a primary source of alleles that facilitate local adaptation. Our results therefore emphasize the importance of migration-selection balance underlying the genetic architecture of key adaptive quantitative traits.

@article{bag_atlas_2021,
	title = {An atlas of the {Norway} spruce needle seasonal transcriptome},
	volume = {108},
	issn = {1365-313X},
	url = {https://onlinelibrary.wiley.com/doi/abs/10.1111/tpj.15530},
	doi = {10.1111/tpj.15530},
	abstract = {Boreal conifers possess a tremendous ability to survive and remain evergreen during harsh winter conditions and resume growth during summer. This is enabled by coordinated regulation of major cellular functions at the level of gene expression, metabolism, and physiology. Here we present a comprehensive characterization of the annual changes in the global transcriptome of Norway spruce (Picea abies) needles as a resource to understand needle development and acclimation processes throughout the year. In young, growing needles (May 15 until June 30), cell walls, organelles, etc., were formed, and this developmental program heavily influenced the transcriptome, explained by over-represented Gene Ontology (GO) categories. Later changes in gene expression were smaller but four phases were recognized: summer (July–August), autumn (September–October), winter (November–February), and spring (March–April), where over-represented GO categories demonstrated how the needles acclimated to the various seasons. Changes in the seasonal global transcriptome profile were accompanied by differential expression of members of the major transcription factor families. We present a tentative model of how cellular activities are regulated over the year in needles of Norway spruce, which demonstrates the value of mining this dataset, accessible in ConGenIE together with advanced visualization tools.},
	language = {en},
	number = {6},
	urldate = {2021-11-04},
	journal = {The Plant Journal},
	author = {Bag, Pushan and Lihavainen, Jenna and Delhomme, Nicolas and Riquelme, Thomas and Robinson, Kathryn M and Jansson, Stefan},
	month = oct,
	year = {2021},
	keywords = {Conifers, Norway spruce, Seasonal adaptation, Transcriptomics, conifers, resource, seasonal adaptation, transcriptomics},
}

Boreal conifers possess a tremendous ability to survive and remain evergreen during harsh winter conditions and resume growth during summer. This is enabled by coordinated regulation of major cellular functions at the level of gene expression, metabolism, and physiology. Here we present a comprehensive characterization of the annual changes in the global transcriptome of Norway spruce (Picea abies) needles as a resource to understand needle development and acclimation processes throughout the year. In young, growing needles (May 15 until June 30), cell walls, organelles, etc., were formed, and this developmental program heavily influenced the transcriptome, explained by over-represented Gene Ontology (GO) categories. Later changes in gene expression were smaller but four phases were recognized: summer (July–August), autumn (September–October), winter (November–February), and spring (March–April), where over-represented GO categories demonstrated how the needles acclimated to the various seasons. Changes in the seasonal global transcriptome profile were accompanied by differential expression of members of the major transcription factor families. We present a tentative model of how cellular activities are regulated over the year in needles of Norway spruce, which demonstrates the value of mining this dataset, accessible in ConGenIE together with advanced visualization tools.

@article{fataftah_gigantea_2021,
	title = {{GIGANTEA} influences leaf senescence in trees in two different ways},
	volume = {187},
	issn = {0032-0889},
	url = {https://doi.org/10.1093/plphys/kiab439},
	doi = {10/gnxfqw},
	abstract = {GIGANTEA (GI) genes have a central role in plant development and influence several processes. Hybrid aspen T89 (Populus tremula x tremuloides) trees with low GI expression engineered through RNAi show severely compromised growth. To study the effect of reduced GI expression on leaf traits with special emphasis on leaf senescence, we grafted GI-RNAi scions onto wild-type rootstocks and successfully restored growth of the scions. The RNAi line had a distorted leaf shape and reduced photosynthesis, probably caused by modulation of phloem or stomatal function, increased starch accumulation, a higher carbon-to-nitrogen ratio, and reduced capacity to withstand moderate light stress. GI-RNAi also induced senescence under long day (LD) and moderate light conditions. Furthermore, the GI-RNAi lines were affected in their capacity to respond to “autumn environmental cues” inducing senescence, a type of leaf senescence that has physiological and biochemical characteristics that differ from those of senescence induced directly by stress under LD conditions. Overexpression of GI delayed senescence under simulated autumn conditions. The two different effects on leaf senescence under LD or simulated autumn conditions were not affected by the expression of FLOWERING LOCUS T. GI expression regulated leaf senescence locally—the phenotype followed the genotype of the branch, independent of its position on the tree—and trees with modified gene expression were affected in a similar way when grown in the field as under controlled conditions. Taken together, GI plays a central role in sensing environmental changes during autumn and determining the appropriate timing for leaf senescence in Populus.},
	number = {4},
	urldate = {2021-10-15},
	journal = {Plant Physiology},
	author = {Fataftah, Nazeer and Bag, Pushan and André, Domenique and Lihavainen, Jenna and Zhang, Bo and Ingvarsson, Pär K and Nilsson, Ove and Jansson, Stefan},
	month = sep,
	year = {2021},
	pages = {2435--2450},
}

GIGANTEA (GI) genes have a central role in plant development and influence several processes. Hybrid aspen T89 (Populus tremula x tremuloides) trees with low GI expression engineered through RNAi show severely compromised growth. To study the effect of reduced GI expression on leaf traits with special emphasis on leaf senescence, we grafted GI-RNAi scions onto wild-type rootstocks and successfully restored growth of the scions. The RNAi line had a distorted leaf shape and reduced photosynthesis, probably caused by modulation of phloem or stomatal function, increased starch accumulation, a higher carbon-to-nitrogen ratio, and reduced capacity to withstand moderate light stress. GI-RNAi also induced senescence under long day (LD) and moderate light conditions. Furthermore, the GI-RNAi lines were affected in their capacity to respond to “autumn environmental cues” inducing senescence, a type of leaf senescence that has physiological and biochemical characteristics that differ from those of senescence induced directly by stress under LD conditions. Overexpression of GI delayed senescence under simulated autumn conditions. The two different effects on leaf senescence under LD or simulated autumn conditions were not affected by the expression of FLOWERING LOCUS T. GI expression regulated leaf senescence locally—the phenotype followed the genotype of the branch, independent of its position on the tree—and trees with modified gene expression were affected in a similar way when grown in the field as under controlled conditions. Taken together, GI plays a central role in sensing environmental changes during autumn and determining the appropriate timing for leaf senescence in Populus.

@article{bag_solubilization_2021,
	title = {Solubilization {Method} for {Isolation} of {Photosynthetic} {Mega}- and {Super}-complexes from {Conifer} {Thylakoids}},
	volume = {11},
	url = {https://bio-protocol.org/e4144},
	abstract = {Photosynthesis is the main process by which sunlight is harvested and converted into chemical energy and has been a focal point of fundamental research in plant biology for decades. In higher plants, the process takes place in the thylakoid membranes where the two photosystems (PSI and PSII) are located. In the past few decades, the evolution of biophysical and biochemical techniques allowed detailed studies of the thylakoid organization and the interaction between protein complexes and cofactors. These studies have mainly focused on model plants, such as Arabidopsis, pea, spinach, and tobacco, which are grown in climate chambers even though significant differences between indoor and outdoor growth conditions are present. In this manuscript, we present a new mild-solubilization procedure for use with \“fragile\” samples such as thylakoids from conifers growing outdoors. Here, the solubilization protocol is optimized with two detergents in two species, namely Norway spruce (Picea abies) and Scots pine (Pinus sylvestris). We have optimized the isolation and characterization of PSI and PSII multimeric mega- and super-complexes in a close-to-native condition by Blue-Native gel electrophoresis. Eventually, our protocol will not only help in the characterization of photosynthetic complexes from conifers but also in understanding winter adaptation.},
	number = {17},
	urldate = {2021-10-05},
	journal = {Bio-protocol},
	author = {Bag, Pushan and Schröder, Wolfgang P. and Jansson, Stefan and Farci, Domenica},
	month = sep,
	year = {2021},
	pages = {e4144--e4144},
}

Photosynthesis is the main process by which sunlight is harvested and converted into chemical energy and has been a focal point of fundamental research in plant biology for decades. In higher plants, the process takes place in the thylakoid membranes where the two photosystems (PSI and PSII) are located. In the past few decades, the evolution of biophysical and biochemical techniques allowed detailed studies of the thylakoid organization and the interaction between protein complexes and cofactors. These studies have mainly focused on model plants, such as Arabidopsis, pea, spinach, and tobacco, which are grown in climate chambers even though significant differences between indoor and outdoor growth conditions are present. In this manuscript, we present a new mild-solubilization procedure for use with “fragile” samples such as thylakoids from conifers growing outdoors. Here, the solubilization protocol is optimized with two detergents in two species, namely Norway spruce (Picea abies) and Scots pine (Pinus sylvestris). We have optimized the isolation and characterization of PSI and PSII multimeric mega- and super-complexes in a close-to-native condition by Blue-Native gel electrophoresis. Eventually, our protocol will not only help in the characterization of photosynthetic complexes from conifers but also in understanding winter adaptation.

@article{lihavainen_stem_2021,
	title = {Stem girdling affects the onset of autumn senescence in aspen in interaction with metabolic signals},
	volume = {172},
	issn = {0031-9317, 1399-3054},
	url = {https://onlinelibrary.wiley.com/doi/10.1111/ppl.13319},
	doi = {10.1111/ppl.13319},
	language = {en},
	number = {1},
	urldate = {2021-06-07},
	journal = {Physiologia Plantarum},
	author = {Lihavainen, Jenna and Edlund, Erik and Björkén, Lars and Bag, Pushan and Robinson, Kathryn M. and Jansson, Stefan},
	month = may,
	year = {2021},
	pages = {201--217},
}

@article{robinson_variation_2021,
	title = {Variation in non-target traits in genetically modified hybrid aspens does not exceed natural variation},
	volume = {64},
	issn = {1871-6784},
	url = {https://www.sciencedirect.com/science/article/pii/S1871678421000625},
	doi = {10.1016/j.nbt.2021.05.005},
	abstract = {Genetically modified hybrid aspens (Populus tremula L. x P. tremuloides Michx.), selected for increased growth under controlled conditions, have been grown in highly replicated field trials to evaluate how the target trait (growth) translated to natural conditions. Moreover, the variation was compared among genotypes of ecologically important non-target traits: number of shoots, bud set, pathogen infection, amount of insect herbivory, composition of the insect herbivore community and flower bud induction. This variation was compared with the variation in a population of randomly selected natural accessions of P. tremula grown in common garden trials, to estimate how the “unintended variation” present in transgenic trees, which in the future may be commercialized, compares with natural variation. The natural variation in the traits was found to be typically significantly greater. The data suggest that when authorities evaluate the potential risks associated with a field experiment or commercial introduction of transgenic trees, risk evaluation should focus on target traits and that unintentional variation in non-target traits is of less concern.},
	language = {en},
	urldate = {2021-09-21},
	journal = {New Biotechnology},
	author = {Robinson, Kathryn M. and Möller, Linus and Bhalerao, Rishikesh P. and Hertzberg, Magnus and Nilsson, Ove and Jansson, Stefan},
	month = sep,
	year = {2021},
	keywords = {European aspen, Field experiment, Genetically modified, Hybrid aspen, Natural variation, Non-target traits},
	pages = {27--36},
}

Genetically modified hybrid aspens (Populus tremula L. x P. tremuloides Michx.), selected for increased growth under controlled conditions, have been grown in highly replicated field trials to evaluate how the target trait (growth) translated to natural conditions. Moreover, the variation was compared among genotypes of ecologically important non-target traits: number of shoots, bud set, pathogen infection, amount of insect herbivory, composition of the insect herbivore community and flower bud induction. This variation was compared with the variation in a population of randomly selected natural accessions of P. tremula grown in common garden trials, to estimate how the “unintended variation” present in transgenic trees, which in the future may be commercialized, compares with natural variation. The natural variation in the traits was found to be typically significantly greater. The data suggest that when authorities evaluate the potential risks associated with a field experiment or commercial introduction of transgenic trees, risk evaluation should focus on target traits and that unintentional variation in non-target traits is of less concern.

@article{bag_direct_2020,
	title = {Direct energy transfer from photosystem {II} to photosystem {I} confers winter sustainability in {Scots} {Pine}},
	volume = {11},
	issn = {2041-1723},
	url = {http://www.nature.com/articles/s41467-020-20137-9},
	doi = {10/gjd6p3},
	abstract = {Abstract
            
              Evergreen conifers in boreal forests can survive extremely cold (freezing) temperatures during long dark winter and fully recover during summer. A phenomenon called “sustained quenching” putatively provides photoprotection and enables their survival, but its precise molecular and physiological mechanisms are not understood. To unveil them, here we have analyzed seasonal adjustment of the photosynthetic machinery of Scots pine (
              Pinus sylvestris
              ) trees by monitoring multi-year changes in weather, chlorophyll fluorescence, chloroplast ultrastructure, and changes in pigment-protein composition. Analysis of Photosystem II and Photosystem I performance parameters indicate that highly dynamic structural and functional seasonal rearrangements of the photosynthetic apparatus occur. Although several mechanisms might contribute to ‘sustained quenching’ of winter/early spring pine needles, time-resolved fluorescence analysis shows that extreme down-regulation of photosystem II activity along with direct energy transfer from photosystem II to photosystem I play a major role. This mechanism is enabled by extensive thylakoid destacking allowing for the mixing of PSII with PSI complexes. These two linked phenomena play crucial roles in winter acclimation and protection.},
	language = {en},
	number = {1},
	urldate = {2021-06-07},
	journal = {Nature Communications},
	author = {Bag, Pushan and Chukhutsina, Volha and Zhang, Zishan and Paul, Suman and Ivanov, Alexander G. and Shutova, Tatyana and Croce, Roberta and Holzwarth, Alfred R. and Jansson, Stefan},
	month = dec,
	year = {2020},
	pages = {6388},
}

Abstract Evergreen conifers in boreal forests can survive extremely cold (freezing) temperatures during long dark winter and fully recover during summer. A phenomenon called “sustained quenching” putatively provides photoprotection and enables their survival, but its precise molecular and physiological mechanisms are not understood. To unveil them, here we have analyzed seasonal adjustment of the photosynthetic machinery of Scots pine ( Pinus sylvestris ) trees by monitoring multi-year changes in weather, chlorophyll fluorescence, chloroplast ultrastructure, and changes in pigment-protein composition. Analysis of Photosystem II and Photosystem I performance parameters indicate that highly dynamic structural and functional seasonal rearrangements of the photosynthetic apparatus occur. Although several mechanisms might contribute to ‘sustained quenching’ of winter/early spring pine needles, time-resolved fluorescence analysis shows that extreme down-regulation of photosystem II activity along with direct energy transfer from photosystem II to photosystem I play a major role. This mechanism is enabled by extensive thylakoid destacking allowing for the mixing of PSII with PSI complexes. These two linked phenomena play crucial roles in winter acclimation and protection.

@article{apuli_inferring_2020,
	title = {Inferring the {Genomic} {Landscape} of {Recombination} {Rate} {Variation} in {European} {Aspen} ( {Populus} tremula )},
	volume = {10},
	issn = {2160-1836},
	url = {https://academic.oup.com/g3journal/article/10/1/299/6020315},
	doi = {10/gjctk2},
	abstract = {Abstract
            The rate of meiotic recombination is one of the central factors determining genome-wide levels of linkage disequilibrium which has important consequences for the efficiency of natural selection and for the dissection of quantitative traits. Here we present a new, high-resolution linkage map for Populus tremula that we use to anchor approximately two thirds of the P. tremula draft genome assembly on to the expected 19 chromosomes, providing us with the first chromosome-scale assembly for P. tremula (Table 2). We then use this resource to estimate variation in recombination rates across the P. tremula genome and compare these results to recombination rates based on linkage disequilibrium in a large number of unrelated individuals. We also assess how variation in recombination rates is associated with a number of genomic features, such as gene density, repeat density and methylation levels. We find that recombination rates obtained from the two methods largely agree, although the LD-based method identifies a number of genomic regions with very high recombination rates that the map-based method fails to detect. Linkage map and LD-based estimates of recombination rates are positively correlated and show similar correlations with other genomic features, showing that both methods can accurately infer recombination rate variation across the genome. Recombination rates are positively correlated with gene density and negatively correlated with repeat density and methylation levels, suggesting that recombination is largely directed toward gene regions in P. tremula.},
	language = {en},
	number = {1},
	urldate = {2021-06-07},
	journal = {G3 Genes{\textbar}Genomes{\textbar}Genetics},
	author = {Apuli, Rami-Petteri and Bernhardsson, Carolina and Schiffthaler, Bastian and Robinson, Kathryn M and Jansson, Stefan and Street, Nathaniel R and Ingvarsson, Pär K},
	month = jan,
	year = {2020},
	pages = {299--309},
}

Abstract The rate of meiotic recombination is one of the central factors determining genome-wide levels of linkage disequilibrium which has important consequences for the efficiency of natural selection and for the dissection of quantitative traits. Here we present a new, high-resolution linkage map for Populus tremula that we use to anchor approximately two thirds of the P. tremula draft genome assembly on to the expected 19 chromosomes, providing us with the first chromosome-scale assembly for P. tremula (Table 2). We then use this resource to estimate variation in recombination rates across the P. tremula genome and compare these results to recombination rates based on linkage disequilibrium in a large number of unrelated individuals. We also assess how variation in recombination rates is associated with a number of genomic features, such as gene density, repeat density and methylation levels. We find that recombination rates obtained from the two methods largely agree, although the LD-based method identifies a number of genomic regions with very high recombination rates that the map-based method fails to detect. Linkage map and LD-based estimates of recombination rates are positively correlated and show similar correlations with other genomic features, showing that both methods can accurately infer recombination rate variation across the genome. Recombination rates are positively correlated with gene density and negatively correlated with repeat density and methylation levels, suggesting that recombination is largely directed toward gene regions in P. tremula.

@article{mahler_leaf_2020,
	title = {Leaf shape in {Populus} tremula is a complex, omnigenic trait},
	volume = {10},
	issn = {2045-7758, 2045-7758},
	url = {https://onlinelibrary.wiley.com/doi/10.1002/ece3.6691},
	doi = {10.1002/ece3.6691},
	language = {en},
	number = {21},
	urldate = {2021-06-07},
	journal = {Ecology and Evolution},
	author = {Mähler, Niklas and Schiffthaler, Bastian and Robinson, Kathryn M. and Terebieniec, Barbara K. and Vučak, Matej and Mannapperuma, Chanaka and Bailey, Mark E. S. and Jansson, Stefan and Hvidsten, Torgeir R. and Street, Nathaniel R.},
	month = nov,
	year = {2020},
	pages = {11922--11940},
}

@article{grebe_specific_2020,
	title = {Specific thylakoid protein phosphorylations are prerequisites for overwintering of {Norway} spruce ( \textit{{Picea} abies} ) photosynthesis},
	volume = {117},
	issn = {0027-8424, 1091-6490},
	url = {http://www.pnas.org/lookup/doi/10.1073/pnas.2004165117},
	doi = {10.1073/pnas.2004165117},
	abstract = {Coping of evergreen conifers in boreal forests with freezing temperatures on bright winter days puts the photosynthetic machinery in great risk of oxidative damage. To survive harsh winter conditions, conifers have evolved a unique but poorly characterized photoprotection mechanism, a sustained form of nonphotochemical quenching (sustained NPQ). Here we focused on functional properties and underlying molecular mechanisms related to the development of sustained NPQ in Norway spruce (
              Picea abies
              ). Data were collected during 4 consecutive years (2016 to 2019) from trees growing in sun and shade habitats. When day temperatures dropped below −4 °C, the specific N-terminally triply phosphorylated LHCB1 isoform (3p-LHCII) and phosphorylated PSBS (p-PSBS) could be detected in the thylakoid membrane. Development of sustained NPQ coincided with the highest level of 3p-LHCII and p-PSBS, occurring after prolonged coincidence of bright winter days and temperatures close to −10 °C. Artificial induction of both the sustained NPQ and recovery from naturally induced sustained NPQ provided information on differential dynamics and light-dependence of 3p-LHCII and p-PSBS accumulation as prerequisites for sustained NPQ. Data obtained collectively suggest three components related to sustained NPQ in spruce: 1) Freezing temperatures induce 3p-LHCII accumulation independently of light, which is suggested to initiate destacking of appressed thylakoid membranes due to increased electrostatic repulsion of adjacent membranes; 2) p-PSBS accumulation is both light- and temperature-dependent and closely linked to the initiation of sustained NPQ, which 3) in concert with PSII photoinhibition, is suggested to trigger sustained NPQ in spruce.},
	language = {en},
	number = {30},
	urldate = {2021-06-07},
	journal = {Proceedings of the National Academy of Sciences},
	author = {Grebe, Steffen and Trotta, Andrea and Bajwa, Azfar Ali and Mancini, Ilaria and Bag, Pushan and Jansson, Stefan and Tikkanen, Mikko and Aro, Eva-Mari},
	month = jul,
	year = {2020},
	pages = {17499--17509},
}

Coping of evergreen conifers in boreal forests with freezing temperatures on bright winter days puts the photosynthetic machinery in great risk of oxidative damage. To survive harsh winter conditions, conifers have evolved a unique but poorly characterized photoprotection mechanism, a sustained form of nonphotochemical quenching (sustained NPQ). Here we focused on functional properties and underlying molecular mechanisms related to the development of sustained NPQ in Norway spruce ( Picea abies ). Data were collected during 4 consecutive years (2016 to 2019) from trees growing in sun and shade habitats. When day temperatures dropped below −4 °C, the specific N-terminally triply phosphorylated LHCB1 isoform (3p-LHCII) and phosphorylated PSBS (p-PSBS) could be detected in the thylakoid membrane. Development of sustained NPQ coincided with the highest level of 3p-LHCII and p-PSBS, occurring after prolonged coincidence of bright winter days and temperatures close to −10 °C. Artificial induction of both the sustained NPQ and recovery from naturally induced sustained NPQ provided information on differential dynamics and light-dependence of 3p-LHCII and p-PSBS accumulation as prerequisites for sustained NPQ. Data obtained collectively suggest three components related to sustained NPQ in spruce: 1) Freezing temperatures induce 3p-LHCII accumulation independently of light, which is suggested to initiate destacking of appressed thylakoid membranes due to increased electrostatic repulsion of adjacent membranes; 2) p-PSBS accumulation is both light- and temperature-dependent and closely linked to the initiation of sustained NPQ, which 3) in concert with PSII photoinhibition, is suggested to trigger sustained NPQ in spruce.

@article{grebe_unique_2019,
	title = {The unique photosynthetic apparatus of {Pinaceae}: analysis of photosynthetic complexes in {Picea} abies},
	volume = {70},
	issn = {0022-0957, 1460-2431},
	shorttitle = {The unique photosynthetic apparatus of {Pinaceae}},
	url = {https://academic.oup.com/jxb/article/70/12/3211/5425460},
	doi = {10/gjdz35},
	abstract = {Abstract
            Pinaceae are the predominant photosynthetic species in boreal forests, but so far no detailed description of the protein components of the photosynthetic apparatus of these gymnosperms has been available. In this study we report a detailed characterization of the thylakoid photosynthetic machinery of Norway spruce (Picea abies (L.) Karst). We first customized a spruce thylakoid protein database from translated transcript sequences combined with existing protein sequences derived from gene models, which enabled reliable tandem mass spectrometry identification of P. abies thylakoid proteins from two-dimensional large pore blue-native/SDS-PAGE. This allowed a direct comparison of the two-dimensional protein map of thylakoid protein complexes from P. abies with the model angiosperm Arabidopsis thaliana. Although the subunit composition of P. abies core PSI and PSII complexes is largely similar to that of Arabidopsis, there was a high abundance of a smaller PSI subcomplex, closely resembling the assembly intermediate PSI* complex. In addition, the evolutionary distribution of light-harvesting complex (LHC) family members of Pinaceae was compared in silico with other land plants, revealing that P. abies and other Pinaceae (also Gnetaceae and Welwitschiaceae) have lost LHCB4, but retained LHCB8 (formerly called LHCB4.3). The findings reported here show the composition of the photosynthetic apparatus of P. abies and other Pinaceae members to be unique among land plants.},
	language = {en},
	number = {12},
	urldate = {2021-06-07},
	journal = {Journal of Experimental Botany},
	author = {Grebe, Steffen and Trotta, Andrea and Bajwa, Azfar A and Suorsa, Marjaana and Gollan, Peter J and Jansson, Stefan and Tikkanen, Mikko and Aro, Eva-Mari},
	month = jun,
	year = {2019},
	pages = {3211--3225},
}

Abstract Pinaceae are the predominant photosynthetic species in boreal forests, but so far no detailed description of the protein components of the photosynthetic apparatus of these gymnosperms has been available. In this study we report a detailed characterization of the thylakoid photosynthetic machinery of Norway spruce (Picea abies (L.) Karst). We first customized a spruce thylakoid protein database from translated transcript sequences combined with existing protein sequences derived from gene models, which enabled reliable tandem mass spectrometry identification of P. abies thylakoid proteins from two-dimensional large pore blue-native/SDS-PAGE. This allowed a direct comparison of the two-dimensional protein map of thylakoid protein complexes from P. abies with the model angiosperm Arabidopsis thaliana. Although the subunit composition of P. abies core PSI and PSII complexes is largely similar to that of Arabidopsis, there was a high abundance of a smaller PSI subcomplex, closely resembling the assembly intermediate PSI* complex. In addition, the evolutionary distribution of light-harvesting complex (LHC) family members of Pinaceae was compared in silico with other land plants, revealing that P. abies and other Pinaceae (also Gnetaceae and Welwitschiaceae) have lost LHCB4, but retained LHCB8 (formerly called LHCB4.3). The findings reported here show the composition of the photosynthetic apparatus of P. abies and other Pinaceae members to be unique among land plants.

@article{wang_major_2018,
	title = {A major locus controls local adaptation and adaptive life history variation in a perennial plant},
	volume = {19},
	issn = {1474-760X},
	url = {https://genomebiology.biomedcentral.com/articles/10.1186/s13059-018-1444-y},
	doi = {10.1186/s13059-018-1444-y},
	language = {en},
	number = {1},
	urldate = {2021-06-07},
	journal = {Genome Biology},
	author = {Wang, Jing and Ding, Jihua and Tan, Biyue and Robinson, Kathryn M. and Michelson, Ingrid H. and Johansson, Anna and Nystedt, Björn and Scofield, Douglas G. and Nilsson, Ove and Jansson, Stefan and Street, Nathaniel R. and Ingvarsson, Pär K.},
	month = dec,
	year = {2018},
	pages = {72},
}

@article{michelson_autumn_2018,
	title = {Autumn senescence in aspen is not triggered by day length},
	volume = {162},
	issn = {00319317},
	url = {http://doi.wiley.com/10.1111/ppl.12593},
	doi = {10.1111/ppl.12593},
	language = {en},
	number = {1},
	urldate = {2021-06-07},
	journal = {Physiologia Plantarum},
	author = {Michelson, Ingrid H. and Ingvarsson, Pär K. and Robinson, Kathryn M. and Edlund, Erik and Eriksson, Maria E. and Nilsson, Ove and Jansson, Stefan},
	month = jan,
	year = {2018},
	pages = {123--134},
}

@article{law_darkened_2018,
	title = {Darkened {Leaves} {Use} {Different} {Metabolic} {Strategies} for {Senescence} and {Survival}},
	volume = {177},
	issn = {0032-0889, 1532-2548},
	url = {https://academic.oup.com/plphys/article/177/1/132-150/6116945},
	doi = {10.1104/pp.18.00062},
	language = {en},
	number = {1},
	urldate = {2021-06-07},
	journal = {Plant Physiology},
	author = {Law, Simon R. and Chrobok, Daria and Juvany, Marta and Delhomme, Nicolas and Lindén, Pernilla and Brouwer, Bastiaan and Ahad, Abdul and Moritz, Thomas and Jansson, Stefan and Gardeström, Per and Keech, Olivier},
	month = may,
	year = {2018},
	pages = {132--150},
}

@article{pribil_fine-tuning_2018,
	title = {Fine-{Tuning} of {Photosynthesis} {Requires} {CURVATURE} {THYLAKOID1}-{Mediated} {Thylakoid} {Plasticity}},
	volume = {176},
	issn = {0032-0889, 1532-2548},
	url = {https://academic.oup.com/plphys/article/176/3/2351-2364/6117159},
	doi = {10.1104/pp.17.00863},
	language = {en},
	number = {3},
	urldate = {2021-06-07},
	journal = {Plant Physiology},
	author = {Pribil, Mathias and Sandoval-Ibáñez, Omar and Xu, Wenteng and Sharma, Anurag and Labs, Mathias and Liu, Qiuping and Galgenmüller, Carolina and Schneider, Trang and Wessels, Malgorzata and Matsubara, Shizue and Jansson, Stefan and Wanner, Gerhard and Leister, Dario},
	month = mar,
	year = {2018},
	pages = {2351--2364},
}

@article{lin_functional_2018,
	title = {Functional and evolutionary genomic inferences in \textit{{Populus}} through genome and population sequencing of {American} and {European} aspen},
	volume = {115},
	issn = {0027-8424, 1091-6490},
	url = {http://www.pnas.org/lookup/doi/10.1073/pnas.1801437115},
	doi = {10.1073/pnas.1801437115},
	abstract = {The
              Populus
              genus is one of the major plant model systems, but genomic resources have thus far primarily been available for poplar species, and primarily
              Populus trichocarpa
              (Torr. \& Gray), which was the first tree with a whole-genome assembly. To further advance evolutionary and functional genomic analyses in
              Populus
              , we produced genome assemblies and population genetics resources of two aspen species,
              Populus tremula
              L. and
              Populus tremuloides
              Michx. The two aspen species have distributions spanning the Northern Hemisphere, where they are keystone species supporting a wide variety of dependent communities and produce a diverse array of secondary metabolites. Our analyses show that the two aspens share a similar genome structure and a highly conserved gene content with
              P. trichocarpa
              but display substantially higher levels of heterozygosity. Based on population resequencing data, we observed widespread positive and negative selection acting on both coding and noncoding regions. Furthermore, patterns of genetic diversity and molecular evolution in aspen are influenced by a number of features, such as expression level, coexpression network connectivity, and regulatory variation. To maximize the community utility of these resources, we have integrated all presented data within the PopGenIE web resource (
              PopGenIE.org
              ).},
	language = {en},
	number = {46},
	urldate = {2021-06-07},
	journal = {Proceedings of the National Academy of Sciences},
	author = {Lin, Yao-Cheng and Wang, Jing and Delhomme, Nicolas and Schiffthaler, Bastian and Sundström, Görel and Zuccolo, Andrea and Nystedt, Björn and Hvidsten, Torgeir R. and de la Torre, Amanda and Cossu, Rosa M. and Hoeppner, Marc P. and Lantz, Henrik and Scofield, Douglas G. and Zamani, Neda and Johansson, Anna and Mannapperuma, Chanaka and Robinson, Kathryn M. and Mähler, Niklas and Leitch, Ilia J. and Pellicer, Jaume and Park, Eung-Jun and Van Montagu, Marc and Van de Peer, Yves and Grabherr, Manfred and Jansson, Stefan and Ingvarsson, Pär K. and Street, Nathaniel R.},
	month = nov,
	year = {2018},
	pages = {E10970--E10978},
}

The Populus genus is one of the major plant model systems, but genomic resources have thus far primarily been available for poplar species, and primarily Populus trichocarpa (Torr. & Gray), which was the first tree with a whole-genome assembly. To further advance evolutionary and functional genomic analyses in Populus , we produced genome assemblies and population genetics resources of two aspen species, Populus tremula L. and Populus tremuloides Michx. The two aspen species have distributions spanning the Northern Hemisphere, where they are keystone species supporting a wide variety of dependent communities and produce a diverse array of secondary metabolites. Our analyses show that the two aspens share a similar genome structure and a highly conserved gene content with P. trichocarpa but display substantially higher levels of heterozygosity. Based on population resequencing data, we observed widespread positive and negative selection acting on both coding and noncoding regions. Furthermore, patterns of genetic diversity and molecular evolution in aspen are influenced by a number of features, such as expression level, coexpression network connectivity, and regulatory variation. To maximize the community utility of these resources, we have integrated all presented data within the PopGenIE web resource ( PopGenIE.org ).

@article{jansson_gene-edited_2018,
	title = {Gene-edited plants on the plate: the ‘{CRISPR} cabbage story’},
	volume = {164},
	issn = {00319317},
	shorttitle = {Gene-edited plants on the plate},
	url = {http://doi.wiley.com/10.1111/ppl.12754},
	doi = {10.1111/ppl.12754},
	language = {en},
	number = {4},
	urldate = {2021-06-07},
	journal = {Physiologia Plantarum},
	author = {Jansson, Stefan},
	month = dec,
	year = {2018},
	pages = {396--405},
}

@article{jansson_gene-edited_2018,
	title = {Gene-edited plants: {What} is happening now?},
	volume = {164},
	issn = {00319317},
	shorttitle = {Gene-edited plants},
	url = {http://doi.wiley.com/10.1111/ppl.12853},
	doi = {10.1111/ppl.12853},
	language = {en},
	number = {4},
	urldate = {2021-06-07},
	journal = {Physiologia Plantarum},
	author = {Jansson, Stefan},
	month = dec,
	year = {2018},
	pages = {370--371},
}

@article{myouga_stable_2018,
	title = {Stable {Accumulation} of {Photosystem} {II} {Requires} {ONE}-{HELIX} {PROTEIN1} ({OHP1}) of the {Light} {Harvesting}-{Like} {Family}},
	volume = {176},
	issn = {0032-0889, 1532-2548},
	url = {https://academic.oup.com/plphys/article/176/3/2277-2291/6117119},
	doi = {10.1104/pp.17.01782},
	language = {en},
	number = {3},
	urldate = {2021-06-07},
	journal = {Plant Physiology},
	author = {Myouga, Fumiyoshi and Takahashi, Kaori and Tanaka, Ryoichi and Nagata, Noriko and Kiss, Anett Z. and Funk, Christiane and Nomura, Yuko and Nakagami, Hirofumi and Jansson, Stefan and Shinozaki, Kazuo},
	month = mar,
	year = {2018},
	pages = {2277--2291},
}

@article{mishra_active-site_2017,
	title = {Active-site plasticity revealed in the asymmetric dimer of {AnPrx6} the 1-{Cys} peroxiredoxin and molecular chaperone from {Anabaena} sp. {PCC} 7120},
	volume = {7},
	issn = {2045-2322},
	url = {http://www.nature.com/articles/s41598-017-17044-3},
	doi = {10/gc2fwt},
	language = {en},
	number = {1},
	urldate = {2021-06-07},
	journal = {Scientific Reports},
	author = {Mishra, Yogesh and Hall, Michael and Locmelis, Roland and Nam, Kwangho and Söderberg, Christopher A. G. and Storm, Patrik and Chaurasia, Neha and Rai, Lal Chand and Jansson, Stefan and Schröder, Wolfgang P. and Sauer, Uwe H.},
	month = dec,
	year = {2017},
	pages = {17151},
}

@article{edlund_contrasting_2017,
	title = {Contrasting patterns of cytokinins between years in senescing aspen leaves},
	volume = {40},
	issn = {0140-7791, 1365-3040},
	url = {https://onlinelibrary.wiley.com/doi/abs/10.1111/pce.12899},
	doi = {10.1111/pce.12899},
	language = {en},
	number = {5},
	urldate = {2021-06-07},
	journal = {Plant, Cell \& Environment},
	author = {Edlund, Erik and Novak, Ondrej and Karady, Michal and Ljung, Karin and Jansson, Stefan},
	month = may,
	year = {2017},
	pages = {622--634},
}

@article{zas_genetic_2017,
	title = {Genetic variation in resistance of {Norway} spruce seedlings to damage by the pine weevil {Hylobius} abietis},
	volume = {13},
	issn = {1614-2942, 1614-2950},
	url = {http://link.springer.com/10.1007/s11295-017-1193-1},
	doi = {10/gcps32},
	language = {en},
	number = {5},
	urldate = {2021-06-07},
	journal = {Tree Genetics \& Genomes},
	author = {Zas, Rafael and Björklund, Niklas and Sampedro, Luis and Hellqvist, Claes and Karlsson, Bo and Jansson, Stefan and Nordlander, Göran},
	month = oct,
	year = {2017},
	pages = {111},
}

@article{ricroch_challenges_2016,
	title = {Challenges facing {European} agriculture and possible biotechnological solutions},
	volume = {36},
	issn = {0738-8551, 1549-7801},
	url = {https://www.tandfonline.com/doi/full/10.3109/07388551.2015.1055707},
	doi = {10.3109/07388551.2015.1055707},
	language = {en},
	number = {5},
	urldate = {2021-06-07},
	journal = {Critical Reviews in Biotechnology},
	author = {Ricroch, Agnès and Harwood, Wendy and Svobodová, Zdeňka and Sági, László and Hundleby, Penelope and Badea, Elena Marcela and Rosca, Ioan and Cruz, Gabriela and Salema Fevereiro, Manuel Pedro and Marfà Riera, Victoria and Jansson, Stefan and Morandini, Piero and Bojinov, Bojin and Cetiner, Selim and Custers, René and Schrader, Uwe and Jacobsen, Hans-Joerg and Martin-Laffon, Jacqueline and Boisron, Audrey and Kuntz, Marcel},
	month = sep,
	year = {2016},
	pages = {875--883},
}

@article{zulfugarov_enhanced_2016,
	title = {Enhanced resistance of {PsbS}-deficient rice ({Oryza} sativa {L}.) to fungal and bacterial pathogens},
	volume = {59},
	issn = {1226-9239, 1867-0725},
	url = {http://link.springer.com/10.1007/s12374-016-0068-6},
	doi = {10.1007/s12374-016-0068-6},
	language = {en},
	number = {6},
	urldate = {2021-06-07},
	journal = {Journal of Plant Biology},
	author = {Zulfugarov, Ismayil S. and Tovuu, Altanzaya and Kim, Chi-Yeol and Xuan Vo, Kieu Thi and Ko, Soo Yeon and Hall, Michael and Seok, Hye-Yeon and Kim, Yeon-Ki and Skogstrom, Oscar and Moon, Yong-Hwan and Jansson, Stefan and Jeon, Jong-Seong and Lee, Choon-Hwan},
	month = dec,
	year = {2016},
	pages = {616--626},
}

@article{benson_intact_2015,
	title = {An intact light harvesting complex {I} antenna system is required for complete state transitions in {Arabidopsis}},
	volume = {1},
	issn = {2055-0278 (Electronic) 2055-0278 (Linking)},
	url = {https://www.ncbi.nlm.nih.gov/pubmed/27251716},
	doi = {10.1038/nplants.2015.176},
	abstract = {Efficient photosynthesis depends on maintaining balance between the rate of light-driven electron transport occurring in photosystem I (PSI) and photosystem II (PSII), located in the chloroplast thylakoid membranes. Balance is achieved through a process of 'state transitions' that increases energy transfer towards PSI when PSII is overexcited (state II), and towards PSII when PSI is overexcited (state I). This is achieved through redox control of the phosphorylation state of light-harvesting antenna complex II (LHCII). PSI is served by both LHCII and four light-harvesting antenna complex I (LHCI) subunits, Lhca1, 2, 3 and 4. Here we demonstrate that despite unchanged levels of LHCII phosphorylation, absence of specific Lhca subunits reduces state transitions in Arabidopsis. The severest phenotype-observed in a mutant lacking Lhca4 (DeltaLhca4)-displayed a 69\% reduction compared with the wild type. Yet, surprisingly, the amounts of the PSI-LHCI-LHCII supercomplex isolated by blue native polyacrylamide gel electrophoresis (BN-PAGE) from digitonin-solubilized thylakoids were similar in the wild type and DeltaLhca mutants. Fluorescence excitation spectroscopy revealed that in the wild type this PSI-LHCI-LHCII supercomplex is supplemented by energy transfer from additional LHCII trimers in state II, whose binding is sensitive to digitonin, and which are absent in DeltaLhca4. The grana margins of the thylakoid membrane were found to be the primary site of interaction between this 'extra' LHCII and the PSI-LHCI-LHCII supercomplex in state II. The results suggest that the LHCI complexes mediate energetic interactions between LHCII and PSI in the intact membrane.},
	language = {en},
	number = {12},
	urldate = {2021-06-07},
	journal = {Nat Plants},
	author = {Benson, S. L. and Maheswaran, P. and Ware, M. A. and Hunter, C. N. and Horton, P. and Jansson, S. and Ruban, A. V. and Johnson, M. P.},
	month = nov,
	year = {2015},
	note = {Edition: 2015/01/01},
	pages = {15176},
}

Efficient photosynthesis depends on maintaining balance between the rate of light-driven electron transport occurring in photosystem I (PSI) and photosystem II (PSII), located in the chloroplast thylakoid membranes. Balance is achieved through a process of 'state transitions' that increases energy transfer towards PSI when PSII is overexcited (state II), and towards PSII when PSI is overexcited (state I). This is achieved through redox control of the phosphorylation state of light-harvesting antenna complex II (LHCII). PSI is served by both LHCII and four light-harvesting antenna complex I (LHCI) subunits, Lhca1, 2, 3 and 4. Here we demonstrate that despite unchanged levels of LHCII phosphorylation, absence of specific Lhca subunits reduces state transitions in Arabidopsis. The severest phenotype-observed in a mutant lacking Lhca4 (DeltaLhca4)-displayed a 69% reduction compared with the wild type. Yet, surprisingly, the amounts of the PSI-LHCI-LHCII supercomplex isolated by blue native polyacrylamide gel electrophoresis (BN-PAGE) from digitonin-solubilized thylakoids were similar in the wild type and DeltaLhca mutants. Fluorescence excitation spectroscopy revealed that in the wild type this PSI-LHCI-LHCII supercomplex is supplemented by energy transfer from additional LHCII trimers in state II, whose binding is sensitive to digitonin, and which are absent in DeltaLhca4. The grana margins of the thylakoid membrane were found to be the primary site of interaction between this 'extra' LHCII and the PSI-LHCI-LHCII supercomplex in state II. The results suggest that the LHCI complexes mediate energetic interactions between LHCII and PSI in the intact membrane.

@article{soolanayakanahally_comparative_2015,
	title = {Comparative physiology of allopatric {Populus} species: geographic clines in photosynthesis, height growth, and carbon isotope discrimination in common gardens},
	volume = {6},
	issn = {1664-462X (Print) 1664-462X (Linking)},
	shorttitle = {Comparative physiology of allopatric {Populus} species},
	url = {https://www.ncbi.nlm.nih.gov/pubmed/26236324},
	doi = {10.3389/fpls.2015.00528},
	abstract = {Populus species with wide geographic ranges display strong adaptation to local environments. We studied the clinal patterns in phenology and ecophysiology in allopatric Populus species adapted to similar environments on different continents under common garden settings. As a result of climatic adaptation, both Populus tremula L. and Populus balsamifera L. display latitudinal clines in photosynthetic rates (A), whereby high-latitude trees of P. tremula had higher A compared to low-latitude trees and nearly so in P. balsamifera (p = 0.06). Stomatal conductance (g s) and chlorophyll content index (CCI) follow similar latitudinal trends. However, foliar nitrogen was positively correlated with latitude in P. balsamifera and negatively correlated in P. tremula. No significant trends in carbon isotope composition of the leaf tissue (delta(13)C) were observed for both species; but, intrinsic water-use efficiency (WUEi) was negatively correlated with the latitude of origin in P. balsamifera. In spite of intrinsically higher A, high-latitude trees in both common gardens accomplished less height gain as a result of early bud set. Thus, shoot biomass was determined by height elongation duration (HED), which was well approximated by the number of days available for free growth between bud flush and bud set. We highlight the shortcoming of unreplicated outdoor common gardens for tree improvement and the crucial role of photoperiod in limiting height growth, further complicating interpretation of other secondary effects.},
	language = {English},
	urldate = {2021-06-07},
	journal = {Front Plant Sci},
	author = {Soolanayakanahally, R. Y. and Guy, R. D. and Street, N. R. and Robinson, K. M. and Silim, S. N. and Albrectsen, B. R. and Jansson, S.},
	year = {2015},
	note = {Edition: 2015/08/04},
	keywords = {Photosynthesis, bud set, carbon isotope discrimination, common garden, comparative physiology, latitude, photosynthesis, poplar, water-use efficiency},
	pages = {528},
}

Populus species with wide geographic ranges display strong adaptation to local environments. We studied the clinal patterns in phenology and ecophysiology in allopatric Populus species adapted to similar environments on different continents under common garden settings. As a result of climatic adaptation, both Populus tremula L. and Populus balsamifera L. display latitudinal clines in photosynthetic rates (A), whereby high-latitude trees of P. tremula had higher A compared to low-latitude trees and nearly so in P. balsamifera (p = 0.06). Stomatal conductance (g s) and chlorophyll content index (CCI) follow similar latitudinal trends. However, foliar nitrogen was positively correlated with latitude in P. balsamifera and negatively correlated in P. tremula. No significant trends in carbon isotope composition of the leaf tissue (delta(13)C) were observed for both species; but, intrinsic water-use efficiency (WUEi) was negatively correlated with the latitude of origin in P. balsamifera. In spite of intrinsically higher A, high-latitude trees in both common gardens accomplished less height gain as a result of early bud set. Thus, shoot biomass was determined by height elongation duration (HED), which was well approximated by the number of days available for free growth between bud flush and bud set. We highlight the shortcoming of unreplicated outdoor common gardens for tree improvement and the crucial role of photoperiod in limiting height growth, further complicating interpretation of other secondary effects.

@article{sundell_plant_2015,
	title = {The {Plant} {Genome} {Integrative} {Explorer} {Resource}: {PlantGenIE}.org},
	volume = {208},
	issn = {1469-8137 (Electronic) 0028-646X (Linking)},
	shorttitle = {The {Plant} {Genome} {Integrative} {Explorer} {Resource}},
	url = {https://www.ncbi.nlm.nih.gov/pubmed/26192091},
	doi = {10.1111/nph.13557},
	abstract = {Accessing and exploring large-scale genomics data sets remains a significant challenge to researchers without specialist bioinformatics training. We present the integrated PlantGenIE.org platform for exploration of Populus, conifer and Arabidopsis genomics data, which includes expression networks and associated visualization tools. Standard features of a model organism database are provided, including genome browsers, gene list annotation, Blast homology searches and gene information pages. Community annotation updating is supported via integration of WebApollo. We have produced an RNA-sequencing (RNA-Seq) expression atlas for Populus tremula and have integrated these data within the expression tools. An updated version of the ComPlEx resource for performing comparative plant expression analyses of gene coexpression network conservation between species has also been integrated. The PlantGenIE.org platform provides intuitive access to large-scale and genome-wide genomics data from model forest tree species, facilitating both community contributions to annotation improvement and tools supporting use of the included data resources to inform biological insight.},
	language = {en},
	number = {4},
	urldate = {2021-06-07},
	journal = {New Phytol},
	author = {Sundell, D. and Mannapperuma, C. and Netotea, S. and Delhomme, N. and Lin, Y. C. and Sjodin, A. and Van de Peer, Y. and Jansson, S. and Hvidsten, T. R. and Street, N. R.},
	month = dec,
	year = {2015},
	note = {Edition: 2015/07/21},
	keywords = {*Databases, Factual, *Genes, Plant, *Genome, Plant, Arabidopsis/*genetics, Computational Biology, Forests, Gene Expression, Genomics/methods, Internet, Models, Biological, Populus, Populus/*genetics, RNA, Plant, Sequence Analysis, DNA, Tracheophyta/*genetics, Trees/*genetics, annotation, coexpression, conifer, database, genome browser, transcriptomics, web resource},
	pages = {1149--56},
}

Accessing and exploring large-scale genomics data sets remains a significant challenge to researchers without specialist bioinformatics training. We present the integrated PlantGenIE.org platform for exploration of Populus, conifer and Arabidopsis genomics data, which includes expression networks and associated visualization tools. Standard features of a model organism database are provided, including genome browsers, gene list annotation, Blast homology searches and gene information pages. Community annotation updating is supported via integration of WebApollo. We have produced an RNA-sequencing (RNA-Seq) expression atlas for Populus tremula and have integrated these data within the expression tools. An updated version of the ComPlEx resource for performing comparative plant expression analyses of gene coexpression network conservation between species has also been integrated. The PlantGenIE.org platform provides intuitive access to large-scale and genome-wide genomics data from model forest tree species, facilitating both community contributions to annotation improvement and tools supporting use of the included data resources to inform biological insight.

@article{de_la_torre_insights_2014,
	title = {Insights into {Conifer} {Giga}-{Genomes}},
	volume = {166},
	issn = {0032-0889, 1532-2548},
	url = {https://academic.oup.com/plphys/article/166/4/1724-1732/6113514},
	doi = {10/f25hfn},
	language = {en},
	number = {4},
	urldate = {2021-06-08},
	journal = {Plant Physiology},
	author = {De La Torre, Amanda R. and Birol, Inanc and Bousquet, Jean and Ingvarsson, Pär K. and Jansson, Stefan and Jones, Steven J.M. and Keeling, Christopher I. and MacKay, John and Nilsson, Ove and Ritland, Kermit and Street, Nathaniel and Yanchuk, Alvin and Zerbe, Philipp and Bohlmann, Jörg},
	month = dec,
	year = {2014},
	pages = {1724--1732},
}

@article{keefover-ring_no_2014,
	title = {No {Evidence} of {Geographical} {Structure} of {Salicinoid} {Chemotypes} within {Populus} {Tremula}},
	volume = {9},
	issn = {1932-6203},
	url = {https://dx.plos.org/10.1371/journal.pone.0107189},
	doi = {10/f25fhm},
	language = {en},
	number = {10},
	urldate = {2021-06-08},
	journal = {PLoS ONE},
	author = {Keefover-Ring, Ken and Ahnlund, Maria and Abreu, Ilka Nacif and Jansson, Stefan and Moritz, Thomas and Albrectsen, Benedicte Riber},
	editor = {Yin, Tongming},
	month = oct,
	year = {2014},
	pages = {e107189},
}

@article{robinson_populus_2014,
	title = {Populus tremula ({European} aspen) shows no evidence of sexual dimorphism},
	volume = {14},
	issn = {1471-2229},
	url = {http://bmcplantbiol.biomedcentral.com/articles/10.1186/s12870-014-0276-5},
	doi = {10/f25brv},
	language = {en},
	number = {1},
	urldate = {2021-06-08},
	journal = {BMC Plant Biology},
	author = {Robinson, Kathryn M and Delhomme, Nicolas and Mähler, Niklas and Schiffthaler, Bastian and Önskog, Jenny and Albrectsen, Benedicte R and Ingvarsson, Pär K and Hvidsten, Torgeir R and Jansson, Stefan and Street, Nathaniel R},
	month = dec,
	year = {2014},
	pages = {276},
}

@article{zulfugarov_production_2014,
	title = {Production of superoxide from {Photosystem} {II} in a rice ({Oryza} {sativaL}.) mutant lacking {PsbS}},
	volume = {14},
	issn = {1471-2229},
	url = {http://bmcplantbiol.biomedcentral.com/articles/10.1186/s12870-014-0242-2},
	doi = {10/f3m3zb},
	language = {en},
	number = {1},
	urldate = {2021-06-08},
	journal = {BMC Plant Biology},
	author = {Zulfugarov, Ismayil S and Tovuu, Altanzaya and Eu, Young-Jae and Dogsom, Bolormaa and Poudyal, Roshan Sharma and Nath, Krishna and Hall, Michael and Banerjee, Mainak and Yoon, Ung Chan and Moon, Yong-Hwan and An, Gynheung and Jansson, Stefan and Lee, Choon-Hwan},
	month = dec,
	year = {2014},
	pages = {242},
}

@article{pietrzykowska_light-harvesting_2014,
	title = {The {Light}-{Harvesting} {Chlorophyll} a/b {Binding} {Proteins} {Lhcb1} and {Lhcb2} {Play} {Complementary} {Roles} during {State} {Transitions} in {Arabidopsis}},
	volume = {26},
	issn = {1040-4651, 1532-298X},
	url = {https://academic.oup.com/plcell/article/26/9/3646-3660/6100356},
	doi = {10/f25cg8},
	language = {en},
	number = {9},
	urldate = {2021-06-08},
	journal = {The Plant Cell},
	author = {Pietrzykowska, M. and Suorsa, M. and Semchonok, D. A. and Tikkanen, M. and Boekema, E. J. and Aro, E.-M. and Jansson, S.},
	month = sep,
	year = {2014},
	pages = {3646--3660},
}

@article{bernhardsson_geographic_2013,
	title = {Geographic structure in metabolome and herbivore community co-occurs with genetic structure in plant defence genes},
	volume = {16},
	issn = {1461023X},
	url = {http://doi.wiley.com/10.1111/ele.12114},
	doi = {10/f25rz6},
	language = {en},
	number = {6},
	urldate = {2021-06-08},
	journal = {Ecology Letters},
	author = {Bernhardsson, Carolina and Robinson, Kathryn M. and Abreu, Ilka N. and Jansson, Stefan and Albrectsen, Benedicte R. and Ingvarsson, Pär K.},
	editor = {Eubanks, Micky},
	month = jun,
	year = {2013},
	pages = {791--798},
}

@article{johansson_jankanpaa_non-photochemical_2013,
	title = {Non-{Photochemical} {Quenching} {Capacity} in {Arabidopsis} thaliana {Affects} {Herbivore} {Behaviour}},
	volume = {8},
	issn = {1932-6203},
	url = {https://dx.plos.org/10.1371/journal.pone.0053232},
	doi = {10/f22s4s},
	language = {en},
	number = {1},
	urldate = {2021-06-08},
	journal = {PLoS ONE},
	author = {Johansson Jänkänpää, Hanna and Frenkel, Martin and Zulfugarov, Ismayil and Reichelt, Michael and Krieger-Liszkay, Anja and Mishra, Yogesh and Gershenzon, Jonathan and Moen, Jon and Lee, Choon-Hwan and Jansson, Stefan},
	editor = {Tran, Lam-Son Phan},
	month = jan,
	year = {2013},
	pages = {e53232},
}

@article{nystedt_norway_2013,
	title = {The {Norway} spruce genome sequence and conifer genome evolution},
	volume = {497},
	issn = {0028-0836, 1476-4687},
	url = {http://www.nature.com/articles/nature12211},
	doi = {10/f2zsx6},
	language = {en},
	number = {7451},
	urldate = {2021-06-08},
	journal = {Nature},
	author = {Nystedt, Björn and Street, Nathaniel R. and Wetterbom, Anna and Zuccolo, Andrea and Lin, Yao-Cheng and Scofield, Douglas G. and Vezzi, Francesco and Delhomme, Nicolas and Giacomello, Stefania and Alexeyenko, Andrey and Vicedomini, Riccardo and Sahlin, Kristoffer and Sherwood, Ellen and Elfstrand, Malin and Gramzow, Lydia and Holmberg, Kristina and Hällman, Jimmie and Keech, Olivier and Klasson, Lisa and Koriabine, Maxim and Kucukoglu, Melis and Käller, Max and Luthman, Johannes and Lysholm, Fredrik and Niittylä, Totte and Olson, Åke and Rilakovic, Nemanja and Ritland, Carol and Rosselló, Josep A. and Sena, Juliana and Svensson, Thomas and Talavera-López, Carlos and Theißen, Günter and Tuominen, Hannele and Vanneste, Kevin and Wu, Zhi-Qiang and Zhang, Bo and Zerbe, Philipp and Arvestad, Lars and Bhalerao, Rishikesh P. and Bohlmann, Joerg and Bousquet, Jean and Garcia Gil, Rosario and Hvidsten, Torgeir R. and de Jong, Pieter and MacKay, John and Morgante, Michele and Ritland, Kermit and Sundberg, Björn and Lee Thompson, Stacey and Van de Peer, Yves and Andersson, Björn and Nilsson, Ove and Ingvarsson, Pär K. and Lundeberg, Joakim and Jansson, Stefan},
	month = may,
	year = {2013},
	pages = {579--584},
}

@article{leoni_very_2013,
	title = {Very rapid phosphorylation kinetics suggest a unique role for {Lhcb2} during state transitions in {Arabidopsis}},
	volume = {76},
	issn = {0960-7412, 1365-313X},
	shorttitle = {Very rapid phosphorylation kinetics suggest a unique role for {\textless}span style="font-variant},
	url = {https://onlinelibrary.wiley.com/doi/10.1111/tpj.12297},
	doi = {10/f23mzn},
	language = {en},
	number = {2},
	urldate = {2021-06-08},
	journal = {The Plant Journal},
	author = {Leoni, Claudia and Pietrzykowska, Malgorzata and Kiss, Anett Z. and Suorsa, Marjaana and Ceci, Luigi R. and Aro, Eva‐Mari and Jansson, Stefan},
	month = oct,
	year = {2013},
	pages = {236--246},
}

@article{mishra_arabidopsis_2012,
	title = {Arabidopsis plants grown in the field and climate chambers significantly differ in leaf morphology and photosystem components},
	volume = {12},
	issn = {1471-2229},
	url = {http://bmcplantbiol.biomedcentral.com/articles/10.1186/1471-2229-12-6},
	doi = {10/fx7f9h},
	language = {en},
	number = {1},
	urldate = {2021-06-08},
	journal = {BMC Plant Biology},
	author = {Mishra, Yogesh and Johansson Jänkänpää, Hanna and Kiss, Anett Z and Funk, Christiane and Schröder, Wolfgang P and Jansson, Stefan},
	year = {2012},
	pages = {6},
}

@article{ismail_comparative_2012,
	title = {Comparative {Nucleotide} {Diversity} {Across} {North} {American} and {European} {Populus} {Species}},
	volume = {74},
	issn = {0022-2844, 1432-1432},
	url = {http://link.springer.com/10.1007/s00239-012-9504-5},
	doi = {10/f23j7s},
	language = {en},
	number = {5-6},
	urldate = {2021-06-08},
	journal = {Journal of Molecular Evolution},
	author = {Ismail, Mohamed and Soolanayakanahally, Raju Y. and Ingvarsson, Pär K. and Guy, Robert D. and Jansson, Stefan and Silim, Salim N. and El-Kassaby, Yousry A.},
	month = jun,
	year = {2012},
	pages = {257--272},
}

@article{robinson_genetic_2012,
	title = {Genetic {Variation} in {Functional} {Traits} {Influences} {Arthropod} {Community} {Composition} in {Aspen} ({Populus} tremula {L}.)},
	volume = {7},
	issn = {1932-6203},
	url = {https://dx.plos.org/10.1371/journal.pone.0037679},
	doi = {10/f24ksj},
	language = {en},
	number = {5},
	urldate = {2021-06-08},
	journal = {PLoS ONE},
	author = {Robinson, Kathryn M. and Ingvarsson, Pär K. and Jansson, Stefan and Albrectsen, Benedicte R.},
	editor = {Kliebenstein, Daniel J.},
	month = may,
	year = {2012},
	pages = {e37679},
}

@incollection{dunwell_how_2012,
	address = {Totowa, NJ},
	title = {How to {Grow} {Transgenic} {Arabidopsis} in the {Field}},
	volume = {847},
	isbn = {978-1-61779-557-2 978-1-61779-558-9},
	url = {http://link.springer.com/10.1007/978-1-61779-558-9_37},
	doi = {10.1007/978-1-61779-558-9_37},
	urldate = {2021-06-08},
	booktitle = {Transgenic {Plants}},
	publisher = {Humana Press},
	author = {Jänkänpää, Hanna Johansson and Jansson, Stefan},
	editor = {Dunwell, Jim M. and Wetten, Andy C.},
	year = {2012},
	note = {Series Title: Methods in Molecular Biology},
	pages = {483--494},
}

@article{jankanpaa_metabolic_2012,
	title = {Metabolic profiling reveals metabolic shifts in {Arabidopsis} plants grown under different light conditions: {Metabolic} profiling under different light regime},
	volume = {35},
	issn = {01407791},
	shorttitle = {Metabolic profiling reveals metabolic shifts in {Arabidopsis} plants grown under different light conditions},
	url = {http://doi.wiley.com/10.1111/j.1365-3040.2012.02519.x},
	doi = {10/f2z77r},
	language = {en},
	number = {10},
	urldate = {2021-06-08},
	journal = {Plant, Cell \& Environment},
	author = {Jänkänpää, Hanna Johansson and Mishra, Yogesh and Schröder, Wolfgang P. and Jansson, Stefan},
	month = oct,
	year = {2012},
	pages = {1824--1836},
}

@article{suorsa_proton_2012,
	title = {{PROTON} {GRADIENT} {REGULATION5} {Is} {Essential} for {Proper} {Acclimation} of {Arabidopsis} {Photosystem} {I} to {Naturally} and {Artificially} {Fluctuating} {Light} {Conditions}},
	volume = {24},
	issn = {1040-4651, 1532-298X},
	url = {https://academic.oup.com/plcell/article/24/7/2934-2948/6100862},
	doi = {10/f242kc},
	language = {en},
	number = {7},
	urldate = {2021-06-08},
	journal = {The Plant Cell},
	author = {Suorsa, Marjaana and Järvi, Sari and Grieco, Michele and Nurmi, Markus and Pietrzykowska, Malgorzata and Rantala, Marjaana and Kangasjärvi, Saijaliisa and Paakkarinen, Virpi and Tikkanen, Mikko and Jansson, Stefan and Aro, Eva-Mari},
	month = jul,
	year = {2012},
	pages = {2934--2948},
}

@article{street_systems_2011,
	title = {A systems biology model of the regulatory network in {Populusleaves} reveals interacting regulators and conserved regulation},
	volume = {11},
	issn = {1471-2229},
	url = {https://doi.org/10.1186/1471-2229-11-13},
	doi = {10/dkhmhb},
	abstract = {Green plant leaves have always fascinated biologists as hosts for photosynthesis and providers of basic energy to many food webs. Today, comprehensive databases of gene expression data enable us to apply increasingly more advanced computational methods for reverse-engineering the regulatory network of leaves, and to begin to understand the gene interactions underlying complex emergent properties related to stress-response and development. These new systems biology methods are now also being applied to organisms such as Populus, a woody perennial tree, in order to understand the specific characteristics of these species.},
	number = {1},
	urldate = {2021-06-08},
	journal = {BMC Plant Biology},
	author = {Street, Nathaniel Robert and Jansson, Stefan and Hvidsten, Torgeir R.},
	month = jan,
	year = {2011},
	keywords = {Biotic Infection, Drought Stress, Nucleosome Assembly, System Biology Model, Transcriptional Module},
	pages = {13},
}

Green plant leaves have always fascinated biologists as hosts for photosynthesis and providers of basic energy to many food webs. Today, comprehensive databases of gene expression data enable us to apply increasingly more advanced computational methods for reverse-engineering the regulatory network of leaves, and to begin to understand the gene interactions underlying complex emergent properties related to stress-response and development. These new systems biology methods are now also being applied to organisms such as Populus, a woody perennial tree, in order to understand the specific characteristics of these species.

@article{mishra_expression_2011,
	title = {Expression, purification, crystallization and preliminary {X}-ray crystallographic studies of alkyl hydroperoxide reductase ({AhpC}) from the cyanobacterium \textit{{Anabaena}} sp. {PCC} 7120},
	volume = {67},
	issn = {1744-3091},
	url = {http://scripts.iucr.org/cgi-bin/paper?S1744309111025747},
	doi = {10/djxscc},
	number = {10},
	urldate = {2021-06-08},
	journal = {Acta Crystallographica Section F Structural Biology and Crystallization Communications},
	author = {Mishra, Yogesh and Hall, Michael and Chaurasia, Neha and Rai, Lal Chand and Jansson, Stefan and Schröder, Wolfgang P. and Sauer, Uwe H.},
	month = oct,
	year = {2011},
	pages = {1203--1206},
}

@article{wagner_fitness_2011,
	title = {Fitness analyses of \textit{{Arabidopsis} thaliana} mutants depleted of {FtsH} metalloproteases and characterization of three {FtsH6} deletion mutants exposed to high light stress, senescence and chilling},
	volume = {191},
	issn = {0028-646X, 1469-8137},
	url = {https://onlinelibrary.wiley.com/doi/10.1111/j.1469-8137.2011.03684.x},
	doi = {10/d4frq4},
	language = {en},
	number = {2},
	urldate = {2021-06-08},
	journal = {New Phytologist},
	author = {Wagner, Raik and Aigner, Harald and Pružinská, Adriana and Jänkänpää, Hanna Johansson and Jansson, Stefan and Funk, Christiane},
	month = jul,
	year = {2011},
	pages = {449--458},
}

@article{albrectsen_endophytic_2010,
	title = {Endophytic fungi in {European} aspen ({Populus} tremula) leaves—diversity, detection, and a suggested correlation with herbivory resistance},
	volume = {41},
	issn = {1560-2745, 1878-9129},
	url = {http://link.springer.com/10.1007/s13225-009-0011-y},
	doi = {10/cg5zgd},
	language = {en},
	number = {1},
	urldate = {2021-06-08},
	journal = {Fungal Diversity},
	author = {Albrectsen, Benedicte R. and Björkén, Lars and Varad, Akkamahadevi and Hagner, Åsa and Wedin, Mats and Karlsson, Jan and Jansson, Stefan},
	month = mar,
	year = {2010},
	pages = {17--28},
}

@article{ma_genetic_2010,
	title = {Genetic {Differentiation}, {Clinal} {Variation} and {Phenotypic} {Associations} {With} {Growth} {Cessation} {Across} the \textit{{Populus} tremula} {Photoperiodic} {Pathway}},
	volume = {186},
	issn = {1943-2631},
	url = {https://academic.oup.com/genetics/article/186/3/1033/6063664},
	doi = {10/c7k7hc},
	abstract = {Abstract
            Perennial plants monitor seasonal changes through changes in environmental conditions such as the quantity and quality of light. To ensure a correct initiation of critical developmental processes, such as the initiation and cessation of growth, plants have adapted to a spatially variable light regime and genes in the photoperiodic pathway have been implicated as likely sources for these adaptations. Here we examine genetic variation in genes from the photoperiodic pathway in Populus tremula (Salicaceae) for signatures diversifying selection in response to varying light regimes across a latitudinal gradient. We fail to identify any loci with unusually high levels of genetic differentiation among populations despite identifying four SNPs that show significant allele frequency clines with latitude. We do, however, observe large covariance in allelic effects across populations for growth cessation, a highly adaptive trait in P. tremula. High covariance in allelic effects is a signature compatible with diversifying selection along an environmental gradient. We also observe significantly higher heterogeneity in genetic differentiation among SNPs from the photoperiod genes than among SNPs from randomly chosen genes. This suggests that spatially variable selection could be affecting genes from the photoperiod pathway even if selection is not strong enough to cause individual loci to be identified as outliers. SNPs from three genes in the photoperiod pathway (PHYB2, LHY1, and LHY2) show significant associations with natural variation in growth cessation. Collectively these SNPs explain 10–15\% of the phenotypic variation in growth cessation. Covariances in allelic effects across populations help explain an additional 5–7\% of the phenotypic variation in growth cessation.},
	language = {en},
	number = {3},
	urldate = {2021-06-08},
	journal = {Genetics},
	author = {Ma, Xiao-Fei and Hall, David and Onge, Katherine R St and Jansson, Stefan and Ingvarsson, Pär K},
	month = nov,
	year = {2010},
	pages = {1033--1044},
}

Abstract Perennial plants monitor seasonal changes through changes in environmental conditions such as the quantity and quality of light. To ensure a correct initiation of critical developmental processes, such as the initiation and cessation of growth, plants have adapted to a spatially variable light regime and genes in the photoperiodic pathway have been implicated as likely sources for these adaptations. Here we examine genetic variation in genes from the photoperiodic pathway in Populus tremula (Salicaceae) for signatures diversifying selection in response to varying light regimes across a latitudinal gradient. We fail to identify any loci with unusually high levels of genetic differentiation among populations despite identifying four SNPs that show significant allele frequency clines with latitude. We do, however, observe large covariance in allelic effects across populations for growth cessation, a highly adaptive trait in P. tremula. High covariance in allelic effects is a signature compatible with diversifying selection along an environmental gradient. We also observe significantly higher heterogeneity in genetic differentiation among SNPs from the photoperiod genes than among SNPs from randomly chosen genes. This suggests that spatially variable selection could be affecting genes from the photoperiod pathway even if selection is not strong enough to cause individual loci to be identified as outliers. SNPs from three genes in the photoperiod pathway (PHYB2, LHY1, and LHY2) show significant associations with natural variation in growth cessation. Collectively these SNPs explain 10–15% of the phenotypic variation in growth cessation. Covariances in allelic effects across populations help explain an additional 5–7% of the phenotypic variation in growth cessation.

@article{courtois-moreau_unique_2009,
	title = {A unique program for cell death in xylem fibers of \textit{{Populus}} stem},
	volume = {58},
	issn = {09607412, 1365313X},
	url = {http://doi.wiley.com/10.1111/j.1365-313X.2008.03777.x},
	doi = {10/bqdrgm},
	language = {en},
	number = {2},
	urldate = {2021-06-08},
	journal = {The Plant Journal},
	author = {Courtois-Moreau, Charleen L. and Pesquet, Edouard and Sjödin, Andreas and Muñiz, Luis and Bollhöner, Benjamin and Kaneda, Minako and Samuels, Lacey and Jansson, Stefan and Tuominen, Hannele},
	month = apr,
	year = {2009},
	pages = {260--274},
}

@article{garcia-cerdan_antisense_2009,
	title = {Antisense {Inhibition} of the {PsbX} {Protein} {Affects} {PSII} {Integrity} in the {Higher} {Plant} {Arabidopsis} thaliana},
	volume = {50},
	issn = {1471-9053, 0032-0781},
	url = {https://academic.oup.com/pcp/article-lookup/doi/10.1093/pcp/pcn188},
	doi = {10/fbkmdx},
	language = {en},
	number = {2},
	urldate = {2021-06-08},
	journal = {Plant and Cell Physiology},
	author = {García-Cerdán, José G. and Sveshnikov, Dmitry and Dewez, David and Jansson, Stefan and Funk, Christiane and Schröder, Wolfgang P.},
	month = feb,
	year = {2009},
	pages = {191--202},
}

@article{klevebring_genome-wide_2009,
	title = {Genome-wide profiling of populus small {RNAs}},
	volume = {10},
	issn = {1471-2164},
	doi = {10/d7t35k},
	abstract = {BACKGROUND: Short RNAs, and in particular microRNAs, are important regulators of gene expression both within defined regulatory pathways and at the epigenetic scale. We investigated the short RNA (sRNA) population (18-24 nt) of the transcriptome of green leaves from the sequenced Populus trichocarpa using a concatenation strategy in combination with 454 sequencing.
RESULTS: The most abundant size class of sRNAs were 24 nt. Long Terminal Repeats were particularly associated with 24 nt sRNAs. Additionally, some repetitive elements were associated with 22 nt sRNAs. We identified an sRNA hot-spot on chromosome 19, overlapping a region containing both the proposed sex-determining locus and a major cluster of NBS-LRR genes. A number of phased siRNA loci were identified, a subset of which are predicted to target PPR and NBS-LRR disease resistance genes, classes of genes that have been significantly expanded in Populus. Additional loci enriched for sRNA production were identified and characterised. We identified 15 novel predicted microRNAs (miRNAs), including miRNA*sequences, and identified a novel locus that may encode a dual miRNA or a miRNA and short interfering RNAs (siRNAs).
CONCLUSIONS: The short RNA population of P. trichocarpa is at least as complex as that of Arabidopsis thaliana. We provide a first genome-wide view of short RNA production for P. trichocarpa and identify new, non-conserved miRNAs.},
	language = {eng},
	journal = {BMC genomics},
	author = {Klevebring, Daniel and Street, Nathaniel R. and Fahlgren, Noah and Kasschau, Kristin D. and Carrington, James C. and Lundeberg, Joakim and Jansson, Stefan},
	month = dec,
	year = {2009},
	keywords = {Chromosomes, Plant, Genome, Plant, Genome-Wide Association Study, MicroRNAs, Plant Leaves, Populus, RNA, Plant, RNA, Small Interfering},
	pages = {620},
}

BACKGROUND: Short RNAs, and in particular microRNAs, are important regulators of gene expression both within defined regulatory pathways and at the epigenetic scale. We investigated the short RNA (sRNA) population (18-24 nt) of the transcriptome of green leaves from the sequenced Populus trichocarpa using a concatenation strategy in combination with 454 sequencing. RESULTS: The most abundant size class of sRNAs were 24 nt. Long Terminal Repeats were particularly associated with 24 nt sRNAs. Additionally, some repetitive elements were associated with 22 nt sRNAs. We identified an sRNA hot-spot on chromosome 19, overlapping a region containing both the proposed sex-determining locus and a major cluster of NBS-LRR genes. A number of phased siRNA loci were identified, a subset of which are predicted to target PPR and NBS-LRR disease resistance genes, classes of genes that have been significantly expanded in Populus. Additional loci enriched for sRNA production were identified and characterised. We identified 15 novel predicted microRNAs (miRNAs), including miRNA*sequences, and identified a novel locus that may encode a dual miRNA or a miRNA and short interfering RNAs (siRNAs). CONCLUSIONS: The short RNA population of P. trichocarpa is at least as complex as that of Arabidopsis thaliana. We provide a first genome-wide view of short RNA production for P. trichocarpa and identify new, non-conserved miRNAs.

@article{frenkel_improper_2009,
	title = {Improper excess light energy dissipation in {Arabidopsis} results in a metabolic reprogramming},
	volume = {9},
	issn = {1471-2229},
	url = {https://doi.org/10.1186/1471-2229-9-12},
	doi = {10/ffdbr8},
	abstract = {Plant performance is affected by the level of expression of PsbS, a key photoprotective protein involved in the process of feedback de-excitation (FDE), or the qE component of non-photochemical quenching, NPQ.},
	number = {1},
	urldate = {2021-06-08},
	journal = {BMC Plant Biology},
	author = {Frenkel, Martin and Külheim, Carsten and Jänkänpää, Hanna Johansson and Skogström, Oskar and Dall'Osto, Luca and Ågren, Jon and Bassi, Roberto and Moritz, Thomas and Moen, Jon and Jansson, Stefan},
	month = jan,
	year = {2009},
	keywords = {Herbivore Preference, Partial Little Square Discriminant Analysis, Partial Little Square Discriminant Analysis Model, Photooxidative Stress, Photosynthetic Light Reaction},
	pages = {12},
}

Plant performance is affected by the level of expression of PsbS, a key photoprotective protein involved in the process of feedback de-excitation (FDE), or the qE component of non-photochemical quenching, NPQ.

@article{bylesjo_integrated_2009,
	title = {Integrated {Analysis} of {Transcript}, {Protein} and {Metabolite} {Data} {To} {Study} {Lignin} {Biosynthesis} in {Hybrid} {Aspen}},
	volume = {8},
	issn = {1535-3893, 1535-3907},
	url = {https://pubs.acs.org/doi/10.1021/pr800298s},
	doi = {10/ddqkpn},
	language = {en},
	number = {1},
	urldate = {2021-06-08},
	journal = {Journal of Proteome Research},
	author = {Bylesjö, Max and Nilsson, Robert and Srivastava, Vaibhav and Grönlund, Andreas and Johansson, Annika I. and Jansson, Stefan and Karlsson, Jan and Moritz, Thomas and Wingsle, Gunnar and Trygg, Johan},
	month = jan,
	year = {2009},
	pages = {199--210},
}

@article{albrectsen_large_2009,
	title = {Large scale geographic clines of parasite damage to \textit{{Populus} tremula} {L}},
	issn = {09067590, 16000587},
	url = {http://doi.wiley.com/10.1111/j.1600-0587.2009.05982.x},
	doi = {10/c38874},
	language = {en},
	urldate = {2021-06-08},
	journal = {Ecography},
	author = {Albrectsen, Benedicte R. and Witzell, Johanna and Robinson, Kathryn M. and Wulff, Sören and Luquez, Virginia M. C. and Ågren, Rickard and Jansson, Stefan},
	month = oct,
	year = {2009},
}

@article{babst_local_2009,
	title = {Local and systemic transcriptome responses to herbivory and jasmonic acid in {Populus}},
	volume = {5},
	issn = {1614-2942, 1614-2950},
	url = {http://link.springer.com/10.1007/s11295-009-0200-6},
	doi = {10/fmhhv9},
	language = {en},
	number = {3},
	urldate = {2021-06-08},
	journal = {Tree Genetics \& Genomes},
	author = {Babst, Benjamin A. and Sjödin, Andreas and Jansson, Stefan and Orians, Colin M.},
	month = jul,
	year = {2009},
	pages = {459--474},
}

@article{sjodin_populus_2009,
	title = {The \textit{{Populus}} {Genome} {Integrative} {Explorer} ({PopGenIE}): a new resource for exploring the \textit{{Populus}} genome},
	volume = {182},
	issn = {0028-646X, 1469-8137},
	shorttitle = {The \textit{{Populus}} {Genome} {Integrative} {Explorer} ({PopGenIE})},
	url = {https://onlinelibrary.wiley.com/doi/10.1111/j.1469-8137.2009.02807.x},
	doi = {10/bwmrwk},
	language = {en},
	number = {4},
	urldate = {2021-06-08},
	journal = {New Phytologist},
	author = {Sjödin, Andreas and Street, Nathaniel Robert and Sandberg, Göran and Gustafsson, Petter and Jansson, Stefan},
	month = jun,
	year = {2009},
	pages = {1013--1025},
}

@article{fracheboud_control_2009,
	title = {The {Control} of {Autumn} {Senescence} in {European} {Aspen}},
	volume = {149},
	issn = {1532-2548},
	url = {https://academic.oup.com/plphys/article/149/4/1982/6107938},
	doi = {10/b8n86h},
	abstract = {Abstract
            The initiation, progression, and natural variation of autumn senescence in European aspen (Populus tremula) was investigated by monitoring chlorophyll degradation in (1) trees growing in natural stands and (2) cloned trees growing in a greenhouse under various light regimes. The main trigger for the initiation of autumn senescence in aspen is the shortening photoperiod, but there was a large degree of variation in the onset of senescence, both within local populations and among trees originating from different populations, where it correlated with the latitude of their respective origins. The variation for onset of senescence with a population was much larger than the variation of bud set. Once started, autumn senescence was accelerated by low temperature and longer nights, and clones that started to senescence late had a faster senescence. Bud set and autumn senescence appeared to be under the control of two independent critical photoperiods, but senescence could not be initiated until a certain time after bud set, suggesting that bud set and growth arrest are important for the trees to acquire competence to respond to the photoperiodic trigger to undergo autumn senescence. A timetable of events related to bud set and autumn senescence is presented.},
	language = {en},
	number = {4},
	urldate = {2021-06-08},
	journal = {Plant Physiology},
	author = {Fracheboud, Yvan and Luquez, Virginia and Björkén, Lars and Sjödin, Andreas and Tuominen, Hannele and Jansson, Stefan},
	month = apr,
	year = {2009},
	pages = {1982--1991},
}

Abstract The initiation, progression, and natural variation of autumn senescence in European aspen (Populus tremula) was investigated by monitoring chlorophyll degradation in (1) trees growing in natural stands and (2) cloned trees growing in a greenhouse under various light regimes. The main trigger for the initiation of autumn senescence in aspen is the shortening photoperiod, but there was a large degree of variation in the onset of senescence, both within local populations and among trees originating from different populations, where it correlated with the latitude of their respective origins. The variation for onset of senescence with a population was much larger than the variation of bud set. Once started, autumn senescence was accelerated by low temperature and longer nights, and clones that started to senescence late had a faster senescence. Bud set and autumn senescence appeared to be under the control of two independent critical photoperiods, but senescence could not be initiated until a certain time after bud set, suggesting that bud set and growth arrest are important for the trees to acquire competence to respond to the photoperiodic trigger to undergo autumn senescence. A timetable of events related to bud set and autumn senescence is presented.

@article{damkjaer_photosystem_2009,
	title = {The {Photosystem} {II} {Light}-{Harvesting} {Protein} {Lhcb3} {Affects} the {Macrostructure} of {Photosystem} {II} and the {Rate} of {State} {Transitions} in \textit{{Arabidopsis}}},
	volume = {21},
	issn = {1532-298X, 1040-4651},
	url = {https://academic.oup.com/plcell/article/21/10/3245/6096237},
	doi = {10/fb96fz},
	abstract = {Abstract
            The main trimeric light-harvesting complex of higher plants (LHCII) consists of three different Lhcb proteins (Lhcb1-3). We show that Arabidopsis thaliana T-DNA knockout plants lacking Lhcb3 (koLhcb3) compensate for the lack of Lhcb3 by producing increased amounts of Lhcb1 and Lhcb2. As in wild-type plants, LHCII-photosystem II (PSII) supercomplexes were present in Lhcb3 knockout plants (koLhcb3), and preservation of the LHCII trimers (M trimers) indicates that the Lhcb3 in M trimers has been replaced by Lhcb1 and/or Lhcb2. However, the rotational position of the M LHCII trimer was altered, suggesting that the Lhcb3 subunit affects the macrostructural arrangement of the LHCII antenna. The absence of Lhcb3 did not result in any significant alteration in PSII efficiency or qE type of nonphotochemical quenching, but the rate of transition from State 1 to State 2 was increased in koLhcb3, although the final extent of state transition was unchanged. The level of phosphorylation of LHCII was increased in the koLhcb3 plants compared with wild-type plants in both State 1 and State 2. The relative increase in phosphorylation upon transition from State 1 to State 2 was also significantly higher in koLhcb3. It is suggested that the main function of Lhcb3 is to modulate the rate of state transitions.},
	language = {en},
	number = {10},
	urldate = {2021-06-08},
	journal = {The Plant Cell},
	author = {Damkjær, Jakob T. and Kereïche, Sami and Johnson, Matthew P. and Kovacs, Laszlo and Kiss, Anett Z. and Boekema, Egbert J. and Ruban, Alexander V. and Horton, Peter and Jansson, Stefan},
	month = dec,
	year = {2009},
	pages = {3245--3256},
}

Abstract The main trimeric light-harvesting complex of higher plants (LHCII) consists of three different Lhcb proteins (Lhcb1-3). We show that Arabidopsis thaliana T-DNA knockout plants lacking Lhcb3 (koLhcb3) compensate for the lack of Lhcb3 by producing increased amounts of Lhcb1 and Lhcb2. As in wild-type plants, LHCII-photosystem II (PSII) supercomplexes were present in Lhcb3 knockout plants (koLhcb3), and preservation of the LHCII trimers (M trimers) indicates that the Lhcb3 in M trimers has been replaced by Lhcb1 and/or Lhcb2. However, the rotational position of the M LHCII trimer was altered, suggesting that the Lhcb3 subunit affects the macrostructural arrangement of the LHCII antenna. The absence of Lhcb3 did not result in any significant alteration in PSII efficiency or qE type of nonphotochemical quenching, but the rate of transition from State 1 to State 2 was increased in koLhcb3, although the final extent of state transition was unchanged. The level of phosphorylation of LHCII was increased in the koLhcb3 plants compared with wild-type plants in both State 1 and State 2. The relative increase in phosphorylation upon transition from State 1 to State 2 was also significantly higher in koLhcb3. It is suggested that the main function of Lhcb3 is to modulate the rate of state transitions.

@article{wientjes_role_2009,
	title = {The {Role} of {Lhca} {Complexes} in the {Supramolecular} {Organization} of {Higher} {Plant} {Photosystem} {I}},
	volume = {284},
	issn = {00219258},
	url = {https://linkinghub.elsevier.com/retrieve/pii/S0021925820324923},
	doi = {10/bpvfwk},
	language = {en},
	number = {12},
	urldate = {2021-06-08},
	journal = {Journal of Biological Chemistry},
	author = {Wientjes, Emilie and Oostergetel, Gert T. and Jansson, Stefan and Boekema, Egbert J. and Croce, Roberta},
	month = mar,
	year = {2009},
	pages = {7803--7810},
}

@article{street_cross-species_2008,
	title = {A cross-species transcriptomics approach to identify genes involved in leaf development},
	volume = {9},
	issn = {1471-2164},
	url = {http://bmcgenomics.biomedcentral.com/articles/10.1186/1471-2164-9-589},
	doi = {10/d5c8qb},
	language = {en},
	number = {1},
	urldate = {2021-06-10},
	journal = {BMC Genomics},
	author = {Street, Nathaniel and Sjödin, Andreas and Bylesjö, Max and Gustafsson, Petter and Trygg, Johan and Jansson, Stefan},
	year = {2008},
	pages = {589},
}

@article{frenkel_illustrated_2008,
	title = {An illustrated gardener's guide to transgenic \textit{{Arabidopsis}} field experiments},
	volume = {180},
	issn = {0028-646X, 1469-8137},
	url = {https://onlinelibrary.wiley.com/doi/10.1111/j.1469-8137.2008.02591.x},
	doi = {10/ds43gk},
	language = {en},
	number = {2},
	urldate = {2021-06-10},
	journal = {New Phytologist},
	author = {Frenkel, Martin and Johansson Jänkänpää, Hanna and Moen, Jon and Jansson, Stefan},
	month = oct,
	year = {2008},
	pages = {545--555},
}

@article{sjodin_global_2008,
	title = {Global expression profiling in leaves of free-growing aspen},
	volume = {8},
	issn = {1471-2229},
	url = {http://bmcplantbiol.biomedcentral.com/articles/10.1186/1471-2229-8-61},
	doi = {10/dsf6k8},
	language = {en},
	number = {1},
	urldate = {2021-06-10},
	journal = {BMC Plant Biology},
	author = {Sjodin, Andreas and Wissel, Kirsten and Bylesjo, Max and Trygg, Johan and Jansson, Stefan},
	year = {2008},
	pages = {61},
}

@article{bylesjo_lamina_2008,
	title = {{LAMINA}: a tool for rapid quantification of leaf size and shape parameters},
	volume = {8},
	issn = {1471-2229},
	shorttitle = {{LAMINA}},
	url = {http://bmcplantbiol.biomedcentral.com/articles/10.1186/1471-2229-8-82},
	doi = {10/dg9gsg},
	language = {en},
	number = {1},
	urldate = {2021-06-10},
	journal = {BMC Plant Biology},
	author = {Bylesjö, Max and Segura, Vincent and Soolanayakanahally, Raju Y and Rae, Anne M and Trygg, Johan and Gustafsson, Petter and Jansson, Stefan and Street, Nathaniel R},
	year = {2008},
	pages = {82},
}

@article{luquez_natural_2008,
	title = {Natural phenological variation in aspen ({Populus} tremula): the {SwAsp} collection},
	volume = {4},
	issn = {1614-2942, 1614-2950},
	shorttitle = {Natural phenological variation in aspen ({Populus} tremula)},
	url = {http://link.springer.com/10.1007/s11295-007-0108-y},
	doi = {10/bwk27s},
	language = {en},
	number = {2},
	urldate = {2021-06-10},
	journal = {Tree Genetics \& Genomes},
	author = {Luquez, Virginia and Hall, David and Albrectsen, Benedicte R. and Karlsson, Jan and Ingvarsson, Pär and Jansson, Stefan},
	month = apr,
	year = {2008},
	pages = {279--292},
}

@article{ingvarsson_nucleotide_2008,
	title = {Nucleotide {Polymorphism} and {Phenotypic} {Associations} {Within} and {Around} the \textit{phytochrome {B2}} {Locus} in {European} {Aspen} ( \textit{{Populus} tremula} , {Salicaceae})},
	volume = {178},
	issn = {1943-2631},
	url = {https://academic.oup.com/genetics/article/178/4/2217/6073872},
	doi = {10/bd8hh3},
	abstract = {Abstract
            We investigated the utility of association mapping to dissect the genetic basis of naturally occurring variation in bud phenology in European aspen (Populus tremula). With this aim, we surveyed nucleotide polymorphism in 13 fragments spanning an 80-kb region surrounding the phytochrome B2 (phyB2) locus. Although polymorphism varies substantially across the phyB2 region, we detected no signs for deviations from neutral expectations. We also identified a total of 41 single nucleotide polymorphisms (SNPs) that were subsequently scored in a mapping population consisting of 120 trees. We identified two nonsynonymous SNPs in the phytochrome B2 gene that were independently associated with variation in the timing of bud set and that explained between 1.5 and 5\% of the observed phenotypic variation in bud set. Earlier studies have shown that the frequencies of both these SNPs vary clinally with latitude. Linkage disequilibrium across the region was low, suggesting that the SNPs we identified are strong candidates for being causally linked to variation in bud set in our mapping populations. One of the SNPs (T608N) is located in the “hinge region,” close to the chromophore binding site of the phyB2 protein. The other SNP (L1078P) is located in a region supposed to mediate downstream signaling from the phyB2 locus. The lack of population structure, combined with low levels of linkage disequilibrium, suggests that association mapping is a fruitful method for dissecting naturally occurring variation in Populus tremula.},
	language = {en},
	number = {4},
	urldate = {2021-06-10},
	journal = {Genetics},
	author = {Ingvarsson, Pär K and Garcia, M Victoria and Luquez, Virginia and Hall, David and Jansson, Stefan},
	month = apr,
	year = {2008},
	pages = {2217--2226},
}

Abstract We investigated the utility of association mapping to dissect the genetic basis of naturally occurring variation in bud phenology in European aspen (Populus tremula). With this aim, we surveyed nucleotide polymorphism in 13 fragments spanning an 80-kb region surrounding the phytochrome B2 (phyB2) locus. Although polymorphism varies substantially across the phyB2 region, we detected no signs for deviations from neutral expectations. We also identified a total of 41 single nucleotide polymorphisms (SNPs) that were subsequently scored in a mapping population consisting of 120 trees. We identified two nonsynonymous SNPs in the phytochrome B2 gene that were independently associated with variation in the timing of bud set and that explained between 1.5 and 5% of the observed phenotypic variation in bud set. Earlier studies have shown that the frequencies of both these SNPs vary clinally with latitude. Linkage disequilibrium across the region was low, suggesting that the SNPs we identified are strong candidates for being causally linked to variation in bud set in our mapping populations. One of the SNPs (T608N) is located in the “hinge region,” close to the chromophore binding site of the phyB2 protein. The other SNP (L1078P) is located in a region supposed to mediate downstream signaling from the phyB2 locus. The lack of population structure, combined with low levels of linkage disequilibrium, suggests that association mapping is a fruitful method for dissecting naturally occurring variation in Populus tremula.

@article{jansson_senescence_2008,
	title = {Senescence: developmental program or timetable?},
	volume = {179},
	issn = {0028-646X, 1469-8137},
	shorttitle = {Senescence},
	url = {https://onlinelibrary.wiley.com/doi/10.1111/j.1469-8137.2008.02471.x},
	doi = {10/drc9xn},
	language = {en},
	number = {3},
	urldate = {2021-06-10},
	journal = {New Phytologist},
	author = {Jansson, Stefan and Thomas, Howard},
	month = aug,
	year = {2008},
	pages = {575--579},
}

@article{hall_adaptive_2007,
	title = {Adaptive {Population} {Differentiation} in {Phenology} across a {Latitudinal} {Gradient} in {European} {Aspen} ({Populus} tremula, {L}.): {A} {Comparison} of {Neutral} {Markers}, {Candidate} {Genes} and {Phenotypic} {Traits}},
	volume = {61},
	issn = {0014-3820, 1558-5646},
	shorttitle = {Adaptive {Population} {Differentiation} in {Phenology} across a {Latitudinal} {Gradient} in {European} {Aspen} ({Populus} tremula, {L}.)},
	url = {http://doi.wiley.com/10.1111/j.1558-5646.2007.00230.x},
	doi = {10/bv9gz6},
	language = {en},
	number = {12},
	urldate = {2021-06-10},
	journal = {Evolution},
	author = {Hall, David and Luquez, Virginia and Garcia, Victoria M. and St Onge, Kate R. and Jansson, Stefan and Ingvarsson, Pär K.},
	month = dec,
	year = {2007},
	pages = {2849--2860},
}

@article{segerman_characterization_2007,
	title = {Characterization of genes with tissue-specific differential expression patterns in {Populus}},
	volume = {3},
	issn = {1614-2942, 1614-2950},
	url = {http://link.springer.com/10.1007/s11295-006-0077-6},
	doi = {10/ct8snb},
	language = {en},
	number = {4},
	urldate = {2021-06-10},
	journal = {Tree Genetics \& Genomes},
	author = {Segerman, Bo and Jansson, Stefan and Karlsson, Jan},
	month = aug,
	year = {2007},
	pages = {351--362},
}

@article{lee_growth-phase-dependent_2007,
	title = {Growth-phase-dependent gene expression profiling of poplar ({Populus} alba × {Populus} tremula var. glandulosa) suspension cells},
	volume = {131},
	issn = {0031-9317, 1399-3054},
	url = {http://doi.wiley.com/10.1111/j.1399-3054.2007.00987.x},
	doi = {10/b8dzcg},
	language = {en},
	number = {4},
	urldate = {2021-06-10},
	journal = {Physiologia Plantarum},
	author = {Lee, Hyoshin and Bae, Eun-Kyung and Park, So-Young and Sjödin, Andreas and Lee, Jae-Soon and Noh, Eun-Woon and Jansson, Stefan},
	month = dec,
	year = {2007},
	pages = {599--613},
}

@article{frenkel_hierarchy_2007,
	title = {Hierarchy amongst photosynthetic acclimation responses for plant fitness},
	volume = {129},
	issn = {1399-3054},
	url = {https://onlinelibrary.wiley.com/doi/abs/10.1111/j.1399-3054.2006.00831.x},
	doi = {10.1111/j.1399-3054.2006.00831.x},
	abstract = {We have compared the seed production of Arabidopsis wild-type and mutant plants impaired in the regulation of the photosynthetic light reactions grown under natural conditions in the field. Mutant plants (npq4) lacking feedback de-excitation were, as previously demonstrated, severely affected in seed production. Seed sets of plants deficient in state transitions (stn7) were 19\% smaller than those of wild-type plants, whereas plants missing the STN8 kinase required for the phosphorylation of the core photosystem II reaction centre polypeptides (stn8) had a normal seed production. Plants lacking both STN7 and STN8 kinases were strongly affected, indicating that these mutations act synergistically. In contrast, npq4×stn7 double mutants had the same seed set as npq4 mutants.},
	language = {en},
	number = {2},
	urldate = {2024-06-28},
	journal = {Physiologia Plantarum},
	author = {Frenkel, Martin and Bellafiore, Stephane and Rochaix, Jean-David and Jansson, Stefan},
	year = {2007},
	note = {\_eprint: https://onlinelibrary.wiley.com/doi/pdf/10.1111/j.1399-3054.2006.00831.x},
	pages = {455--459},
}

We have compared the seed production of Arabidopsis wild-type and mutant plants impaired in the regulation of the photosynthetic light reactions grown under natural conditions in the field. Mutant plants (npq4) lacking feedback de-excitation were, as previously demonstrated, severely affected in seed production. Seed sets of plants deficient in state transitions (stn7) were 19% smaller than those of wild-type plants, whereas plants missing the STN8 kinase required for the phosphorylation of the core photosystem II reaction centre polypeptides (stn8) had a normal seed production. Plants lacking both STN7 and STN8 kinases were strongly affected, indicating that these mutations act synergistically. In contrast, npq4×stn7 double mutants had the same seed set as npq4 mutants.

@article{bylesjo_orthogonal_2007,
	title = {Orthogonal projections to latent structures as a strategy for microarray data normalization},
	volume = {8},
	issn = {1471-2105},
	url = {https://bmcbioinformatics.biomedcentral.com/articles/10.1186/1471-2105-8-207},
	doi = {10/dfs78z},
	language = {en},
	number = {1},
	urldate = {2021-06-10},
	journal = {BMC Bioinformatics},
	author = {Bylesjö, Max and Eriksson, Daniel and Sjödin, Andreas and Jansson, Stefan and Moritz, Thomas and Trygg, Johan},
	month = dec,
	year = {2007},
	pages = {207},
}

@article{jansson_populus_2007,
	title = {Populus: {A} {Model} {System} for {Plant} {Biology}},
	volume = {58},
	issn = {1543-5008},
	shorttitle = {Populus},
	url = {https://www.annualreviews.org/doi/10.1146/annurev.arplant.58.032806.103956},
	doi = {10/d42zfw},
	abstract = {With the completion of the Populus trichocarpa genome sequence and the development of various genetic, genomic, and biochemical tools, Populus now offers many possibilities to study questions that cannot be as easily addressed in Arabidopsis and rice, the two prime model systems of plant biology and genomics. Tree-specific traits such as wood formation, long-term perennial growth, and seasonality are obvious areas of research, but research in other areas such as control of flowering, biotic interactions, and evolution of adaptive traits is enriched by adding a tree to the suite of model systems. Furthermore, the reproductive biology of Populus (a dioeceous wind-pollinated long-lived tree) offers both new possibilities and challenges in the study and analysis of natural genetic and phenotypic variation. The relatively close phylogenetic relationship of Populus to Arabidopsis in the Eurosid clade of Eudicotyledonous plants aids in comparative functional studies and comparative genomics, and has the potential to greatly facilitate studies on genome and gene family evolution in eudicots.},
	number = {1},
	urldate = {2021-06-21},
	journal = {Annual Review of Plant Biology},
	publisher = {Annual Reviews},
	author = {Jansson, Stefan and Douglas, Carl J.},
	month = jun,
	year = {2007},
	pages = {435--458},
}

With the completion of the Populus trichocarpa genome sequence and the development of various genetic, genomic, and biochemical tools, Populus now offers many possibilities to study questions that cannot be as easily addressed in Arabidopsis and rice, the two prime model systems of plant biology and genomics. Tree-specific traits such as wood formation, long-term perennial growth, and seasonality are obvious areas of research, but research in other areas such as control of flowering, biotic interactions, and evolution of adaptive traits is enriched by adding a tree to the suite of model systems. Furthermore, the reproductive biology of Populus (a dioeceous wind-pollinated long-lived tree) offers both new possibilities and challenges in the study and analysis of natural genetic and phenotypic variation. The relatively close phylogenetic relationship of Populus to Arabidopsis in the Eurosid clade of Eudicotyledonous plants aids in comparative functional studies and comparative genomics, and has the potential to greatly facilitate studies on genome and gene family evolution in eudicots.

@article{jensen_structure_2007,
	title = {Structure, function and regulation of plant photosystem {I}},
	volume = {1767},
	issn = {00052728},
	url = {https://linkinghub.elsevier.com/retrieve/pii/S0005272807000722},
	doi = {10/fdc7p3},
	language = {en},
	number = {5},
	urldate = {2021-06-10},
	journal = {Biochimica et Biophysica Acta (BBA) - Bioenergetics},
	author = {Jensen, Poul Erik and Bassi, Roberto and Boekema, Egbert J. and Dekker, Jan P. and Jansson, Stefan and Leister, Dario and Robinson, Colin and Scheller, Henrik Vibe},
	month = may,
	year = {2007},
	pages = {335--352},
}

@article{klimmek_abundantly_2006,
	title = {Abundantly and rarely expressed {Lhc} protein genes exhibit distinct regulation patterns in plants},
	volume = {140},
	issn = {0032-0889},
	doi = {10/fbrp2z},
	abstract = {We have analyzed gene regulation of the Lhc supergene family in poplar ( Populus spp.) and Arabidopsis ( Arabidopsis thaliana) using digital expression profiling. Multivariate analysis of the tissue-specific, environmental, and developmental Lhc expression patterns in Arabidopsis and poplar was employed to characterize four rarely expressed Lhc genes, Lhca5, Lhca6, Lhcb7, and Lhcb4.3. Those genes have high expression levels under different conditions and in different tissues than the abundantly expressed Lhca1 to 4 and Lhcb1 to 6 genes that code for the 10 major types of higher plant light-harvesting proteins. However, in some of the datasets analyzed, the Lhcb4 and Lhcb6 genes as well as an Arabidopsis gene not present in poplar ( Lhcb2.3) exhibited minor differences to the main cooperative Lhc gene expression pattern. The pattern of the rarely expressed Lhc genes was always found to be more similar to that of PsbS and the various light-harvesting- like genes, which might indicate distinct physiological functions for the rarely and abundantly expressed Lhc proteins. The previously undetected Lhcb7 gene encodes a novel plant Lhcb-type protein that possibly contains an additional, fourth, transmembrane N-terminal helix with a highly conserved motif. As the Lhcb4.3 gene seems to be present only in Eurosid species and as its regulation pattern varies significantly from that of Lhcb4.1 and Lhcb4.2, we conclude it to encode a distinct Lhc protein type, Lhcb8.},
	language = {English},
	number = {3},
	journal = {Plant Physiology},
	publisher = {Amer Soc Plant Biologists},
	author = {Klimmek, F. and Sjodin, A. and Noutsos, C. and Leister, D. and Jansson, S.},
	month = mar,
	year = {2006},
	note = {Place: Rockville
WOS:000235868900001},
	keywords = {a/b-binding proteins, arabidopsis, chloroplast transit   peptides, draft sequence, energy-dissipation, light-harvesting-complex, membrane-proteins, photosystem-ii, pigment-binding, posttranscriptional   mechanisms},
	pages = {793--804},
}

We have analyzed gene regulation of the Lhc supergene family in poplar ( Populus spp.) and Arabidopsis ( Arabidopsis thaliana) using digital expression profiling. Multivariate analysis of the tissue-specific, environmental, and developmental Lhc expression patterns in Arabidopsis and poplar was employed to characterize four rarely expressed Lhc genes, Lhca5, Lhca6, Lhcb7, and Lhcb4.3. Those genes have high expression levels under different conditions and in different tissues than the abundantly expressed Lhca1 to 4 and Lhcb1 to 6 genes that code for the 10 major types of higher plant light-harvesting proteins. However, in some of the datasets analyzed, the Lhcb4 and Lhcb6 genes as well as an Arabidopsis gene not present in poplar ( Lhcb2.3) exhibited minor differences to the main cooperative Lhc gene expression pattern. The pattern of the rarely expressed Lhc genes was always found to be more similar to that of PsbS and the various light-harvesting- like genes, which might indicate distinct physiological functions for the rarely and abundantly expressed Lhc proteins. The previously undetected Lhcb7 gene encodes a novel plant Lhcb-type protein that possibly contains an additional, fourth, transmembrane N-terminal helix with a highly conserved motif. As the Lhcb4.3 gene seems to be present only in Eurosid species and as its regulation pattern varies significantly from that of Lhcb4.1 and Lhcb4.2, we conclude it to encode a distinct Lhc protein type, Lhcb8.

@article{bohlenius_coft_2006,
	title = {{CO}/{FT} regulatory module controls timing of flowering and seasonal growth cessation in trees},
	volume = {312},
	issn = {0036-8075},
	doi = {10/csznqf},
	abstract = {Forest trees display a perennial growth behavior characterized by a multiple-year delay in flowering and, in temperate regions, an annual cycling between growth and dormancy. We show here that the CO/FT regulatory module, which controls flowering time in response to variations in daylength in annual plants, controls flowering in aspen trees. Unexpectedly, however, it also controls the short-day-induced growth cessation and bud set occurring in the fall. This regulatory mechanism can explain the ecogenetic variation in a highly adaptive trait: the critical daylength for growth cessation displayed by aspen trees sampled across a latitudinal gradient spanning northern Europe.},
	language = {English},
	number = {5776},
	journal = {Science},
	publisher = {Amer Assoc Advancement Science},
	author = {Bohlenius, H. and Huang, T. and Charbonnel-Campaa, L. and Brunner, A. M. and Jansson, S. and Strauss, S. H. and Nilsson, O.},
	month = may,
	year = {2006},
	note = {Place: Washington
WOS:000237628800042},
	keywords = {arabidopsis, aspen populus-tremula, black cottonwood, bud set, candidate gene, ft, induction, phytochrome, protein, shoot   apex},
	pages = {1040--1043},
}

Forest trees display a perennial growth behavior characterized by a multiple-year delay in flowering and, in temperate regions, an annual cycling between growth and dormancy. We show here that the CO/FT regulatory module, which controls flowering time in response to variations in daylength in annual plants, controls flowering in aspen trees. Unexpectedly, however, it also controls the short-day-induced growth cessation and bud set occurring in the fall. This regulatory mechanism can explain the ecogenetic variation in a highly adaptive trait: the critical daylength for growth cessation displayed by aspen trees sampled across a latitudinal gradient spanning northern Europe.

@article{ingvarsson_clinal_2006,
	title = {Clinal variation in {phyB2}, a candidate gene for day-length-induced growth cessation and bud set, across a latitudinal gradient in {European} aspen ({Populus} tremula)},
	volume = {172},
	issn = {0016-6731},
	doi = {10.1534/genetics.105.047522},
	abstract = {The initiation of growth cessation and dormancy represents a Critical ecological and evolutionary tradeoff between survival and growth in most. forest trees. The Most important environmental cue regulating the initiation of dormancy is a shortening of the photoperiod and phytochrome genes have been implicated in short-day-induced bud set and growth cessation in Populus. We characterized patterns of DNA sequence variation at the putative candidate gene phyB2 in 4 populations of European aspen (Populus tremula) and scored single-nucleotide polymorphisms in an additional 12 populations collected along a latitudinal gradient in Sweden. We also measured bud set from a subset Of these trees in a growth chamber experiment. Buds set. showed significant clinal variation With latitude, explaining similar to 90\% Of the population variation in bud Set. A sliding-window scan of phyB2 identified six putative regions with enhanced population differentiation and four SNPs showed significant clinal variation. The clinal variation at individual SNPs is suggestive of all adaptive response in phyB2 to local photoperiodic conditions. Three of four SNPs showing clinal variation were located in regions With excessive genetic differentiation, demonstrating that searching for regions of high genetic differentiation call be useful for identifying sites putatively involved in local adaptation.},
	language = {English},
	number = {3},
	journal = {Genetics},
	publisher = {Genetics Society America},
	author = {Ingvarsson, P. K. and Garcia, M. V. and Hall, D. and Luquez, V. and Jansson, S.},
	month = mar,
	year = {2006},
	note = {Place: Bethesda
WOS:000236668100040},
	keywords = {adaptation, arabidopsis, coalescent, linkage disequilibrium, nucleotide diversity, phenology, polymorphism, populations, quantitative trait loci, selection},
	pages = {1845--1853},
}

The initiation of growth cessation and dormancy represents a Critical ecological and evolutionary tradeoff between survival and growth in most. forest trees. The Most important environmental cue regulating the initiation of dormancy is a shortening of the photoperiod and phytochrome genes have been implicated in short-day-induced bud set and growth cessation in Populus. We characterized patterns of DNA sequence variation at the putative candidate gene phyB2 in 4 populations of European aspen (Populus tremula) and scored single-nucleotide polymorphisms in an additional 12 populations collected along a latitudinal gradient in Sweden. We also measured bud set from a subset Of these trees in a growth chamber experiment. Buds set. showed significant clinal variation With latitude, explaining similar to 90% Of the population variation in bud Set. A sliding-window scan of phyB2 identified six putative regions with enhanced population differentiation and four SNPs showed significant clinal variation. The clinal variation at individual SNPs is suggestive of all adaptive response in phyB2 to local photoperiodic conditions. Three of four SNPs showing clinal variation were located in regions With excessive genetic differentiation, demonstrating that searching for regions of high genetic differentiation call be useful for identifying sites putatively involved in local adaptation.

@article{svalastog_comparative_2006,
	title = {Comparative analysis of the risk-handling procedures for gene technology applications in medical and plant science},
	volume = {12},
	issn = {1353-3452},
	doi = {10/b58tj9},
	abstract = {In this paper we analyse how the risks associated with research on transgenic plants are regulated in Sweden. The paper outlines the way in which pilot projects in the plant sciences are overseen in Sweden, and discusses the international and national background to the current regulatory system. The historical, and hitherto unexplored, reasons for the evolution of current administrative and legislative procedures in plant science are of particular interest. Specifically, we discuss similarities and differences in the regulation of medicine and plant science, and we examine the tendency towards dichotomizing risk-focusing on social/ethical risks in medicine and biological risks in plant science. The context of this article is the Synpraxia research project, an inter-disciplinary program combining expertise in sciences and the humanities.},
	language = {English},
	number = {3},
	journal = {Science and Engineering Ethics},
	publisher = {Opragen Publications},
	author = {Svalastog, Anna Lydia and Gustafsson, Petter and Jansson, Stefan},
	month = jul,
	year = {2006},
	note = {Place: Guildford
WOS:000239947700006},
	keywords = {World War II, gene technology, medical ethics, plant science, public   opinion},
	pages = {465--479},
}

In this paper we analyse how the risks associated with research on transgenic plants are regulated in Sweden. The paper outlines the way in which pilot projects in the plant sciences are overseen in Sweden, and discusses the international and national background to the current regulatory system. The historical, and hitherto unexplored, reasons for the evolution of current administrative and legislative procedures in plant science are of particular interest. Specifically, we discuss similarities and differences in the regulation of medicine and plant science, and we examine the tendency towards dichotomizing risk-focusing on social/ethical risks in medicine and biological risks in plant science. The context of this article is the Synpraxia research project, an inter-disciplinary program combining expertise in sciences and the humanities.

@article{albrectsen_micro_2006,
	title = {From micro towards the macro scale},
	volume = {172},
	issn = {0028-646X},
	doi = {10.1111/j.1469-8137.2006.01869.x},
	language = {English},
	number = {1},
	journal = {New Phytologist},
	publisher = {Wiley},
	author = {Albrectsen, Benedicte R. and Jansson, Stefan},
	year = {2006},
	note = {Place: Hoboken
WOS:000239988100003},
	keywords = {arabidopsis, biofuel, coevolution, developmental biology, diversity, genes, plant defence   strategy, plants, scientific outreach, small RNA},
	pages = {7--10},
}

@article{kovacs_lack_2006,
	title = {Lack of the {Light}-{Harvesting} {Complex} {CP24} {Affects} the {Structure} and {Function} of the {Grana} {Membranes} of {Higher} {Plant} {Chloroplasts}},
	volume = {18},
	issn = {1040-4651},
	url = {https://doi.org/10.1105/tpc.106.045641},
	doi = {10.1105/tpc.106.045641},
	abstract = {The photosystem II (PSII) light-harvesting antenna in higher plants contains a number of highly conserved gene products whose function is unknown. Arabidopsis thaliana plants depleted of one of these, the CP24 light-harvesting complex, have been analyzed. CP24-deficient plants showed a decrease in light-limited photosynthetic rate and growth, but the pigment and protein content of the thylakoid membranes were otherwise almost unchanged. However, there was a major change in the macroorganization of PSII within these membranes; electron microscopy and image analysis revealed the complete absence of the C2S2M2 light-harvesting complex II (LHCII)/PSII supercomplex predominant in wild-type plants. Instead, only C2S2 supercomplexes, which are deficient in the LHCIIb M-trimers, were found. Spectroscopic analysis confirmed the disruption of the wild-type macroorganization of PSII. It was found that the functions of the PSII antenna were disturbed: connectivity between PSII centers was reduced, and maximum photochemical yield was lowered; rapidly reversible nonphotochemical quenching was inhibited; and the state transitions were altered kinetically. CP24 is therefore an important factor in determining the structure and function of the PSII light-harvesting antenna, providing the linker for association of the M-trimer into the PSII complex, allowing a specific macroorganization that is necessary both for maximum quantum efficiency and for photoprotective dissipation of excess excitation energy.},
	number = {11},
	urldate = {2021-06-11},
	journal = {The Plant Cell},
	author = {Kovács, László and Damkjær, Jakob and Kereïche, Sami and Ilioaia, Cristian and Ruban, Alexander V. and Boekema, Egbert J. and Jansson, Stefan and Horton, Peter},
	month = nov,
	year = {2006},
	pages = {3106--3120},
}

The photosystem II (PSII) light-harvesting antenna in higher plants contains a number of highly conserved gene products whose function is unknown. Arabidopsis thaliana plants depleted of one of these, the CP24 light-harvesting complex, have been analyzed. CP24-deficient plants showed a decrease in light-limited photosynthetic rate and growth, but the pigment and protein content of the thylakoid membranes were otherwise almost unchanged. However, there was a major change in the macroorganization of PSII within these membranes; electron microscopy and image analysis revealed the complete absence of the C2S2M2 light-harvesting complex II (LHCII)/PSII supercomplex predominant in wild-type plants. Instead, only C2S2 supercomplexes, which are deficient in the LHCIIb M-trimers, were found. Spectroscopic analysis confirmed the disruption of the wild-type macroorganization of PSII. It was found that the functions of the PSII antenna were disturbed: connectivity between PSII centers was reduced, and maximum photochemical yield was lowered; rapidly reversible nonphotochemical quenching was inhibited; and the state transitions were altered kinetically. CP24 is therefore an important factor in determining the structure and function of the PSII light-harvesting antenna, providing the linker for association of the M-trimer into the PSII complex, allowing a specific macroorganization that is necessary both for maximum quantum efficiency and for photoprotective dissipation of excess excitation energy.

@article{lucinski_lhca5_2006,
	title = {Lhca5 interaction with plant photosystem {I}},
	volume = {580},
	copyright = {FEBS Letters 580 (2006) 1873-3468 © 2015 Federation of European Biochemical Societies},
	issn = {1873-3468},
	url = {https://febs.onlinelibrary.wiley.com/doi/abs/10.1016/j.febslet.2006.10.063},
	doi = {10.1016/j.febslet.2006.10.063},
	abstract = {In the outer antenna (LHCI) of higher plant photosystem I (PSI) four abundantly expressed light-harvesting protein of photosystem I (Lhca)-type proteins are organized in two heterodimeric domains (Lhca1/Lhca4 and Lhca2/Lhca3). Our cross-linking studies on PSI-LHCI preparations from wildtype Arabidopsis and pea plants indicate an exclusive interaction of the rarely expressed Lhca5 light-harvesting protein with LHCI in the Lhca2/Lhca3-site. In PSI particles with an altered LHCI composition Lhca5 assembles in the Lhca1/Lhca4 site, partly as a homodimer. This flexibility indicates a binding-competitive model for the LHCI assembly in plants regulated by molecular interactions of the Lhca proteins with the PSI core.},
	language = {en},
	number = {27},
	urldate = {2021-06-11},
	journal = {FEBS Letters},
	author = {Lucinski, Robert and Schmid, Volkmar H. R. and Jansson, Stefan and Klimmek, Frank},
	year = {2006},
	note = {\_eprint: https://febs.onlinelibrary.wiley.com/doi/pdf/10.1016/j.febslet.2006.10.063},
	keywords = {Cross-linking, LHCI, Lhca, Lhca5, Light-harvesting complex I, PSI, Photosystem I, chl, chlorophyll, depleted in Lhca protein, light-harvesting complex I, light-harvesting protein of photosystem I, photosystem I, wildtype, wt, ΔLhca},
	pages = {6485--6488},
}

In the outer antenna (LHCI) of higher plant photosystem I (PSI) four abundantly expressed light-harvesting protein of photosystem I (Lhca)-type proteins are organized in two heterodimeric domains (Lhca1/Lhca4 and Lhca2/Lhca3). Our cross-linking studies on PSI-LHCI preparations from wildtype Arabidopsis and pea plants indicate an exclusive interaction of the rarely expressed Lhca5 light-harvesting protein with LHCI in the Lhca2/Lhca3-site. In PSI particles with an altered LHCI composition Lhca5 assembles in the Lhca1/Lhca4 site, partly as a homodimer. This flexibility indicates a binding-competitive model for the LHCI assembly in plants regulated by molecular interactions of the Lhca proteins with the PSI core.

@article{bylesjo_masqot-gui_2006,
	title = {{MASQOT}-{GUI}: spot quality assessment for the two-channel microarray platform},
	volume = {22},
	issn = {1367-4803},
	shorttitle = {{MASQOT}-{GUI}},
	url = {https://doi.org/10.1093/bioinformatics/btl434},
	doi = {10.1093/bioinformatics/btl434},
	abstract = {Summary: MASQOT-GUI provides an open-source, platform-independent software pipeline for two-channel microarray spot quality control. This includes gridding, segmentation, quantification, quality assessment and data visualization. It hosts a set of independent applications, with interactions between the tools as well as import and export support for external software. The implementation of automated multivariate quality control assessment, which is a unique feature of MASQOT-GUI, is based on the previously documented and evaluated MASQOT methodology. Further abilities of the application are outlined and illustrated.Availability: MASQOT-GUI is Java-based and licensed under the GNU LGPL. Source code and installation files are available for download at Contact: This email address is being protected from spambots. You need JavaScript enabled to view it. information: Supplementary data are available at Bioinformatics online},
	number = {20},
	urldate = {2021-06-11},
	journal = {Bioinformatics},
	author = {Bylesjö, Max and Sjödin, Andreas and Eriksson, Daniel and Antti, Henrik and Moritz, Thomas and Jansson, Stefan and Trygg, Johan},
	month = oct,
	year = {2006},
	pages = {2554--2555},
}

Summary: MASQOT-GUI provides an open-source, platform-independent software pipeline for two-channel microarray spot quality control. This includes gridding, segmentation, quantification, quality assessment and data visualization. It hosts a set of independent applications, with interactions between the tools as well as import and export support for external software. The implementation of automated multivariate quality control assessment, which is a unique feature of MASQOT-GUI, is based on the previously documented and evaluated MASQOT methodology. Further abilities of the application are outlined and illustrated.Availability: MASQOT-GUI is Java-based and licensed under the GNU LGPL. Source code and installation files are available for download at Contact: This email address is being protected from spambots. You need JavaScript enabled to view it. information: Supplementary data are available at Bioinformatics online

@article{demmig-adams_modulation_2006,
	title = {Modulation of {PsbS} and flexible vs sustained energy dissipation by light environment in different species},
	volume = {127},
	issn = {0031-9317},
	doi = {10.1111/j.1399-3054.2006.00698.x},
	abstract = {Contrasting acclimation strategies of photosynthesis and photoprotection were identified for annual mesophytes (spinach, pumpkin, and Arabidopsis) vs the tropical evergreen Monstera deliciosa. The annual species utilized full sunlight for photosynthesis to a much greater extent than the evergreen species. Conversely, the evergreen species exhibited a greater capacity for photoprotective thermal energy dissipation as well as a greater expression of the PsbS protein in full sun than the annual species. In all species, the majority of thermal energy dissipation [assessed as non-photochemical fluorescence quenching (NPQ)] was the flexible, Delta pH-dependent form of NPQ over the entire range of growth light environments. However, in response to a transfer of shade-grown plants to high light, the evergreen species exhibited a high level of sustained thermal dissipation (ql), but the annual species did not. This sustained energy dissipation in the evergreen species was not Delta pH-dependent nor did the low level of PsbS in shade leaves increase upon transfer to high light for several days. Sustained Delta pH-independent NPQ was correlated (a) initially, with sustained DI protein phosphorylation and xanthophyll cycle arrest and U subsequently, with an accumulation over several days of PsbS-related one-helix proteins and newly synthesized zeaxanthin and lutein.},
	language = {English},
	number = {4},
	journal = {Physiologia Plantarum},
	publisher = {Wiley-Blackwell},
	author = {Demmig-Adams, Barbara and Ebbert, Volker and Mellman, David L. and Mueh, Kristine E. and Schaffer, Lisa and Funk, Christiane and Zarter, C. Ryan and Adamska, Iwona and Jansson, Stefan and Adams III, William W.},
	month = aug,
	year = {2006},
	note = {Place: Hoboken
WOS:000239561900014},
	keywords = {arabidopsis-thaliana, chlorophyll   fluorescence, excess excitation, inducible polypeptides, overwintering evergreens, photosystem-ii, protein, shade leaves, synechocystis pcc6803, xanthophyll cycle},
	pages = {670--680},
}

Contrasting acclimation strategies of photosynthesis and photoprotection were identified for annual mesophytes (spinach, pumpkin, and Arabidopsis) vs the tropical evergreen Monstera deliciosa. The annual species utilized full sunlight for photosynthesis to a much greater extent than the evergreen species. Conversely, the evergreen species exhibited a greater capacity for photoprotective thermal energy dissipation as well as a greater expression of the PsbS protein in full sun than the annual species. In all species, the majority of thermal energy dissipation [assessed as non-photochemical fluorescence quenching (NPQ)] was the flexible, Delta pH-dependent form of NPQ over the entire range of growth light environments. However, in response to a transfer of shade-grown plants to high light, the evergreen species exhibited a high level of sustained thermal dissipation (ql), but the annual species did not. This sustained energy dissipation in the evergreen species was not Delta pH-dependent nor did the low level of PsbS in shade leaves increase upon transfer to high light for several days. Sustained Delta pH-independent NPQ was correlated (a) initially, with sustained DI protein phosphorylation and xanthophyll cycle arrest and U subsequently, with an accumulation over several days of PsbS-related one-helix proteins and newly synthesized zeaxanthin and lutein.

@article{ruban_plasticity_2006,
	title = {Plasticity in the composition of the light harvesting antenna of higher plants preserves structural integrity and biological function},
	volume = {281},
	issn = {0021-9258},
	doi = {10.1074/jbc.M511415200},
	abstract = {Arabidopsis plants in which the major trimeric light harvesting complex ( LHCIIb) is eliminated by antisense expression still exhibit the typical macrostructure of photosystem II in the granal membranes. Here the detailed analysis of the composition and the functional state of the light harvesting antennae of both photosystem I and II of these plants is presented. Two new populations of trimers were found, both functional in energy transfer to the PSII reaction center, a homotrimer of CP26 and a heterotrimer of CP26 and Lhcb3. These trimers possess characteristic features thought to be specific for the native LHCIIb trimers they are replacing: the long wavelength form of lutein and at least one extra chlorophyll b, but they were less stable. A new population of loosely bound LHCI was also found, contributing to an increased antenna size for photosystem I, which may in part compensate for the loss of the phosphorylated LHCIIb that can associate with this photosystem. Thus, the loss of LHCIIb has triggered concerted compensatory responses in the composition of antennae of both photosystems. These responses clearly show the importance of LHCIIb in the structure and assembly of the photosynthetic membrane and illustrate the extreme plasticity at the level of the composition of the light harvesting system.},
	language = {English},
	number = {21},
	journal = {Journal of Biological Chemistry},
	publisher = {Amer Soc Biochemistry Molecular Biology Inc},
	author = {Ruban, Alexander V. and Solovieva, Svetlana and Lee, Pamela J. and Ilioaia, Cristian and Wentworth, Mark and Ganeteg, Ulrika and Klimmek, Frank and Chow, Wah Soon and Anderson, Jan M. and Jansson, Stefan and Horton, Peter},
	month = may,
	year = {2006},
	note = {Place: Rockville
WOS:000237671300051},
	keywords = {a/b-binding-proteins, acclimation, arabidopsis, complex-ii, crystal-structure, energy, photosystem-ii, spectroscopic analysis, supramolecular organization, xanthophylls},
	pages = {14981--14990},
}

Arabidopsis plants in which the major trimeric light harvesting complex ( LHCIIb) is eliminated by antisense expression still exhibit the typical macrostructure of photosystem II in the granal membranes. Here the detailed analysis of the composition and the functional state of the light harvesting antennae of both photosystem I and II of these plants is presented. Two new populations of trimers were found, both functional in energy transfer to the PSII reaction center, a homotrimer of CP26 and a heterotrimer of CP26 and Lhcb3. These trimers possess characteristic features thought to be specific for the native LHCIIb trimers they are replacing: the long wavelength form of lutein and at least one extra chlorophyll b, but they were less stable. A new population of loosely bound LHCI was also found, contributing to an increased antenna size for photosystem I, which may in part compensate for the loss of the phosphorylated LHCIIb that can associate with this photosystem. Thus, the loss of LHCIIb has triggered concerted compensatory responses in the composition of antennae of both photosystems. These responses clearly show the importance of LHCIIb in the structure and assembly of the photosynthetic membrane and illustrate the extreme plasticity at the level of the composition of the light harvesting system.

@article{garcia-lorenzo_protease_2006,
	title = {Protease gene families in {Populus} and {Arabidopsis}},
	volume = {6},
	issn = {1471-2229},
	url = {https://doi.org/10.1186/1471-2229-6-30},
	doi = {10.1186/1471-2229-6-30},
	abstract = {Proteases play key roles in plants, maintaining strict protein quality control and degrading specific sets of proteins in response to diverse environmental and developmental stimuli. Similarities and differences between the proteases expressed in different species may give valuable insights into their physiological roles and evolution.},
	number = {1},
	urldate = {2021-06-11},
	journal = {BMC Plant Biology},
	author = {García-Lorenzo, Maribel and Sjödin, Andreas and Jansson, Stefan and Funk, Christiane},
	month = dec,
	year = {2006},
	keywords = {Leaf Senescence, Protease Family, Protease Gene, Putative Protease, Tension Wood},
	pages = {30},
}

Proteases play key roles in plants, maintaining strict protein quality control and degrading specific sets of proteins in response to diverse environmental and developmental stimuli. Similarities and differences between the proteases expressed in different species may give valuable insights into their physiological roles and evolution.

@article{street_genetics_2006,
	title = {The genetics and genomics of the drought response in {Populus}},
	volume = {48},
	issn = {1365-313X},
	url = {https://onlinelibrary.wiley.com/doi/abs/10.1111/j.1365-313X.2006.02864.x},
	doi = {10/fj53r5},
	abstract = {The genetic nature of tree adaptation to drought stress was examined by utilizing variation in the drought response of a full-sib second generation (F2) mapping population from a cross between Populus trichocarpa (93-968) and P. deltoides Bart (ILL-129) and known to be highly divergent for a vast range of phenotypic traits. We combined phenotyping, quantitative trait loci (QTL) analysis and microarray experiments to demonstrate that ‘genetical genomics’ can be used to provide information on adaptation at the species level. The grandparents and F2 population were subjected to soil drying, and contrasting responses to drought across genotypes, including leaf coloration, expansion and abscission, were observed, and QTL for these traits mapped. A subset of extreme genotypes exhibiting extreme sensitivity and insensitivity to drought on the basis of leaf abscission were defined, and microarray experiments conducted on these genotypes and the grandparent species. The extreme genotype groups induced a different set of genes: 215 and 125 genes differed in their expression response between groups in control and drought, respectively, suggesting species adaptation at the gene expression level. Co-location of differentially expressed genes with drought-specific and drought-responsive QTLs was examined, and these may represent candidate genes contributing to the variation in drought response.},
	language = {en},
	number = {3},
	urldate = {2021-06-11},
	journal = {The Plant Journal},
	author = {Street, Nathaniel Robert and Skogström, Oskar and Sjödin, Andreas and Tucker, James and Rodríguez-Acosta, Maricela and Nilsson, Peter and Jansson, Stefan and Taylor, Gail},
	year = {2006},
	note = {\_eprint: https://onlinelibrary.wiley.com/doi/pdf/10.1111/j.1365-313X.2006.02864.x},
	keywords = {QTL, drought, microarray, poplar, transcriptome},
	pages = {321--341},
}

The genetic nature of tree adaptation to drought stress was examined by utilizing variation in the drought response of a full-sib second generation (F2) mapping population from a cross between Populus trichocarpa (93-968) and P. deltoides Bart (ILL-129) and known to be highly divergent for a vast range of phenotypic traits. We combined phenotyping, quantitative trait loci (QTL) analysis and microarray experiments to demonstrate that ‘genetical genomics’ can be used to provide information on adaptation at the species level. The grandparents and F2 population were subjected to soil drying, and contrasting responses to drought across genotypes, including leaf coloration, expansion and abscission, were observed, and QTL for these traits mapped. A subset of extreme genotypes exhibiting extreme sensitivity and insensitivity to drought on the basis of leaf abscission were defined, and microarray experiments conducted on these genotypes and the grandparent species. The extreme genotype groups induced a different set of genes: 215 and 125 genes differed in their expression response between groups in control and drought, respectively, suggesting species adaptation at the gene expression level. Co-location of differentially expressed genes with drought-specific and drought-responsive QTLs was examined, and these may represent candidate genes contributing to the variation in drought response.

@article{tuskan_genome_2006,
	title = {The genome of black cottonwood, {Populus} trichocarpa ({Torr}. \& {Gray})},
	volume = {313},
	issn = {0036-8075},
	doi = {10/c7hs34},
	abstract = {We report the draft genome of the black cottonwood tree, Populus trichocarpa. Integration of shotgun sequence assembly with genetic mapping enabled chromosome-scale reconstruction of the genome. More than 45,000 putative protein-coding genes were identified. Analysis of the assembled genome revealed a whole-genome duplication event; about 8000 pairs of duplicated genes from that event survived in the Populus genome. A second, older duplication event is indistinguishably coincident with the divergence of the Populus and Arabidopsis lineages. Nucleotide substitution, tandem gene duplication, and gross chromosomal rearrangement appear to proceed substantially more slowly in Populus than in Arabidopsis. Populus has more protein-coding genes than Arabidopsis, ranging on average from 1.4 to 1.6 putative Populus homologs for each Arabidopsis gene. However, the relative frequency of protein domains in the two genomes is similar. Overrepresented exceptions in Populus include genes associated with lignocellulosic wall biosynthesis, meristem development, disease resistance, and metabolite transport.},
	language = {English},
	number = {5793},
	journal = {Science},
	publisher = {Amer Assoc Advancement Science},
	author = {Tuskan, G. A. and DiFazio, S. and Jansson, S. and Bohlmann, J. and Grigoriev, I. and Hellsten, U. and Putnam, N. and Ralph, S. and Rombauts, S. and Salamov, A. and Schein, J. and Sterck, L. and Aerts, A. and Bhalerao, Rishikesh P. and Bhalerao, R. P. and Blaudez, D. and Boerjan, W. and Brun, A. and Brunner, A. and Busov, V. and Campbell, M. and Carlson, J. and Chalot, M. and Chapman, J. and Chen, G.-L. and Cooper, D. and Coutinho, P. M. and Couturier, J. and Covert, S. and Cronk, Q. and Cunningham, R. and Davis, J. and Degroeve, S. and Dejardin, A. and dePamphilis, C. and Detter, J. and Dirks, B. and Dubchak, I. and Duplessis, S. and Ehlting, J. and Ellis, B. and Gendler, K. and Goodstein, D. and Gribskov, M. and Grimwood, J. and Groover, A. and Gunter, L. and Hamberger, B. and Heinze, B. and Helariutta, Y. and Henrissat, B. and Holligan, D. and Holt, R. and Huang, W. and Islam-Faridi, N. and Jones, S. and Jones-Rhoades, M. and Jorgensen, R. and Joshi, C. and Kangasjarvi, J. and Karlsson, J. and Kelleher, C. and Kirkpatrick, R. and Kirst, M. and Kohler, A. and Kalluri, U. and Larimer, F. and Leebens-Mack, J. and Leple, J.-C. and Locascio, P. and Lou, Y. and Lucas, S. and Martin, F. and Montanini, B. and Napoli, C. and Nelson, D. R. and Nelson, C. and Nieminen, K. and Nilsson, O. and Pereda, V. and Peter, G. and Philippe, R. and Pilate, G. and Poliakov, A. and Razumovskaya, J. and Richardson, P. and Rinaldi, C. and Ritland, K. and Rouze, P. and Ryaboy, D. and Schmutz, J. and Schrader, J. and Segerman, B. and Shin, H. and Siddiqui, A. and Sterky, F. and Terry, A. and Tsai, C.-J. and Uberbacher, E. and Unneberg, P. and Vahala, J. and Wall, K. and Wessler, S. and Yang, G. and Yin, T. and Douglas, C. and Marra, M. and Sandberg, G. and Van de Peer, Y. and Rokhsar, D.},
	month = sep,
	year = {2006},
	note = {Place: Washington
WOS:000240498900035},
	keywords = {arabidopsis-thaliana, cinnamyl alcohol-dehydrogenase, gene-expression, gravitational induction, hybrid poplar, lignin biosynthesis, phenylpropanoid metabolism, quaking   aspen, resistance genes, transcriptional regulators},
	pages = {1596--1604},
}

We report the draft genome of the black cottonwood tree, Populus trichocarpa. Integration of shotgun sequence assembly with genetic mapping enabled chromosome-scale reconstruction of the genome. More than 45,000 putative protein-coding genes were identified. Analysis of the assembled genome revealed a whole-genome duplication event; about 8000 pairs of duplicated genes from that event survived in the Populus genome. A second, older duplication event is indistinguishably coincident with the divergence of the Populus and Arabidopsis lineages. Nucleotide substitution, tandem gene duplication, and gross chromosomal rearrangement appear to proceed substantially more slowly in Populus than in Arabidopsis. Populus has more protein-coding genes than Arabidopsis, ranging on average from 1.4 to 1.6 putative Populus homologs for each Arabidopsis gene. However, the relative frequency of protein domains in the two genomes is similar. Overrepresented exceptions in Populus include genes associated with lignocellulosic wall biosynthesis, meristem development, disease resistance, and metabolite transport.

@article{sjodin_upsc-base_2006,
	title = {{UPSC}-{BASE} - {Populus} transcriptomics online},
	volume = {48},
	issn = {0960-7412},
	doi = {10/cxqkhm},
	abstract = {The increasing accessibility and use of microarrays in transcriptomics has accentuated the need for purpose-designed storage and analysis tools. Here we present UPSC-BASE, a database for analysis and storage of Populus DNA microarray data. A microarray analysis pipeline has also been established to allow consistent and efficient analysis (from small to large scale) of samples in various experimental designs. A range of optimized experimental protocols is provided for each step in generating the data. Within UPSC-BASE, researchers can perform standard and advanced microarray analysis procedures in a user-friendly environment. Background corrections, normalizations, quality-control tools, visualizations, hypothesis tests and export tools are provided without requirements for expert-level knowledge. Although the database has been developed primarily for handling Populus DNA microarrays, most of the tools are generic and can be used for other types of microarray. UPSC-BASE is also a repository of Populus microarray information, providing data from 21 experiments on a total of 407 microarray hybridizations in the public domain of the database. There are also an additional 10 experiments containing 347 hybridizations, where the automatically analysed data are searchable.},
	language = {English},
	number = {5},
	journal = {Plant Journal},
	publisher = {Wiley},
	author = {Sjodin, Andreas and Bylesjo, Max and Skogstrom, Oskar and Eriksson, Daniel and Nilsson, Peter and Ryden, Patrik and Jansson, Stefan and Karlsson, Jan},
	month = dec,
	year = {2006},
	note = {Place: Hoboken
WOS:000242042900013},
	keywords = {bioconductor, cdna microarray data, database, design, expression profiling, functional genomics, gene-expression patterns, genomics, microarray, normalization, poplar, resource, sequence tags, tool, transcriptome},
	pages = {806--817},
}

The increasing accessibility and use of microarrays in transcriptomics has accentuated the need for purpose-designed storage and analysis tools. Here we present UPSC-BASE, a database for analysis and storage of Populus DNA microarray data. A microarray analysis pipeline has also been established to allow consistent and efficient analysis (from small to large scale) of samples in various experimental designs. A range of optimized experimental protocols is provided for each step in generating the data. Within UPSC-BASE, researchers can perform standard and advanced microarray analysis procedures in a user-friendly environment. Background corrections, normalizations, quality-control tools, visualizations, hypothesis tests and export tools are provided without requirements for expert-level knowledge. Although the database has been developed primarily for handling Populus DNA microarrays, most of the tools are generic and can be used for other types of microarray. UPSC-BASE is also a repository of Populus microarray information, providing data from 21 experiments on a total of 407 microarray hybridizations in the public domain of the database. There are also an additional 10 experiments containing 347 hybridizations, where the automatically analysed data are searchable.

@article{zarter_winter_2006,
	title = {Winter acclimation of {PsbS} and related proteins in the evergreen {Arctostaphylos} uva-ursi as influenced by altitude and light environment},
	volume = {29},
	issn = {1365-3040},
	url = {https://onlinelibrary.wiley.com/doi/abs/10.1111/j.1365-3040.2005.01466.x},
	doi = {10/dffrdg},
	abstract = {The evergreen groundcover bearberry (Arctostaphylos uva-ursi[L.] Sprengel) was characterized over two successive years (2002–2004) from both sun-exposed and shaded sites at a montane ponderosa pine and subalpine forest community of 1900- and 2800-m-high altitudes, respectively. During summer, photosynthetic capacities and pre-dawn photosystem II (PSII) efficiency were similarly high in all four populations, and in winter, only the sun-exposed and shaded populations at 2800 m exhibited complete down-regulation of photosynthetic oxygen evolution capacity and consistent sustained down-regulation of PSII efficiency. This photosynthetic down-regulation at high altitude involved a substantial decrease in PSII components [pheophytin, D1 protein, oxygen evolving complex ([OEC)], a strong up-regulation of several anti-early-light-inducible protein (Elip)- and anti-high-light-inducible protein (Hlip)-reactive bands and a warm-sustained retention of zeaxanthin and antheraxanthin (Z + A). PsbS, the protein modulating the rapid engagement and disengagement of Z + A in energy dissipation, exhibited its most pronounced winter increases in the shade at 1900 m, and thus apparently assumes a greater role in providing rapidly reversible zeaxanthin-dependent photoprotection during winter when light becomes excessive in the shaded population, which remains photosynthetically active. It is attractive to hypothesize that PsbS relatives (Elips/Hlips) may be involved in sustained zeaxanthin-dependent photoprotection under the more extreme winter conditions at 2800 m.},
	language = {en},
	number = {5},
	urldate = {2021-06-11},
	journal = {Plant, Cell \& Environment},
	author = {Zarter, C. Ryan and Adams, William W. and Ebbert, Volker and Adamska, Iwona and Jansson, Stefan and Demmig-Adams, Barbara},
	year = {2006},
	note = {\_eprint: https://onlinelibrary.wiley.com/doi/pdf/10.1111/j.1365-3040.2005.01466.x},
	keywords = {D1 protein, Elip, Hlip, OEC, PsbS, energy dissipation, photoinhibition, photosynthesis, winter stress, zeaxanthin},
	pages = {869--878},
}

The evergreen groundcover bearberry (Arctostaphylos uva-ursi[L.] Sprengel) was characterized over two successive years (2002–2004) from both sun-exposed and shaded sites at a montane ponderosa pine and subalpine forest community of 1900- and 2800-m-high altitudes, respectively. During summer, photosynthetic capacities and pre-dawn photosystem II (PSII) efficiency were similarly high in all four populations, and in winter, only the sun-exposed and shaded populations at 2800 m exhibited complete down-regulation of photosynthetic oxygen evolution capacity and consistent sustained down-regulation of PSII efficiency. This photosynthetic down-regulation at high altitude involved a substantial decrease in PSII components [pheophytin, D1 protein, oxygen evolving complex ([OEC)], a strong up-regulation of several anti-early-light-inducible protein (Elip)- and anti-high-light-inducible protein (Hlip)-reactive bands and a warm-sustained retention of zeaxanthin and antheraxanthin (Z + A). PsbS, the protein modulating the rapid engagement and disengagement of Z + A in energy dissipation, exhibited its most pronounced winter increases in the shade at 1900 m, and thus apparently assumes a greater role in providing rapidly reversible zeaxanthin-dependent photoprotection during winter when light becomes excessive in the shaded population, which remains photosynthetically active. It is attractive to hypothesize that PsbS relatives (Elips/Hlips) may be involved in sustained zeaxanthin-dependent photoprotection under the more extreme winter conditions at 2800 m.

@article{keskitalo_cellular_2005,
	title = {A {Cellular} {Timetable} of {Autumn} {Senescence}},
	volume = {139},
	issn = {0032-0889},
	url = {https://doi.org/10.1104/pp.105.066845},
	doi = {10/cdw8rv},
	abstract = {We have studied autumn leaf senescence in a free-growing aspen (Populus tremula) by following changes in pigment, metabolite and nutrient content, photosynthesis, and cell and organelle integrity. The senescence process started on September 11, 2003, apparently initiated solely by the photoperiod, and progressed steadily without any obvious influence of other environmental signals. For example, after this date, senescing leaves accumulated anthocyanins in response to conditions inducing photooxidative stress, but at the beginning of September the leaves did not. Degradation of leaf constituents took place over an 18-d period, and, although the cells in each leaf did not all senesce in parallel, senescence in the tree as a whole was synchronous. Lutein and β-carotene were degraded in parallel with chlorophyll, whereas neoxanthin and the xanthophyll cycle pigments were retained longer. Chloroplasts in each cell were rapidly converted to gerontoplasts and many, although not all, cells died. From September 19, when chlorophyll levels had dropped by 50\%, mitochondrial respiration provided the energy for nutrient remobilization. Remobilization seemed to stop on September 29, probably due to the cessation of phloem transport, but, up to abscission of the last leaves (over 1 week later), some cells were metabolically active and had chlorophyll-containing gerontoplasts. About 80\% of the nitrogen and phosphorus was remobilized, and on September 29 a sudden change occurred in the δ15n of the cellular content, indicating that volatile compounds may have been released.},
	number = {4},
	urldate = {2021-06-11},
	journal = {Plant Physiology},
	author = {Keskitalo, Johanna and Bergquist, Gustaf and Gardeström, Per and Jansson, Stefan},
	month = dec,
	year = {2005},
	pages = {1635--1648},
}

We have studied autumn leaf senescence in a free-growing aspen (Populus tremula) by following changes in pigment, metabolite and nutrient content, photosynthesis, and cell and organelle integrity. The senescence process started on September 11, 2003, apparently initiated solely by the photoperiod, and progressed steadily without any obvious influence of other environmental signals. For example, after this date, senescing leaves accumulated anthocyanins in response to conditions inducing photooxidative stress, but at the beginning of September the leaves did not. Degradation of leaf constituents took place over an 18-d period, and, although the cells in each leaf did not all senesce in parallel, senescence in the tree as a whole was synchronous. Lutein and β-carotene were degraded in parallel with chlorophyll, whereas neoxanthin and the xanthophyll cycle pigments were retained longer. Chloroplasts in each cell were rapidly converted to gerontoplasts and many, although not all, cells died. From September 19, when chlorophyll levels had dropped by 50%, mitochondrial respiration provided the energy for nutrient remobilization. Remobilization seemed to stop on September 29, probably due to the cessation of phloem transport, but, up to abscission of the last leaves (over 1 week later), some cells were metabolically active and had chlorophyll-containing gerontoplasts. About 80% of the nitrogen and phosphorus was remobilized, and on September 29 a sudden change occurred in the δ15n of the cellular content, indicating that volatile compounds may have been released.

@article{moreau_genomic_2005,
	title = {A genomic approach to investigate developmental cell death in woody tissues of {Populus} trees},
	volume = {6},
	issn = {1474-760X},
	doi = {10.1186/gb-2005-6-4-r34},
	abstract = {Background: Poplar ( Populus sp.) has emerged as the main model system for molecular and genetic studies of forest trees. A Populus expressed sequence tag ( EST) database (POPULUSDB) was previously created from 19 cDNA libraries each originating from different Populus tree tissues, and opened to the public in September 2004. We used this dataset for in silico transcript profiling of a particular process in the woody tissues of the Populus stem: the programmed death of xylem fibers. Results: One EST library in POPULUSDB originates from woody tissues of the Populus stem where xylem fibers undergo cell death. Analysis of EST abundances and library distribution within the POPULUSDB revealed a large number of previously uncharacterized transcripts that were unique in this library and possibly related to the death of xylem fibers. The in silico analysis was complemented by a microarray analysis utilizing a novel Populus cDNA array with a unigene set of 25,000 sequences. Conclusions: In silico analysis, combined with the microarray analysis, revealed the usefulness of non-normalized EST libraries in elucidating transcriptional regulation of previously uncharacterized physiological processes. The data suggested the involvement of two novel extracellular serine proteases, nodulin-like proteins and an Arabidopsis thaliana OPEN STOMATA 1 (AtOST1) homolog in signaling fiber-cell death, as well as mechanisms responsible for hormonal control, nutrient remobilization, regulation of vacuolar integrity and autolysis of the dying fibers.},
	language = {English},
	number = {4},
	journal = {Genome Biology},
	publisher = {Bmc},
	author = {Moreau, C. and Aksenov, N. and Lorenzo, M. G. and Segerman, B. and Funk, C. and Nilsson, P. and Jansson, S. and Tuominen, H.},
	year = {2005},
	note = {Place: London
WOS:000228436000011},
	keywords = {arabidopsis, arabinogalactan proteins, expression, poplar, secondary   growth, senescence, serine proteases, tracheary element differentiation, transcriptome, xylogenesis},
	pages = {R34},
}

Background: Poplar ( Populus sp.) has emerged as the main model system for molecular and genetic studies of forest trees. A Populus expressed sequence tag ( EST) database (POPULUSDB) was previously created from 19 cDNA libraries each originating from different Populus tree tissues, and opened to the public in September 2004. We used this dataset for in silico transcript profiling of a particular process in the woody tissues of the Populus stem: the programmed death of xylem fibers. Results: One EST library in POPULUSDB originates from woody tissues of the Populus stem where xylem fibers undergo cell death. Analysis of EST abundances and library distribution within the POPULUSDB revealed a large number of previously uncharacterized transcripts that were unique in this library and possibly related to the death of xylem fibers. The in silico analysis was complemented by a microarray analysis utilizing a novel Populus cDNA array with a unigene set of 25,000 sequences. Conclusions: In silico analysis, combined with the microarray analysis, revealed the usefulness of non-normalized EST libraries in elucidating transcriptional regulation of previously uncharacterized physiological processes. The data suggested the involvement of two novel extracellular serine proteases, nodulin-like proteins and an Arabidopsis thaliana OPEN STOMATA 1 (AtOST1) homolog in signaling fiber-cell death, as well as mechanisms responsible for hormonal control, nutrient remobilization, regulation of vacuolar integrity and autolysis of the dying fibers.

@article{unneberg_analysis_2005,
	title = {Analysis of 70,000 {EST} sequences to study divergence between two closely related {Populus} species},
	volume = {1},
	issn = {1614-2950},
	url = {https://doi.org/10.1007/s11295-005-0014-0},
	doi = {10.1007/s11295-005-0014-0},
	abstract = {The Populus genus has evolved as the model organism for forest tree genomics, which has been further emphasised with the sequencing of the Populus trichocarpa genome. Populus species are widely spread over the Northern Hemisphere and provide a great source of genetic diversity, which can be used for mapping of quantitative trait loci, positional cloning, association mapping and studies in environmental adaptation. Collections of expressed sequence tags (ESTs) are rich sources in studies of genetic diversity. Here, we report on an in-depth analysis of 70,000 ESTs from two Populus species, Populus tremula and Populus trichocarpa. We present data on the level of conservation in transcript sequences and supply a collection of potential single nucleotide polymorphisms.},
	language = {en},
	number = {3},
	urldate = {2021-06-11},
	journal = {Tree Genetics \& Genomes},
	author = {Unneberg, Per and Strömberg, Michael and Lundeberg, Joakim and Jansson, Stefan and Sterky, Fredrik},
	month = nov,
	year = {2005},
	pages = {109--115},
}

The Populus genus has evolved as the model organism for forest tree genomics, which has been further emphasised with the sequencing of the Populus trichocarpa genome. Populus species are widely spread over the Northern Hemisphere and provide a great source of genetic diversity, which can be used for mapping of quantitative trait loci, positional cloning, association mapping and studies in environmental adaptation. Collections of expressed sequence tags (ESTs) are rich sources in studies of genetic diversity. Here, we report on an in-depth analysis of 70,000 ESTs from two Populus species, Populus tremula and Populus trichocarpa. We present data on the level of conservation in transcript sequences and supply a collection of potential single nucleotide polymorphisms.

@article{zelisko_atftsh6_2005,
	chapter = {Biological Sciences},
	title = {{AtFtsH6} is involved in the degradation of the light-harvesting complex {II} during high-light acclimation and senescence},
	volume = {102},
	copyright = {Copyright © 2005, The National Academy of Sciences},
	issn = {0027-8424, 1091-6490},
	url = {https://www.pnas.org/content/102/38/13699},
	doi = {10.1073/pnas.0503472102},
	abstract = {Degradation of the most abundant membrane protein on earth, the light-harvesting complex of Photosystem II (LHC II), is highly regulated under various environmental conditions, e.g., light stress, to prevent photochemical damage to the reaction center. We identified the LHC II degrading protease in Arabidopsis thaliana as a Zn2+-dependent metalloprotease, activated by the removal of unknown extrinsic factors, similar to the proteolytic activity directed against Lhcb3 in barley. By using a reversed genetic approach, the chloroplast-targeted protease FtsH6 was identified as being responsible for the degradation. T-DNA KO A. thaliana mutants, lacking ftsH6, were unable to degrade either Lhcb3 during dark-induced senescence or Lhcb1 and Lhcb3 during highlight acclimation. The A. thaliana ftsH6 gene has a clear orthologue in the genome of Populus trichocarpa. It is likely that FtsH6 is a general LHC II protease and that FtsH6-dependent LHC II proteolysis is a feature of all higher plants.},
	language = {en},
	number = {38},
	urldate = {2021-06-11},
	journal = {Proceedings of the National Academy of Sciences},
	publisher = {National Academy of Sciences},
	author = {Żelisko, Agnieszka and García-Lorenzo, Maribel and Jackowski, Grzegorz and Jansson, Stefan and Funk, Christiane},
	month = sep,
	year = {2005},
	keywords = {membrane protein, photosynthesis, protease},
	pages = {13699--13704},
}

Degradation of the most abundant membrane protein on earth, the light-harvesting complex of Photosystem II (LHC II), is highly regulated under various environmental conditions, e.g., light stress, to prevent photochemical damage to the reaction center. We identified the LHC II degrading protease in Arabidopsis thaliana as a Zn2+-dependent metalloprotease, activated by the removal of unknown extrinsic factors, similar to the proteolytic activity directed against Lhcb3 in barley. By using a reversed genetic approach, the chloroplast-targeted protease FtsH6 was identified as being responsible for the degradation. T-DNA KO A. thaliana mutants, lacking ftsH6, were unable to degrade either Lhcb3 during dark-induced senescence or Lhcb1 and Lhcb3 during highlight acclimation. The A. thaliana ftsH6 gene has a clear orthologue in the genome of Populus trichocarpa. It is likely that FtsH6 is a general LHC II protease and that FtsH6-dependent LHC II proteolysis is a feature of all higher plants.

@article{sterck_est_2005,
	title = {{EST} data suggest that poplar is an ancient polyploid},
	volume = {167},
	issn = {1469-8137},
	url = {https://nph.onlinelibrary.wiley.com/doi/abs/10.1111/j.1469-8137.2005.01378.x},
	doi = {10/c6wh5d},
	abstract = {• We analysed the publicly available expressed sequence tag (EST) collections for the genus Populus to examine whether evidence can be found for large-scale gene-duplication events in the evolutionary past of this genus. • The ESTs were clustered into unigenes for each poplar species examined. Gene families were constructed for all proteins deduced from these unigenes, and KS dating was performed on all paralogs within a gene family. The fraction of paralogs was then plotted against the KS values, which resulted in a distribution reflecting the age of duplicated genes in poplar. • Sufficient EST data were available for seven different poplar species spanning four of the six sections of the genus Populus. For all these species, there was evidence that a large-scale gene-duplication event had occurred. • From our analysis it is clear that all poplar species have shared the same large-scale gene-duplication event, suggesting that this event must have occurred in the ancestor of poplar, or at least very early in the evolution of the Populus genus.},
	language = {en},
	number = {1},
	urldate = {2021-06-11},
	journal = {New Phytologist},
	author = {Sterck, Lieven and Rombauts, Stephane and Jansson, Stefan and Sterky, Fredrik and Rouzé, Pierre and Peer, Yves Van de},
	year = {2005},
	note = {\_eprint: https://nph.onlinelibrary.wiley.com/doi/pdf/10.1111/j.1469-8137.2005.01378.x},
	keywords = {EST (expressed sequence tag) data, KS dating, Populus (poplar), evolution, fossil record, genome duplication, polyploidy},
	pages = {165--170},
}

• We analysed the publicly available expressed sequence tag (EST) collections for the genus Populus to examine whether evidence can be found for large-scale gene-duplication events in the evolutionary past of this genus. • The ESTs were clustered into unigenes for each poplar species examined. Gene families were constructed for all proteins deduced from these unigenes, and KS dating was performed on all paralogs within a gene family. The fraction of paralogs was then plotted against the KS values, which resulted in a distribution reflecting the age of duplicated genes in poplar. • Sufficient EST data were available for seven different poplar species spanning four of the six sections of the genus Populus. For all these species, there was evidence that a large-scale gene-duplication event had occurred. • From our analysis it is clear that all poplar species have shared the same large-scale gene-duplication event, suggesting that this event must have occurred in the ancestor of poplar, or at least very early in the evolution of the Populus genus.

@article{villarejo_evidence_2005,
	title = {Evidence for a protein transported through the secretory pathway en route to the higher plant chloroplast},
	volume = {7},
	copyright = {2005 Nature Publishing Group},
	issn = {1476-4679},
	url = {https://www.nature.com/articles/ncb1330},
	doi = {10/fmrqwn},
	abstract = {In contrast to animal and fungal cells, green plant cells contain one or multiple chloroplasts, the organelle(s) in which photosynthetic reactions take place. Chloroplasts are believed to have originated from an endosymbiotic event and contain DNA that codes for some of their proteins. Most chloroplast proteins are encoded by the nuclear genome and imported with the help of sorting signals that are intrinsic parts of the polypeptides. Here, we show that a chloroplast-located protein in higher plants takes an alternative route through the secretory pathway, and becomes N-glycosylated before entering the chloroplast.},
	language = {en},
	number = {12},
	urldate = {2021-06-11},
	journal = {Nature Cell Biology},
	publisher = {Nature Publishing Group},
	author = {Villarejo, Arsenio and Burén, Stefan and Larsson, Susanne and Déjardin, Annabelle and Monné, Magnus and Rudhe, Charlotta and Karlsson, Jan and Jansson, Stefan and Lerouge, Patrice and Rolland, Norbert and von Heijne, Gunnar and Grebe, Markus and Bakó, Laszlo and Samuelsson, Göran},
	month = dec,
	year = {2005},
	note = {Number: 12},
	pages = {1224--1231},
}

In contrast to animal and fungal cells, green plant cells contain one or multiple chloroplasts, the organelle(s) in which photosynthetic reactions take place. Chloroplasts are believed to have originated from an endosymbiotic event and contain DNA that codes for some of their proteins. Most chloroplast proteins are encoded by the nuclear genome and imported with the help of sorting signals that are intrinsic parts of the polypeptides. Here, we show that a chloroplast-located protein in higher plants takes an alternative route through the secretory pathway, and becomes N-glycosylated before entering the chloroplast.

@article{ihalainen_excitation_2005,
	title = {Excitation energy trapping in photosystem {I} complexes depleted in {Lhca1} and {Lhca4}},
	volume = {579},
	copyright = {FEBS Letters 579 (2005) 1873-3468 © 2015 Federation of European Biochemical Societies},
	issn = {1873-3468},
	url = {https://febs.onlinelibrary.wiley.com/doi/abs/10.1016/j.febslet.2005.06.091},
	doi = {10.1016/j.febslet.2005.06.091},
	abstract = {We report a time-resolved fluorescence spectroscopy characterization of photosystem I (PSI) particles prepared from Arabidopsis lines with knock-out mutations against the peripheral antenna proteins of Lhca1 or Lhca4. The first mutant retains Lhca2 and Lhca3 while the second retains one other light-harvesting protein of photosystem I (Lhca) protein, probably Lhca5. The results indicate that Lhca2/3 and Lhca1/4 each provides about equally effective energy transfer routes to the PSI core complex, and that Lhca5 provides a less effective energy transfer route. We suggest that the specific location of each Lhca protein within the PSI–LHCI supercomplex is more important than the presence of so-called red chlorophylls in the Lhca proteins.},
	language = {en},
	number = {21},
	urldate = {2021-06-11},
	journal = {FEBS Letters},
	author = {Ihalainen, Janne A. and Klimmek, Frank and Ganeteg, Ulrika and Stokkum, Ivo H. M. van and Grondelle, Rienk van and Jansson, Stefan and Dekker, Jan P.},
	year = {2005},
	note = {\_eprint: https://febs.onlinelibrary.wiley.com/doi/pdf/10.1016/j.febslet.2005.06.091},
	keywords = {DAS, Excitation energy trapping, LHCI, Lhca, Light-harvesting, PSI, Photosynthesis, WT, decay-associated spectra, light-harvesting complex I, light-harvesting protein of photosystem I, photosystem I, wild type},
	pages = {4787--4791},
}

We report a time-resolved fluorescence spectroscopy characterization of photosystem I (PSI) particles prepared from Arabidopsis lines with knock-out mutations against the peripheral antenna proteins of Lhca1 or Lhca4. The first mutant retains Lhca2 and Lhca3 while the second retains one other light-harvesting protein of photosystem I (Lhca) protein, probably Lhca5. The results indicate that Lhca2/3 and Lhca1/4 each provides about equally effective energy transfer routes to the PSI core complex, and that Lhca5 provides a less effective energy transfer route. We suggest that the specific location of each Lhca protein within the PSI–LHCI supercomplex is more important than the presence of so-called red chlorophylls in the Lhca proteins.

@article{bylesjo_masqot_2005,
	title = {{MASQOT}: a method for {cDNA} microarray spot quality control},
	volume = {6},
	issn = {1471-2105},
	shorttitle = {{MASQOT}},
	url = {https://doi.org/10.1186/1471-2105-6-250},
	doi = {10.1186/1471-2105-6-250},
	abstract = {cDNA microarray technology has emerged as a major player in the parallel detection of biomolecules, but still suffers from fundamental technical problems. Identifying and removing unreliable data is crucial to prevent the risk of receiving illusive analysis results. Visual assessment of spot quality is still a common procedure, despite the time-consuming work of manually inspecting spots in the range of hundreds of thousands or more.},
	number = {1},
	urldate = {2021-06-11},
	journal = {BMC Bioinformatics},
	author = {Bylesjö, Max and Eriksson, Daniel and Sjödin, Andreas and Sjöström, Michael and Jansson, Stefan and Antti, Henrik and Trygg, Johan},
	month = oct,
	year = {2005},
	keywords = {Classification Training, Foreground Region, Microarray Slide, Partial Little Square, Spot Quality},
	pages = {250},
}

cDNA microarray technology has emerged as a major player in the parallel detection of biomolecules, but still suffers from fundamental technical problems. Identifying and removing unreliable data is crucial to prevent the risk of receiving illusive analysis results. Visual assessment of spot quality is still a common procedure, despite the time-consuming work of manually inspecting spots in the range of hundreds of thousands or more.

@article{storf_pigment_2005,
	title = {Pigment {Binding}, {Fluorescence} {Properties}, and {Oligomerization} {Behavior} of {Lhca5}, a {Novel} {Light}-harvesting {Protein}*},
	volume = {280},
	issn = {0021-9258},
	url = {https://www.sciencedirect.com/science/article/pii/S0021925819630103},
	doi = {10.1074/jbc.M411248200},
	abstract = {A new potential light-harvesting protein, named Lhca5, was recently detected in higher plants. Because of the low amount of Lhca5 in thylakoid membranes, the isolation of a native Lhca5 pigment-protein complex has not been achieved to date. Therefore, we used in vitro reconstitution to analyze whether Lhca5 binds pigments and is actually an additional light-harvesting protein. By this approach we could demonstrate that Lhca5 binds pigments in a unique stoichiometry. Analyses of pigment requirements for light-harvesting complex formation by Lhca5 revealed that chlorophyll b is the only indispensable pigment. Fluorescence measurements showed that ligated chlorophylls and carotenoids are arranged in a way that allows directed energy transfer within the light-harvesting complex. Reconstitutions of Lhca5 together with other Lhca proteins resulted in the formation of heterodimers with Lhca1. This result demonstrates that Lhca5 is indeed a protein belonging to the light-harvesting antenna of photosystem I. The properties of Lhca5 are compared with those of previously characterized Lhca proteins, and the consequences of an additional Lhca protein for the composition of the light-harvesting antenna of photosystem I are discussed in view of the recently published photosystem I structure of the pea.},
	language = {en},
	number = {7},
	urldate = {2021-06-11},
	journal = {Journal of Biological Chemistry},
	author = {Storf, Stefanie and Jansson, Stefan and Schmid, Volkmar H. R.},
	month = feb,
	year = {2005},
	pages = {5163--5168},
}

A new potential light-harvesting protein, named Lhca5, was recently detected in higher plants. Because of the low amount of Lhca5 in thylakoid membranes, the isolation of a native Lhca5 pigment-protein complex has not been achieved to date. Therefore, we used in vitro reconstitution to analyze whether Lhca5 binds pigments and is actually an additional light-harvesting protein. By this approach we could demonstrate that Lhca5 binds pigments in a unique stoichiometry. Analyses of pigment requirements for light-harvesting complex formation by Lhca5 revealed that chlorophyll b is the only indispensable pigment. Fluorescence measurements showed that ligated chlorophylls and carotenoids are arranged in a way that allows directed energy transfer within the light-harvesting complex. Reconstitutions of Lhca5 together with other Lhca proteins resulted in the formation of heterodimers with Lhca1. This result demonstrates that Lhca5 is indeed a protein belonging to the light-harvesting antenna of photosystem I. The properties of Lhca5 are compared with those of previously characterized Lhca proteins, and the consequences of an additional Lhca protein for the composition of the light-harvesting antenna of photosystem I are discussed in view of the recently published photosystem I structure of the pea.

@article{klimmek_structure_2005,
	title = {Structure of the {Higher} {Plant} {Light} {Harvesting} {Complex} {I}:  {In} {Vivo} {Characterization} and {Structural} {Interdependence} of the {Lhca} {Proteins}},
	volume = {44},
	issn = {0006-2960},
	shorttitle = {Structure of the {Higher} {Plant} {Light} {Harvesting} {Complex} {I}},
	url = {https://doi.org/10.1021/bi047873g},
	doi = {10/dfnxgm},
	abstract = {We have investigated the structure of the higher plant light harvesting complex of photosystem I (LHCI) by analyzing PSI−LHCI particles isolated from a set of Arabidopsis plant lines, each lacking a specific Lhca (Lhca1−4) polypeptide. Functional antenna size measurements support the recent finding that there are four Lhca proteins per PSI in the crystal structure [Ben-Shem, A., Frolow, F., and Nelson, N. (2003) Nature 426, 630−635]. According to HPLC analyses the number of pigment molecules bound within the LHCI is higher than expected from reconstitution studies or analyses of isolated native LHCI. Comparison of the spectra of the particles from the different lines reveals chlorophyll absorption bands peaking at 696, 688, 665, and 655 nm that are not present in isolated PSI or LHCI. These bands presumably originate from “gap” or “linker” pigments that are cooperatively coordinated by the Lhca and/or PSI proteins, which we have tentatively localized in the PSI−LHCI complex.},
	number = {8},
	urldate = {2021-06-11},
	journal = {Biochemistry},
	publisher = {American Chemical Society},
	author = {Klimmek, Frank and Ganeteg, Ulrika and Ihalainen, Janne A. and van Roon, Henny and Jensen, Poul E. and Scheller, Henrik V. and Dekker, Jan P. and Jansson, Stefan},
	month = mar,
	year = {2005},
	pages = {3065--3073},
}

We have investigated the structure of the higher plant light harvesting complex of photosystem I (LHCI) by analyzing PSI−LHCI particles isolated from a set of Arabidopsis plant lines, each lacking a specific Lhca (Lhca1−4) polypeptide. Functional antenna size measurements support the recent finding that there are four Lhca proteins per PSI in the crystal structure [Ben-Shem, A., Frolow, F., and Nelson, N. (2003) Nature 426, 630−635]. According to HPLC analyses the number of pigment molecules bound within the LHCI is higher than expected from reconstitution studies or analyses of isolated native LHCI. Comparison of the spectra of the particles from the different lines reveals chlorophyll absorption bands peaking at 696, 688, 665, and 655 nm that are not present in isolated PSI or LHCI. These bands presumably originate from “gap” or “linker” pigments that are cooperatively coordinated by the Lhca and/or PSI proteins, which we have tentatively localized in the PSI−LHCI complex.

@article{morosinotto_association_2005,
	title = {The {Association} of the {Antenna} {System} to {Photosystem} {I} in {Higher} {Plants}: {COOPERATIVE} {INTERACTIONS} {STABILIZE} {THE} {SUPRAMOLECULAR} {COMPLEX} {AND} {ENHANCE} {RED}-{SHIFTED} {SPECTRAL} {FORMS}*},
	volume = {280},
	issn = {0021-9258},
	shorttitle = {The {Association} of the {Antenna} {System} to {Photosystem} {I} in {Higher} {Plants}},
	url = {https://www.sciencedirect.com/science/article/pii/S0021925820793798},
	doi = {10.1074/jbc.M502935200},
	abstract = {We report on the association of the antenna system to the reaction center in Photosystem I. Biochemical analysis of mutants depleted in antenna polypeptides showed that the binding of the antenna moiety is strongly cooperative. The minimal building block for the antenna system was shown to be a dimer. Specific protein-protein interactions play an important role in antenna association, and the gap pigments, bound at the interface between core and antenna, are proposed to mediate these interactions Gap pigments have been characterized by comparing the spectra of the Photosystem I to those of the isolated antenna and core components. CD spectroscopy showed that they are involved in pigment-pigment interactions, supporting their relevance in energy transfer from antenna to the reaction center. Moreover, gap pigments contribute to the red-shifted emission forms of Photosystem I antenna. When compared with Photosystem II, the association of peripheral antenna complexes in PSI appears to be more stable, but far less flexible and functional implications are discussed.},
	language = {en},
	number = {35},
	urldate = {2021-06-11},
	journal = {Journal of Biological Chemistry},
	author = {Morosinotto, Tomas and Ballottari, Matteo and Klimmek, Frank and Jansson, Stefan and Bassi, Roberto},
	month = sep,
	year = {2005},
	pages = {31050--31058},
}

We report on the association of the antenna system to the reaction center in Photosystem I. Biochemical analysis of mutants depleted in antenna polypeptides showed that the binding of the antenna moiety is strongly cooperative. The minimal building block for the antenna system was shown to be a dimer. Specific protein-protein interactions play an important role in antenna association, and the gap pigments, bound at the interface between core and antenna, are proposed to mediate these interactions Gap pigments have been characterized by comparing the spectra of the Photosystem I to those of the isolated antenna and core components. CD spectroscopy showed that they are involved in pigment-pigment interactions, supporting their relevance in energy transfer from antenna to the reaction center. Moreover, gap pigments contribute to the red-shifted emission forms of Photosystem I antenna. When compared with Photosystem II, the association of peripheral antenna complexes in PSI appears to be more stable, but far less flexible and functional implications are discussed.

@article{taylor_transcriptome_2005,
	title = {The transcriptome of {Populus} in elevated {CO2}},
	volume = {167},
	issn = {1469-8137},
	url = {https://nph.onlinelibrary.wiley.com/doi/abs/10.1111/j.1469-8137.2005.01450.x},
	doi = {10/d7g7mz},
	abstract = {• The consequences of increasing atmospheric carbon dioxide for long-term adaptation of forest ecosystems remain uncertain, with virtually no studies undertaken at the genetic level. A global analysis using cDNA microarrays was conducted following 6 yr exposure of Populus × euramericana (clone I-214) to elevated [CO2] in a FACE (free-air CO2 enrichment) experiment. • Gene expression was sensitive to elevated [CO2] but the response depended on the developmental age of the leaves, and {\textless} 50 transcripts differed significantly between different CO2 environments. For young leaves most differentially expressed genes were upregulated in elevated [CO2], while in semimature leaves most were downregulated in elevated [CO2]. • For transcripts related only to the small subunit of Rubisco, upregulation in LPI 3 and downregulation in LPI 6 leaves in elevated CO2 was confirmed by anova. Similar patterns of gene expression for young leaves were also confirmed independently across year 3 and year 6 microarray data, and using real-time RT–PCR. • This study provides the first clues to the long-term genetic expression changes that may occur during long-term plant response to elevated CO2.},
	language = {en},
	number = {1},
	urldate = {2021-06-11},
	journal = {New Phytologist},
	author = {Taylor, Gail and Street, Nathaniel R. and Tricker, Penny J. and Sjödin, Andreas and Graham, Laura and Skogström, Oskar and Calfapietra, Carlo and Scarascia-Mugnozza, Giuseppe and Jansson, Stefan},
	year = {2005},
	note = {\_eprint: https://nph.onlinelibrary.wiley.com/doi/pdf/10.1111/j.1469-8137.2005.01450.x},
	keywords = {FACE (free-air CO2 enrichment), Populus, elevated CO2, gene expression, leaf development, microarray},
	pages = {143--154},
}

• The consequences of increasing atmospheric carbon dioxide for long-term adaptation of forest ecosystems remain uncertain, with virtually no studies undertaken at the genetic level. A global analysis using cDNA microarrays was conducted following 6 yr exposure of Populus × euramericana (clone I-214) to elevated [CO2] in a FACE (free-air CO2 enrichment) experiment. • Gene expression was sensitive to elevated [CO2] but the response depended on the developmental age of the leaves, and \textless 50 transcripts differed significantly between different CO2 environments. For young leaves most differentially expressed genes were upregulated in elevated [CO2], while in semimature leaves most were downregulated in elevated [CO2]. • For transcripts related only to the small subunit of Rubisco, upregulation in LPI 3 and downregulation in LPI 6 leaves in elevated CO2 was confirmed by anova. Similar patterns of gene expression for young leaves were also confirmed independently across year 3 and year 6 microarray data, and using real-time RT–PCR. • This study provides the first clues to the long-term genetic expression changes that may occur during long-term plant response to elevated CO2.

@article{kulheim_what_2005,
	title = {What leads to reduced fitness in non-photochemical quenching mutants?},
	volume = {125},
	issn = {0031-9317},
	doi = {10/djtwsp},
	abstract = {Feedback de-excitation (FDE) is a process that protects photosystem II from damage during short periods of overexcitation. Arabidopsis thaliana mutants lacking this mechanism have reduced fitness in environments with variable light intensities. We have assayed the physiological consequences of mutations resulting in the lack of FDE and analysed the differences between field-grown plants and plants grown under fluctuating light in the laboratory. We show that FDE is an important mechanism in short-term responses to fluctuating light. Anthocyanin and carbohydrate levels indicated that the mutant plants were stressed to a higher degree than wild-type (WT) plants. Field-grown mutants were photo-inactivated to a greater degree than WT, whereas mutant plants in the fluctuating light environment in the laboratory seemed to downregulate the photosynthetic quantum yield, thereby avoiding photo-damage but resulting in impaired growth in the case of one mutant. Finally, we provide evidence that FDE is most important under conditions when photosynthesis limits plant growth, for example during flower and seed development.},
	language = {English},
	number = {2},
	journal = {Physiologia Plantarum},
	publisher = {Blackwell Publishing},
	author = {Kulheim, C. and Jansson, S.},
	month = oct,
	year = {2005},
	note = {Place: Oxford
WOS:000231677000006},
	keywords = {arabidopsis-thaliana, chlorophyll fluorescence, cold-acclimation, energy-dissipation, light-harvesting complex, low-temperature, photoinhibition, photosynthesis, plants, xanthophyll cycle},
	pages = {202--211},
}

Feedback de-excitation (FDE) is a process that protects photosystem II from damage during short periods of overexcitation. Arabidopsis thaliana mutants lacking this mechanism have reduced fitness in environments with variable light intensities. We have assayed the physiological consequences of mutations resulting in the lack of FDE and analysed the differences between field-grown plants and plants grown under fluctuating light in the laboratory. We show that FDE is an important mechanism in short-term responses to fluctuating light. Anthocyanin and carbohydrate levels indicated that the mutant plants were stressed to a higher degree than wild-type (WT) plants. Field-grown mutants were photo-inactivated to a greater degree than WT, whereas mutant plants in the fluctuating light environment in the laboratory seemed to downregulate the photosynthetic quantum yield, thereby avoiding photo-damage but resulting in impaired growth in the case of one mutant. Finally, we provide evidence that FDE is most important under conditions when photosynthesis limits plant growth, for example during flower and seed development.

@article{sterky_populus_2004,
	chapter = {Biological Sciences},
	title = {A {Populus} {EST} resource for plant functional genomics},
	volume = {101},
	copyright = {Copyright © 2004, The National Academy of Sciences},
	issn = {0027-8424, 1091-6490},
	url = {https://www.pnas.org/content/101/38/13951},
	doi = {10/brt6bx},
	abstract = {Trees present a life form of paramount importance for terrestrial ecosystems and human societies because of their ecological structure and physiological function and provision of energy and industrial materials. The genus Populus is the internationally accepted model for molecular tree biology. We have analyzed 102,019 Populus ESTs that clustered into 11,885 clusters and 12,759 singletons. We also provide {\textgreater}4,000 assembled full clone sequences to serve as a basis for the upcoming annotation of the Populus genome sequence. A public web-based EST database (populusdb) provides digital expression profiles for 18 tissues that comprise the majority of differentiated organs. The coding content of Populus and Arabidopsis genomes shows very high similarity, indicating that differences between these annual and perennial angiosperm life forms result primarily from differences in gene regulation. The high similarity between Populus and Arabidopsis will allow studies of Populus to directly benefit from the detailed functional genomic information generated for Arabidopsis, enabling detailed insights into tree development and adaptation. These data will also valuable for functional genomic efforts in Arabidopsis.},
	language = {en},
	number = {38},
	urldate = {2021-06-15},
	journal = {Proceedings of the National Academy of Sciences},
	publisher = {National Academy of Sciences},
	author = {Sterky, Fredrik and Bhalerao, Rupali R. and Unneberg, Per and Segerman, Bo and Nilsson, Peter and Brunner, Amy M. and Charbonnel-Campaa, Laurence and Lindvall, Jenny Jonsson and Tandre, Karolina and Strauss, Steven H. and Sundberg, Björn and Gustafsson, Petter and Uhlén, Mathias and Bhalerao, Rishikesh P. and Nilsson, Ove and Sandberg, Göran and Karlsson, Jan and Lundeberg, Joakim and Jansson, Stefan},
	month = sep,
	year = {2004},
	pages = {13951--13956},
}

Trees present a life form of paramount importance for terrestrial ecosystems and human societies because of their ecological structure and physiological function and provision of energy and industrial materials. The genus Populus is the internationally accepted model for molecular tree biology. We have analyzed 102,019 Populus ESTs that clustered into 11,885 clusters and 12,759 singletons. We also provide \textgreater4,000 assembled full clone sequences to serve as a basis for the upcoming annotation of the Populus genome sequence. A public web-based EST database (populusdb) provides digital expression profiles for 18 tissues that comprise the majority of differentiated organs. The coding content of Populus and Arabidopsis genomes shows very high similarity, indicating that differences between these annual and perennial angiosperm life forms result primarily from differences in gene regulation. The high similarity between Populus and Arabidopsis will allow studies of Populus to directly benefit from the detailed functional genomic information generated for Arabidopsis, enabling detailed insights into tree development and adaptation. These data will also valuable for functional genomic efforts in Arabidopsis.

@article{andersson_transcriptional_2004,
	title = {A transcriptional timetable of autumn senescence},
	volume = {5},
	issn = {1474-760X},
	doi = {10/dw5fcc},
	abstract = {Background: We have developed genomic tools to allow the genus Populus ( aspens and cottonwoods) to be exploited as a full-featured model for investigating fundamental aspects of tree biology. We have undertaken large-scale expressed sequence tag ( EST) sequencing programs and created Populus microarrays with significant gene coverage. One of the important aspects of plant biology that cannot be studied in annual plants is the gene activity involved in the induction of autumn leaf senescence. Results: On the basis of 36,354 Populus ESTs, obtained from seven cDNA libraries, we have created a DNA microarray consisting of 13,490 clones, spotted in duplicate. Of these clones, 12,376 (92\%) were confirmed by resequencing and all sequences were annotated and functionally classified. Here we have used the microarray to study transcript abundance in leaves of a free-growing aspen tree ( Populus tremula) in northern Sweden during natural autumn senescence. Of the 13,490 spotted clones, 3,792 represented genes with significant expression in all leaf samples from the seven studied dates. Conclusions: We observed a major shift in gene expression, coinciding with massive chlorophyll degradation, that reflected a shift from photosynthetic competence to energy generation by mitochondrial respiration, oxidation of fatty acids and nutrient mobilization. Autumn senescence had much in common with senescence in annual plants; for example many proteases were induced. We also found evidence for increased transcriptional activity before the appearance of visible signs of senescence, presumably preparing the leaf for degradation of its components.},
	language = {English},
	number = {4},
	journal = {Genome Biology},
	publisher = {Bmc},
	author = {Andersson, A. and Keskitalo, J. and Sjodin, A. and Bhalerao, Rishikesh P. and Sterky, F. and Wissel, K. and Tandre, K. and Aspeborg, H. and Moyle, R. and Ohmiya, Y. and Bhalerao, R. and Brunner, A. and Gustafsson, P. and Karlsson, J. and Lundeberg, J. and Nilsson, O. and Sandberg, G. and Strauss, S. and Sundberg, B. and Uhlen, M. and Jansson, S. and Nilsson, P.},
	year = {2004},
	note = {Place: London
WOS:000220584700010},
	keywords = {aspen, biology, cytosolic glutamine-synthetase, gene-expression, genomics, leaf senescence, leaves, plants, programmed cell-death, proteins},
	pages = {R24},
}

Background: We have developed genomic tools to allow the genus Populus ( aspens and cottonwoods) to be exploited as a full-featured model for investigating fundamental aspects of tree biology. We have undertaken large-scale expressed sequence tag ( EST) sequencing programs and created Populus microarrays with significant gene coverage. One of the important aspects of plant biology that cannot be studied in annual plants is the gene activity involved in the induction of autumn leaf senescence. Results: On the basis of 36,354 Populus ESTs, obtained from seven cDNA libraries, we have created a DNA microarray consisting of 13,490 clones, spotted in duplicate. Of these clones, 12,376 (92%) were confirmed by resequencing and all sequences were annotated and functionally classified. Here we have used the microarray to study transcript abundance in leaves of a free-growing aspen tree ( Populus tremula) in northern Sweden during natural autumn senescence. Of the 13,490 spotted clones, 3,792 represented genes with significant expression in all leaf samples from the seven studied dates. Conclusions: We observed a major shift in gene expression, coinciding with massive chlorophyll degradation, that reflected a shift from photosynthetic competence to energy generation by mitochondrial respiration, oxidation of fatty acids and nutrient mobilization. Autumn senescence had much in common with senescence in annual plants; for example many proteases were induced. We also found evidence for increased transcriptional activity before the appearance of visible signs of senescence, presumably preparing the leaf for degradation of its components.

@article{lescot_annotation_2004,
	title = {Annotation of a 95-kb {Populus} deltoides genomic sequence reveals a disease resistance gene cluster and novel class {I} and class {II} transposable elements},
	volume = {109},
	issn = {1432-2242},
	url = {https://doi.org/10.1007/s00122-004-1621-0},
	doi = {10/d4g3m9},
	abstract = {Poplar has become a model system for functional genomics in woody plants. Here, we report the sequencing and annotation of the first large contiguous stretch of genomic sequence (95 kb) of poplar, corresponding to a bacterial artificial chromosome clone mapped 0.6 centiMorgan from the Melampsora larici-populina resistance locus. The annotation revealed 15 putative genetic objects, of which five were classified as hypothetical genes that were similar only with expressed sequence tags from poplar. Ten putative objects showed similarity with known genes, of which one was similar to a kinase. Three other objects corresponded to the toll/interleukin-1 receptor/nucleotide-binding site/leucine-rich repeat class of plant disease resistance genes, of which two were predicted to encode an amino terminal nuclear localization signal. Four objects were homologous to the Ty1/copia family of class I transposable elements, one of which was designated Retropop and interrupted one of the disease resistance genes. Two other objects constituted a novel Spm-like class II transposable element, which we designated Magali.},
	language = {en},
	number = {1},
	urldate = {2021-06-30},
	journal = {Theoretical and Applied Genetics},
	author = {Lescot, M. and Rombauts, S. and Zhang, J. and Aubourg, S. and Mathé, C. and Jansson, S. and Rouzé, P. and Boerjan, W.},
	month = jun,
	year = {2004},
	pages = {10--22},
}

Poplar has become a model system for functional genomics in woody plants. Here, we report the sequencing and annotation of the first large contiguous stretch of genomic sequence (95 kb) of poplar, corresponding to a bacterial artificial chromosome clone mapped 0.6 centiMorgan from the Melampsora larici-populina resistance locus. The annotation revealed 15 putative genetic objects, of which five were classified as hypothetical genes that were similar only with expressed sequence tags from poplar. Ten putative objects showed similarity with known genes, of which one was similar to a kinase. Three other objects corresponded to the toll/interleukin-1 receptor/nucleotide-binding site/leucine-rich repeat class of plant disease resistance genes, of which two were predicted to encode an amino terminal nuclear localization signal. Four objects were homologous to the Ty1/copia family of class I transposable elements, one of which was designated Retropop and interrupted one of the disease resistance genes. Two other objects constituted a novel Spm-like class II transposable element, which we designated Magali.

@article{ensminger_intermittent_2004,
	title = {Intermittent low temperatures constrain spring recovery of photosynthesis in boreal {Scots} pine forests},
	volume = {10},
	issn = {1354-1013},
	doi = {10/bg8q75},
	abstract = {During winter and early spring, evergreen boreal conifers are severely stressed because light energy cannot be used when photosynthesis is pre-empted by low ambient temperatures. To study photosynthetic performance dynamics in a severe boreal climate, seasonal changes in photosynthetic pigments, chloroplast proteins and photochemical efficiency were studied in a Scots pine forest near Zotino, Central Siberia. In winter, downregulation of photosynthesis involved loss of chlorophylls, a twofold increase in xanthophyll cycle pigments and sustained high levels of the light stress-induced zeaxanthin pigment. The highest levels of xanthophylls and zeaxanthin did not occur during the coldest winter period, but rather in April when light was increasing, indicating an increased capacity for thermal dissipation of excitation energy at that time. Concomitantly, in early spring the D1 protein of the photosystem II (PSII) reaction centre and the light-harvesting complex of PSII dropped to their lowest annual levels. In April and May, recovery of PSII activity, chloroplast protein synthesis and rearrangements of pigments were observed as air temperatures increased above 0degreesC. Nevertheless, severe intermittent low-temperature episodes during this period not only halted but actually reversed the physiological recovery. During these spring low-temperature episodes, protective processes involved a complementary function of the PsbS and early light-induced protein thylakoid proteins. Full recovery of photosynthesis did not occur until the end of May. Our results show that even after winter cold hardening, photosynthetic activity in evergreens responds opportunistically to environmental change throughout the cold season. Therefore, climate change effects potentially improve the sink capacity of boreal forests for atmospheric carbon. However, earlier photosynthesis in spring in response to warmer temperatures is strongly constrained by environmental variation, counteracting the positive effects of an early recovery process.},
	language = {English},
	number = {6},
	journal = {Global Change Biology},
	publisher = {Wiley},
	author = {Ensminger, I. and Sveshnikov, D. and Campbell, D. A. and Funk, C. and Jansson, S. and Lloyd, J. and Shibistova, O. and Oquist, G.},
	month = jun,
	year = {2004},
	note = {Place: Hoboken
WOS:000221741800006},
	keywords = {Pinus sylvestris, carbon balance, chlorophyll   fluorescence, cold stress, light-use efficiency, northern forests, photoinhibition, photosystem-ii, pigment composition, psbs protein, seasonal variations, seasonal-changes, snow cover, stress, xanthophyll cycle},
	pages = {995--1008},
}

During winter and early spring, evergreen boreal conifers are severely stressed because light energy cannot be used when photosynthesis is pre-empted by low ambient temperatures. To study photosynthetic performance dynamics in a severe boreal climate, seasonal changes in photosynthetic pigments, chloroplast proteins and photochemical efficiency were studied in a Scots pine forest near Zotino, Central Siberia. In winter, downregulation of photosynthesis involved loss of chlorophylls, a twofold increase in xanthophyll cycle pigments and sustained high levels of the light stress-induced zeaxanthin pigment. The highest levels of xanthophylls and zeaxanthin did not occur during the coldest winter period, but rather in April when light was increasing, indicating an increased capacity for thermal dissipation of excitation energy at that time. Concomitantly, in early spring the D1 protein of the photosystem II (PSII) reaction centre and the light-harvesting complex of PSII dropped to their lowest annual levels. In April and May, recovery of PSII activity, chloroplast protein synthesis and rearrangements of pigments were observed as air temperatures increased above 0degreesC. Nevertheless, severe intermittent low-temperature episodes during this period not only halted but actually reversed the physiological recovery. During these spring low-temperature episodes, protective processes involved a complementary function of the PsbS and early light-induced protein thylakoid proteins. Full recovery of photosynthesis did not occur until the end of May. Our results show that even after winter cold hardening, photosynthetic activity in evergreens responds opportunistically to environmental change throughout the cold season. Therefore, climate change effects potentially improve the sink capacity of boreal forests for atmospheric carbon. However, earlier photosynthesis in spring in response to warmer temperatures is strongly constrained by environmental variation, counteracting the positive effects of an early recovery process.

@article{ganeteg_is_2004,
	title = {Is {Each} {Light}-{Harvesting} {Complex} {Protein} {Important} for {Plant} {Fitness}?},
	volume = {134},
	issn = {0032-0889},
	url = {https://doi.org/10.1104/pp.103.033324},
	doi = {10/bmspz3},
	abstract = {Many of the photosynthetic genes are conserved among all higher plants, indicating that there is strong selective pressure to maintain the genes of each protein. However, mutants of these genes often lack visible growth phenotypes, suggesting that they are important only under certain conditions or have overlapping functions. To assess the importance of specific genes encoding the light-harvesting complex (LHC) proteins for the survival of the plant in the natural environment, we have combined two different scientific traditions by using an ecological fitness assay on a set of genetically modified Arabidopsis plants with differing LHC protein contents. The fitness of all of the LHC-deficient plants was reduced in some of the growth environments, supporting the hypothesis that each of the genes has been conserved because they provide ecological flexibility, which is of great adaptive value given the highly variable conditions encountered in nature.},
	number = {1},
	urldate = {2021-06-15},
	journal = {Plant Physiology},
	author = {Ganeteg, Ulrika and Külheim, Carsten and Andersson, Jenny and Jansson, Stefan},
	month = jan,
	year = {2004},
	pages = {502--509},
}

Many of the photosynthetic genes are conserved among all higher plants, indicating that there is strong selective pressure to maintain the genes of each protein. However, mutants of these genes often lack visible growth phenotypes, suggesting that they are important only under certain conditions or have overlapping functions. To assess the importance of specific genes encoding the light-harvesting complex (LHC) proteins for the survival of the plant in the natural environment, we have combined two different scientific traditions by using an ecological fitness assay on a set of genetically modified Arabidopsis plants with differing LHC protein contents. The fitness of all of the LHC-deficient plants was reduced in some of the growth environments, supporting the hypothesis that each of the genes has been conserved because they provide ecological flexibility, which is of great adaptive value given the highly variable conditions encountered in nature.

@article{ganeteg_lhca5_2004,
	title = {Lhca5 – an {LHC}-{Type} {Protein} {Associated} with {Photosystem} {I}},
	volume = {54},
	issn = {1573-5028},
	url = {https://doi.org/10.1023/B:PLAN.0000040813.05224.94},
	doi = {10/bkhvhq},
	abstract = {The light-harvesting antenna of higher plant photosystem (PS) I is known to be composed of four different types of light-harvesting complex (LHC) proteins (Lhca1–4). However, the genomic sequence of Arabidopsis thaliana contains open reading frames coding for two additional LHC type proteins (Lhca5–6) that are presumably associated with PSI. While Lhca6 might not be expressed at all, ESTs have been detected for the Lhca5 gene in Arabidopsis and a number of other plant species. Here we demonstrate the presence of the Lhca5 gene product in the thylakoid membrane of Arabidopsis as an additional type of Lhca-protein associated with PSI. Lhca5 seems to be regulated differently from the other LHC proteins since Lhca5 mRNA levels increase under high light conditions. Analyses reported here of Lhca5 in plants lacking individual Lhca1–4 proteins show that it is more abundant in plants lacking Lhca1/4, and suggest that it interacts in a direct physical fashion with Lhca2 or Lhca3. We propose that Lhca5 binds chlorophylls in a similar fashion to the other Lhca proteins and is associated with PSI only in sub-stoichiometric amounts.},
	language = {en},
	number = {5},
	urldate = {2021-06-15},
	journal = {Plant Molecular Biology},
	author = {Ganeteg, Ulrika and Klimmek, Frank and Jansson, Stefan},
	month = mar,
	year = {2004},
	pages = {641--651},
}

The light-harvesting antenna of higher plant photosystem (PS) I is known to be composed of four different types of light-harvesting complex (LHC) proteins (Lhca1–4). However, the genomic sequence of Arabidopsis thaliana contains open reading frames coding for two additional LHC type proteins (Lhca5–6) that are presumably associated with PSI. While Lhca6 might not be expressed at all, ESTs have been detected for the Lhca5 gene in Arabidopsis and a number of other plant species. Here we demonstrate the presence of the Lhca5 gene product in the thylakoid membrane of Arabidopsis as an additional type of Lhca-protein associated with PSI. Lhca5 seems to be regulated differently from the other LHC proteins since Lhca5 mRNA levels increase under high light conditions. Analyses reported here of Lhca5 in plants lacking individual Lhca1–4 proteins show that it is more abundant in plants lacking Lhca1/4, and suggest that it interacts in a direct physical fashion with Lhca2 or Lhca3. We propose that Lhca5 binds chlorophylls in a similar fashion to the other Lhca proteins and is associated with PSI only in sub-stoichiometric amounts.

@article{andersson_absence_2003,
	title = {Absence of the {Lhcb1} and {Lhcb2} proteins of the light-harvesting complex of photosystem {II} – effects on photosynthesis, grana stacking and fitness},
	volume = {35},
	issn = {1365-313X},
	url = {https://onlinelibrary.wiley.com/doi/abs/10.1046/j.1365-313X.2003.01811.x},
	doi = {10.1046/j.1365-313X.2003.01811.x},
	abstract = {We have constructed Arabidopsis thaliana plants that are virtually devoid of the major light-harvesting complex, LHC II. This was accomplished by introducing the Lhcb2.1 coding region in the antisense orientation into the genome by Agrobacterium-mediated transformation. Lhcb1 and Lhcb2 were absent, while Lhcb3, a protein present in LHC II associated with photosystem (PS) II, was retained. Plants had a pale green appearance and showed reduced chlorophyll content and an elevated chlorophyll a/b ratio. The content of PS II reaction centres was unchanged on a leaf area basis, but there was evidence for increases in the relative levels of other light harvesting proteins, notably CP26, associated with PS II, and Lhca4, associated with PS I. Electron microscopy showed the presence of grana. Photosynthetic rates at saturating irradiance were the same in wild-type and antisense plants, but there was a 10–15\% reduction in quantum yield that reflected the decrease in light absorption by the leaf. The antisense plants were not able to perform state transitions, and their capacity for non-photochemical quenching was reduced. There was no difference in growth between wild-type and antisense plants under controlled climate conditions, but the antisense plants performed worse compared to the wild type in the field, with decreases in seed production of up to 70\%.},
	language = {en},
	number = {3},
	urldate = {2024-06-28},
	journal = {The Plant Journal},
	author = {Andersson, Jenny and Wentworth, Mark and Walters, Robin G. and Howard, Caroline A. and Ruban, Alexander V. and Horton, Peter and Jansson, Stefan},
	year = {2003},
	note = {\_eprint: https://onlinelibrary.wiley.com/doi/pdf/10.1046/j.1365-313X.2003.01811.x},
	keywords = {Arabidopsis, LHC II, antisense, fitness, photosynthesis, state transitions},
	pages = {350--361},
}

We have constructed Arabidopsis thaliana plants that are virtually devoid of the major light-harvesting complex, LHC II. This was accomplished by introducing the Lhcb2.1 coding region in the antisense orientation into the genome by Agrobacterium-mediated transformation. Lhcb1 and Lhcb2 were absent, while Lhcb3, a protein present in LHC II associated with photosystem (PS) II, was retained. Plants had a pale green appearance and showed reduced chlorophyll content and an elevated chlorophyll a/b ratio. The content of PS II reaction centres was unchanged on a leaf area basis, but there was evidence for increases in the relative levels of other light harvesting proteins, notably CP26, associated with PS II, and Lhca4, associated with PS I. Electron microscopy showed the presence of grana. Photosynthetic rates at saturating irradiance were the same in wild-type and antisense plants, but there was a 10–15% reduction in quantum yield that reflected the decrease in light absorption by the leaf. The antisense plants were not able to perform state transitions, and their capacity for non-photochemical quenching was reduced. There was no difference in growth between wild-type and antisense plants under controlled climate conditions, but the antisense plants performed worse compared to the wild type in the field, with decreases in seed production of up to 70%.

@article{bhalerao_gene_2003,
	title = {Gene {Expression} in {Autumn} {Leaves}},
	volume = {131},
	issn = {0032-0889},
	url = {https://doi.org/10.1104/pp.012732},
	doi = {10.1104/pp.012732},
	abstract = {Two cDNA libraries were prepared, one from leaves of a field-grown aspen (Populus tremula) tree, harvested just before any visible sign of leaf senescence in the autumn, and one from young but fully expanded leaves of greenhouse-grown aspen (Populus tremula × tremuloides). Expressed sequence tags (ESTs; 5,128 and 4,841, respectively) were obtained from the two libraries. A semiautomatic method of annotation and functional classification of the ESTs, according to a modified Munich Institute of Protein Sequences classification scheme, was developed, utilizing information from three different databases. The patterns of gene expression in the two libraries were strikingly different. In the autumn leaf library, ESTs encoding metallothionein, early light-inducible proteins, and cysteine proteases were most abundant. Clones encoding other proteases and proteins involved in respiration and breakdown of lipids and pigments, as well as stress-related genes, were also well represented. We identified homologs to many known senescence-associated genes, as well as seven different genes encoding cysteine proteases, two encoding aspartic proteases, five encoding metallothioneins, and 35 additional genes that were up-regulated in autumn leaves. We also indirectly estimated the rate of plastid protein synthesis in the autumn leaves to be less that 10\% of that in young leaves.},
	number = {2},
	urldate = {2024-06-28},
	journal = {Plant Physiology},
	author = {Bhalerao, Rupali and Keskitalo, Johanna and Sterky, Fredrik and Erlandsson, Rikard and Björkbacka, Harry and Birve, Simon Jonsson and Karlsson, Jan and Gardeström, Per and Gustafsson, Petter and Lundeberg, Joakim and Jansson, Stefan},
	month = feb,
	year = {2003},
	pages = {430--442},
}

Two cDNA libraries were prepared, one from leaves of a field-grown aspen (Populus tremula) tree, harvested just before any visible sign of leaf senescence in the autumn, and one from young but fully expanded leaves of greenhouse-grown aspen (Populus tremula × tremuloides). Expressed sequence tags (ESTs; 5,128 and 4,841, respectively) were obtained from the two libraries. A semiautomatic method of annotation and functional classification of the ESTs, according to a modified Munich Institute of Protein Sequences classification scheme, was developed, utilizing information from three different databases. The patterns of gene expression in the two libraries were strikingly different. In the autumn leaf library, ESTs encoding metallothionein, early light-inducible proteins, and cysteine proteases were most abundant. Clones encoding other proteases and proteins involved in respiration and breakdown of lipids and pigments, as well as stress-related genes, were also well represented. We identified homologs to many known senescence-associated genes, as well as seven different genes encoding cysteine proteases, two encoding aspartic proteases, five encoding metallothioneins, and 35 additional genes that were up-regulated in autumn leaves. We also indirectly estimated the rate of plastid protein synthesis in the autumn leaves to be less that 10% of that in young leaves.

@article{ruban_plants_2003,
	title = {Plants lacking the main light-harvesting complex retain photosystem {II} macro-organization},
	volume = {421},
	copyright = {2003 Macmillan Magazines Ltd.},
	issn = {1476-4687},
	url = {https://www.nature.com/articles/nature01344},
	doi = {10.1038/nature01344},
	abstract = {Photosystem II (PSII) is a key component of photosynthesis, the process of converting sunlight into the chemical energy of life. In plant cells, it forms a unique oligomeric macrostructure in membranes of the chloroplasts1. Several light-harvesting antenna complexes are organized precisely in the PSII macrostructure—the major trimeric complexes (LHCII)2 that bind 70\% of PSII chlorophyll and three minor monomeric complexes3—which together form PSII supercomplexes4,5,6. The antenna complexes are essential for collecting sunlight and regulating photosynthesis7,8,9, but the relationship between these functions and their molecular architecture is unresolved. Here we report that antisense Arabidopsis plants lacking the proteins that form LHCII trimers10 have PSII supercomplexes with almost identical abundance and structure to those found in wild-type plants. The place of LHCII is taken by a normally minor and monomeric complex, CP26, which is synthesized in large amounts and organized into trimers. Trimerization is clearly not a specific attribute of LHCII. Our results highlight the importance of the PSII macrostructure: in the absence of one of its main components, another protein is recruited to allow it to assemble and function.},
	language = {en},
	number = {6923},
	urldate = {2024-06-28},
	journal = {Nature},
	publisher = {Nature Publishing Group},
	author = {Ruban, A. V. and Wentworth, M. and Yakushevska, A. E. and Andersson, J. and Lee, P. J. and Keegstra, W. and Dekker, J. P. and Boekema, E. J. and Jansson, S. and Horton, P.},
	month = feb,
	year = {2003},
	keywords = {Humanities and Social Sciences, Science, multidisciplinary},
	pages = {648--652},
}

Photosystem II (PSII) is a key component of photosynthesis, the process of converting sunlight into the chemical energy of life. In plant cells, it forms a unique oligomeric macrostructure in membranes of the chloroplasts1. Several light-harvesting antenna complexes are organized precisely in the PSII macrostructure—the major trimeric complexes (LHCII)2 that bind 70% of PSII chlorophyll and three minor monomeric complexes3—which together form PSII supercomplexes4,5,6. The antenna complexes are essential for collecting sunlight and regulating photosynthesis7,8,9, but the relationship between these functions and their molecular architecture is unresolved. Here we report that antisense Arabidopsis plants lacking the proteins that form LHCII trimers10 have PSII supercomplexes with almost identical abundance and structure to those found in wild-type plants. The place of LHCII is taken by a normally minor and monomeric complex, CP26, which is synthesized in large amounts and organized into trimers. Trimerization is clearly not a specific attribute of LHCII. Our results highlight the importance of the PSII macrostructure: in the absence of one of its main components, another protein is recruited to allow it to assemble and function.

@article{yakushevska_structure_2003,
	title = {The {Structure} of {Photosystem} {II} in {Arabidopsis}: {Localization} of the {CP26} and {CP29} {Antenna} {Complexes}},
	volume = {42},
	issn = {0006-2960},
	shorttitle = {The {Structure} of {Photosystem} {II} in {Arabidopsis}},
	url = {https://doi.org/10.1021/bi027109z},
	doi = {10/c63zsj},
	abstract = {A genetic approach has been adopted to investigate the organization of the light-harvesting proteins in the photosystem II (PSII) complex in plants. PSII membrane fragments were prepared from wild-type Arabidopis thaliana and plants expressing antisense constructs to Lhcb4 and Lhcb5 genes, lacking CP29 and CP26, respectively (Andersson et al. (2001) Plant Cell 13, 1193−1204). Ordered PS II arrays and PS II supercomplexes were isolated from the membranes of plants lacking CP26 but could not be prepared from those lacking CP29. Membranes and supercomplexes lacking CP26 were less stable than those prepared from the wild type. Transmission electron microscopy aided by single-particle image analysis was applied to the ordered arrays and the isolated PSII complexes. The difference between the images obtained from wild type and antisense plants showed the location of CP26 to be near CP43 and one of the light-harvesting complex trimers. Therefore, the location of the CP26 within PSII was directly established for the first time, and the location of the CP29 complex was determined by elimination. Alterations in the packing of the PSII complexes in the thylakoid membrane also resulted from the absence of CP26. The minor light-harvesting complexes each have a unique location and important roles in the stabilization of the oligomeric PSII structure.},
	number = {3},
	urldate = {2021-07-05},
	journal = {Biochemistry},
	publisher = {American Chemical Society},
	author = {Yakushevska, Alevtyna E. and Keegstra, Wilko and Boekema, Egbert J. and Dekker, Jan P. and Andersson, Jenny and Jansson, Stefan and Ruban, Alexander V. and Horton, Peter},
	month = jan,
	year = {2003},
	pages = {608--613},
}

A genetic approach has been adopted to investigate the organization of the light-harvesting proteins in the photosystem II (PSII) complex in plants. PSII membrane fragments were prepared from wild-type Arabidopis thaliana and plants expressing antisense constructs to Lhcb4 and Lhcb5 genes, lacking CP29 and CP26, respectively (Andersson et al. (2001) Plant Cell 13, 1193−1204). Ordered PS II arrays and PS II supercomplexes were isolated from the membranes of plants lacking CP26 but could not be prepared from those lacking CP29. Membranes and supercomplexes lacking CP26 were less stable than those prepared from the wild type. Transmission electron microscopy aided by single-particle image analysis was applied to the ordered arrays and the isolated PSII complexes. The difference between the images obtained from wild type and antisense plants showed the location of CP26 to be near CP43 and one of the light-harvesting complex trimers. Therefore, the location of the CP26 within PSII was directly established for the first time, and the location of the CP29 complex was determined by elimination. Alterations in the packing of the PSII complexes in the thylakoid membrane also resulted from the absence of CP26. The minor light-harvesting complexes each have a unique location and important roles in the stabilization of the oligomeric PSII structure.