Publications 2024

@article{hasan_redox_2024,
	title = {Redox signalling in plant–nematode interactions: {Insights} into molecular crosstalk and defense mechanisms},
	volume = {47},
	copyright = {© 2024 John Wiley \& Sons Ltd.},
	issn = {1365-3040},
	shorttitle = {Redox signalling in plant–nematode interactions},
	url = {https://onlinelibrary.wiley.com/doi/abs/10.1111/pce.14925},
	doi = {10.1111/pce.14925},
	abstract = {Plant–parasitic nematodes, specifically cyst nematodes (CNs) and root-knot nematodes (RKNs), pose significant threats to global agriculture, leading to substantial crop losses. Both CNs and RKNs induce permanent feeding sites in the root of their host plants, which then serve as their only source of nutrients throughout their lifecycle. Plants deploy reactive oxygen species (ROS) as a primary defense mechanism against nematode invasion. Notably, both CNs and RKNs have evolved sophisticated strategies to manipulate the host's redox environment to their advantage, with each employing distinct tactics to combat ROS. In this review, we have focused on the role of ROS and its scavenging network in interactions between host plants and CNs and RKNs. Overall, this review emphasizes the complex interplay between plant defense mechanism, redox signalling and nematode survival tactics, suggesting potential avenues for developing innovative nematode management strategies in agriculture.},
	language = {en},
	number = {8},
	urldate = {2024-07-19},
	journal = {Plant, Cell \& Environment},
	author = {Hasan, M. Shamim and Lin, Ching-Jung and Marhavy, Peter and Kyndt, Tina and Siddique, Shahid},
	year = {2024},
	note = {\_eprint: https://onlinelibrary.wiley.com/doi/pdf/10.1111/pce.14925},
	keywords = {ROS, antioxidants, cyst nematodes, effectors, root-knot nematodes},
	pages = {2811--2820},
}

Plant–parasitic nematodes, specifically cyst nematodes (CNs) and root-knot nematodes (RKNs), pose significant threats to global agriculture, leading to substantial crop losses. Both CNs and RKNs induce permanent feeding sites in the root of their host plants, which then serve as their only source of nutrients throughout their lifecycle. Plants deploy reactive oxygen species (ROS) as a primary defense mechanism against nematode invasion. Notably, both CNs and RKNs have evolved sophisticated strategies to manipulate the host's redox environment to their advantage, with each employing distinct tactics to combat ROS. In this review, we have focused on the role of ROS and its scavenging network in interactions between host plants and CNs and RKNs. Overall, this review emphasizes the complex interplay between plant defense mechanism, redox signalling and nematode survival tactics, suggesting potential avenues for developing innovative nematode management strategies in agriculture.

@article{lecoutre_reduced_2024,
	title = {Reduced adipocyte glutaminase activity promotes energy expenditure and metabolic health},
	copyright = {2024 The Author(s)},
	issn = {2522-5812},
	url = {https://www.nature.com/articles/s42255-024-01083-y},
	doi = {10.1038/s42255-024-01083-y},
	abstract = {Glutamine and glutamate are interconverted by several enzymes and alterations in this metabolic cycle are linked to cardiometabolic traits. Herein, we show that obesity-associated insulin resistance is characterized by decreased plasma and white adipose tissue glutamine-to-glutamate ratios. We couple these stoichiometric changes to perturbed fat cell glutaminase and glutamine synthase messenger RNA and protein abundance, which together promote glutaminolysis. In human white adipocytes, reductions in glutaminase activity promote aerobic glycolysis and mitochondrial oxidative capacity via increases in hypoxia-inducible factor 1α abundance, lactate levels and p38 mitogen-activated protein kinase signalling. Systemic glutaminase inhibition in male and female mice, or genetically in adipocytes of male mice, triggers the activation of thermogenic gene programs in inguinal adipocytes. Consequently, the knockout mice display higher energy expenditure and improved glucose tolerance compared to control littermates, even under high-fat diet conditions. Altogether, our findings highlight white adipocyte glutamine turnover as an important determinant of energy expenditure and metabolic health.},
	language = {en},
	urldate = {2024-07-19},
	journal = {Nature Metabolism},
	author = {Lecoutre, Simon and Maqdasy, Salwan and Rizo-Roca, David and Renzi, Gianluca and Vlassakev, Ivan and Alaeddine, Lynn M. and Higos, Romane and Jalkanen, Jutta and Zhong, Jiawei and Zareifi, Danae S. and Frendo-Cumbo, Scott and Massier, Lucas and Hodek, Ondrej and Juvany, Marta and Moritz, Thomas and de Castro Barbosa, Thais and Omar-Hmeadi, Muhmmad and López-Yus, Marta and Merabtene, Fatiha and Abatan, Jimon Boniface and Marcelin, Geneviève and El Hachem, Elie-Julien and Rouault, Christine and Bergo, Martin O. and Petrus, Paul and Zierath, Juleen R. and Clément, Karine and Krook, Anna and Mejhert, Niklas and Rydén, Mikael},
	month = jul,
	year = {2024},
	note = {Publisher: Nature Publishing Group},
	keywords = {Fat metabolism, Obesity},
	pages = {1--18},
}

Glutamine and glutamate are interconverted by several enzymes and alterations in this metabolic cycle are linked to cardiometabolic traits. Herein, we show that obesity-associated insulin resistance is characterized by decreased plasma and white adipose tissue glutamine-to-glutamate ratios. We couple these stoichiometric changes to perturbed fat cell glutaminase and glutamine synthase messenger RNA and protein abundance, which together promote glutaminolysis. In human white adipocytes, reductions in glutaminase activity promote aerobic glycolysis and mitochondrial oxidative capacity via increases in hypoxia-inducible factor 1α abundance, lactate levels and p38 mitogen-activated protein kinase signalling. Systemic glutaminase inhibition in male and female mice, or genetically in adipocytes of male mice, triggers the activation of thermogenic gene programs in inguinal adipocytes. Consequently, the knockout mice display higher energy expenditure and improved glucose tolerance compared to control littermates, even under high-fat diet conditions. Altogether, our findings highlight white adipocyte glutamine turnover as an important determinant of energy expenditure and metabolic health.

@article{guo_closing_2024,
	title = {Closing {Kok}’s cycle of nature’s water oxidation catalysis},
	volume = {15},
	copyright = {2024 The Author(s)},
	issn = {2041-1723},
	url = {https://www.nature.com/articles/s41467-024-50210-6},
	doi = {10.1038/s41467-024-50210-6},
	abstract = {The Mn4CaO5(6) cluster in photosystem II catalyzes water splitting through the Si state cycle (i = 0–4). Molecular O2 is formed and the natural catalyst is reset during the final S3 → (S4) → S0 transition. Only recently experimental breakthroughs have emerged for this transition but without explicit information on the S0-state reconstitution, thus the progression after O2 release remains elusive. In this report, our molecular dynamics simulations combined with density functional calculations suggest a likely missing link for closing the cycle, i.e., restoring the first catalytic state. Specifically, the formation of closed-cubane intermediates with all hexa-coordinate Mn is observed, which would undergo proton release, water dissociation, and ligand transfer to produce the open-cubane structure of the S0 state. Thereby, we theoretically identify the previously unknown structural isomerism in the S0 state that acts as the origin of the proposed structural flexibility prevailing in the cycle, which may be functionally important for nature’s water oxidation catalysis.},
	language = {en},
	number = {1},
	urldate = {2024-07-19},
	journal = {Nature Communications},
	author = {Guo, Yu and He, Lanlan and Ding, Yunxuan and Kloo, Lars and Pantazis, Dimitrios A. and Messinger, Johannes and Sun, Licheng},
	month = jul,
	year = {2024},
	note = {Publisher: Nature Publishing Group},
	keywords = {Bioinorganic chemistry, Catalytic mechanisms, Reaction mechanisms},
	pages = {5982},
}

The Mn4CaO5(6) cluster in photosystem II catalyzes water splitting through the Si state cycle (i = 0–4). Molecular O2 is formed and the natural catalyst is reset during the final S3 → (S4) → S0 transition. Only recently experimental breakthroughs have emerged for this transition but without explicit information on the S0-state reconstitution, thus the progression after O2 release remains elusive. In this report, our molecular dynamics simulations combined with density functional calculations suggest a likely missing link for closing the cycle, i.e., restoring the first catalytic state. Specifically, the formation of closed-cubane intermediates with all hexa-coordinate Mn is observed, which would undergo proton release, water dissociation, and ligand transfer to produce the open-cubane structure of the S0 state. Thereby, we theoretically identify the previously unknown structural isomerism in the S0 state that acts as the origin of the proposed structural flexibility prevailing in the cycle, which may be functionally important for nature’s water oxidation catalysis.

@article{davis_toward_2024,
	title = {Toward uncovering an operating system in plant organs},
	volume = {29},
	issn = {1360-1385},
	url = {https://www.sciencedirect.com/science/article/pii/S1360138523003655},
	doi = {10.1016/j.tplants.2023.11.006},
	abstract = {Molecular motifs can explain information processing within single cells, while how assemblies of cells collectively achieve this remains less well understood. Plant fitness and survival depend upon robust and accurate decision-making in their decentralised multicellular organ systems. Mobile agents, including hormones, metabolites, and RNAs, have a central role in coordinating multicellular collective decision-making, yet mechanisms describing how cell–cell communication scales to organ-level transitions is poorly understood. Here, we explore how unified outputs may emerge in plant organs by distributed information processing across different scales and using different modalities. Mathematical and computational representations of these events are also explored toward understanding how these events take place and are leveraged to manipulate plant development in response to the environment.},
	number = {7},
	urldate = {2024-07-17},
	journal = {Trends in Plant Science},
	author = {Davis, Gwendolyn V. and de Souza Moraes, Tatiana and Khanapurkar, Swanand and Dromiack, Hannah and Ahmad, Zaki and Bayer, Emmanuelle M. and Bhalerao, Rishikesh P. and Walker, Sara I. and Bassel, George W.},
	month = jul,
	year = {2024},
	keywords = {Cellular Automata, collective behaviour, decentralised information processing, decision-making, plant development},
	pages = {742--753},
}

Molecular motifs can explain information processing within single cells, while how assemblies of cells collectively achieve this remains less well understood. Plant fitness and survival depend upon robust and accurate decision-making in their decentralised multicellular organ systems. Mobile agents, including hormones, metabolites, and RNAs, have a central role in coordinating multicellular collective decision-making, yet mechanisms describing how cell–cell communication scales to organ-level transitions is poorly understood. Here, we explore how unified outputs may emerge in plant organs by distributed information processing across different scales and using different modalities. Mathematical and computational representations of these events are also explored toward understanding how these events take place and are leveraged to manipulate plant development in response to the environment.

@article{graca_obscurity_2024,
	title = {Obscurity of chlorophyll tails - {Is} chlorophyll with farnesyl tail incorporated into {PSII} complexes?},
	volume = {176},
	issn = {0031-9317},
	url = {https://onlinelibrary.wiley.com/doi/10.1111/ppl.14428},
	doi = {10.1111/ppl.14428},
	abstract = {Abstract Chlorophyll is essential in photosynthesis, converting sunlight into chemical energy in plants, algae, and certain bacteria. Its structure, featuring a porphyrin ring enclosing a central magnesium ion, varies in forms like chlorophyll a, b, c, d, and f, allowing light absorption at a broader spectrum. With a 20-carbon phytyl tail (except for chlorophyll c), chlorophyll is anchored to proteins. Previous findings suggested the presence of chlorophyll with a modified farnesyl tail in thermophilic cyanobacteria Thermosynechoccocus vestitus. In our Arabidopsis thaliana PSII cryo-EM map, specific chlorophylls showed incomplete phytyl tails, suggesting potential farnesyl modifications. However, further high-resolution mass spectrometry (HRMS) analysis in A. thaliana and T. vestitus did not confirm the presence of any farnesyl tails. Instead, we propose the truncated tails in PSII models may result from binding pocket flexibility rather than actual modifications.},
	number = {4},
	urldate = {2024-07-17},
	journal = {Physiologia Plantarum},
	author = {Graça, André T. and Lihavainen, Jenna and Hussein, Rana and Schröder, Wolfgang P.},
	month = jul,
	year = {2024},
	note = {Publisher: John Wiley \& Sons, Ltd},
	pages = {e14428},
}

Abstract Chlorophyll is essential in photosynthesis, converting sunlight into chemical energy in plants, algae, and certain bacteria. Its structure, featuring a porphyrin ring enclosing a central magnesium ion, varies in forms like chlorophyll a, b, c, d, and f, allowing light absorption at a broader spectrum. With a 20-carbon phytyl tail (except for chlorophyll c), chlorophyll is anchored to proteins. Previous findings suggested the presence of chlorophyll with a modified farnesyl tail in thermophilic cyanobacteria Thermosynechoccocus vestitus. In our Arabidopsis thaliana PSII cryo-EM map, specific chlorophylls showed incomplete phytyl tails, suggesting potential farnesyl modifications. However, further high-resolution mass spectrometry (HRMS) analysis in A. thaliana and T. vestitus did not confirm the presence of any farnesyl tails. Instead, we propose the truncated tails in PSII models may result from binding pocket flexibility rather than actual modifications.

@article{barbut_integrity_2024,
	title = {Integrity of xylan backbone affects plant responses to drought},
	volume = {15},
	issn = {1664-462X},
	url = {https://www.frontiersin.org/journals/plant-science/articles/10.3389/fpls.2024.1422701/full},
	doi = {10.3389/fpls.2024.1422701},
	abstract = {{\textless}p{\textgreater}Drought is a major factor affecting crops, thus efforts are needed to increase plant resilience to this abiotic stress. The overlapping signaling pathways between drought and cell wall integrity maintenance responses create a possibility of increasing drought resistance by modifying cell walls. Here, using herbaceous and woody plant model species, {\textless}italic{\textgreater}Arabidopsis{\textless}/italic{\textgreater} and hybrid aspen, respectively, we investigated how the integrity of xylan in secondary walls affects the responses of plants to drought stress. Plants, in which secondary wall xylan integrity was reduced by expressing fungal GH10 and GH11 xylanases or by affecting genes involved in xylan backbone biosynthesis, were subjected to controlled drought while their physiological responses were continuously monitored by RGB, fluorescence, and/or hyperspectral cameras. For {\textless}italic{\textgreater}Arabidopsis{\textless}/italic{\textgreater}, this was supplemented with survival test after complete water withdrawal and analyses of stomatal function and stem conductivity. All {\textless}italic{\textgreater}Arabidopsis{\textless}/italic{\textgreater} xylan-impaired lines showed better survival upon complete watering withdrawal, increased stomatal density and delayed growth inhibition by moderate drought, indicating increased resilience to moderate drought associated with modified xylan integrity. Subtle differences were recorded between xylan biosynthesis mutants ({\textless}italic{\textgreater}irx9{\textless}/italic{\textgreater}, {\textless}italic{\textgreater}irx10{\textless}/italic{\textgreater} and {\textless}italic{\textgreater}irx14{\textless}/italic{\textgreater}) and xylanase-expressing lines. {\textless}italic{\textgreater}irx14{\textless}/italic{\textgreater} was the most drought resistant genotype, and the only genotype with increased lignin content and unaltered xylem conductivity despite its {\textless}italic{\textgreater}irx{\textless}/italic{\textgreater} phenotype. Rosette growth was more affected by drought in GH11- than in GH10-expressing plants. In aspen, mild downregulation of {\textless}italic{\textgreater}GT43B{\textless}/italic{\textgreater} and {\textless}italic{\textgreater}C{\textless}/italic{\textgreater} genes did not affect drought responses and the transgenic plants grew better than the wild-type in drought and well-watered conditions. Both GH10 and GH11 xylanases strongly inhibited stem elongation and root growth in well-watered conditions but growth was less inhibited by drought in GH11-expressing plants than in wild-type. Overall, plants with xylan integrity impairment in secondary walls were less affected than wild-type by moderately reduced water availability but their responses also varied among genotypes and species. Thus, modifying the secondary cell wall integrity can be considered as a potential strategy for developing crops better suited to withstand water scarcity, but more research is needed to address the underlying molecular causes of this variability.{\textless}/p{\textgreater}},
	language = {English},
	urldate = {2024-07-17},
	journal = {Frontiers in Plant Science},
	author = {Barbut, Félix R. and Cavel, Emilie and Donev, Evgeniy N. and Gaboreanu, Ioana and Urbancsok, János and Pandey, Garima and Demailly, Hervé and Jiao, Dianyi and Yassin, Zakiya and Derba-Maceluch, Marta and Master, Emma R. and Scheepers, Gerhard and Gutierrez, Laurent and Mellerowicz, Ewa J.},
	month = jun,
	year = {2024},
	note = {Publisher: Frontiers},
	keywords = {Arabidopsis, Drought stress, Glucuronoxylan, Populus, cell wall integrity, high-throughput phenotyping, hyperspectral imaging, secondary cell wall},
}

\textlessp\textgreaterDrought is a major factor affecting crops, thus efforts are needed to increase plant resilience to this abiotic stress. The overlapping signaling pathways between drought and cell wall integrity maintenance responses create a possibility of increasing drought resistance by modifying cell walls. Here, using herbaceous and woody plant model species, \textlessitalic\textgreaterArabidopsis\textless/italic\textgreater and hybrid aspen, respectively, we investigated how the integrity of xylan in secondary walls affects the responses of plants to drought stress. Plants, in which secondary wall xylan integrity was reduced by expressing fungal GH10 and GH11 xylanases or by affecting genes involved in xylan backbone biosynthesis, were subjected to controlled drought while their physiological responses were continuously monitored by RGB, fluorescence, and/or hyperspectral cameras. For \textlessitalic\textgreaterArabidopsis\textless/italic\textgreater, this was supplemented with survival test after complete water withdrawal and analyses of stomatal function and stem conductivity. All \textlessitalic\textgreaterArabidopsis\textless/italic\textgreater xylan-impaired lines showed better survival upon complete watering withdrawal, increased stomatal density and delayed growth inhibition by moderate drought, indicating increased resilience to moderate drought associated with modified xylan integrity. Subtle differences were recorded between xylan biosynthesis mutants (\textlessitalic\textgreaterirx9\textless/italic\textgreater, \textlessitalic\textgreaterirx10\textless/italic\textgreater and \textlessitalic\textgreaterirx14\textless/italic\textgreater) and xylanase-expressing lines. \textlessitalic\textgreaterirx14\textless/italic\textgreater was the most drought resistant genotype, and the only genotype with increased lignin content and unaltered xylem conductivity despite its \textlessitalic\textgreaterirx\textless/italic\textgreater phenotype. Rosette growth was more affected by drought in GH11- than in GH10-expressing plants. In aspen, mild downregulation of \textlessitalic\textgreaterGT43B\textless/italic\textgreater and \textlessitalic\textgreaterC\textless/italic\textgreater genes did not affect drought responses and the transgenic plants grew better than the wild-type in drought and well-watered conditions. Both GH10 and GH11 xylanases strongly inhibited stem elongation and root growth in well-watered conditions but growth was less inhibited by drought in GH11-expressing plants than in wild-type. Overall, plants with xylan integrity impairment in secondary walls were less affected than wild-type by moderately reduced water availability but their responses also varied among genotypes and species. Thus, modifying the secondary cell wall integrity can be considered as a potential strategy for developing crops better suited to withstand water scarcity, but more research is needed to address the underlying molecular causes of this variability.\textless/p\textgreater

@article{sivan_unraveling_2024,
	title = {Unraveling the unique structural motifs of glucuronoxylan from hybrid aspen wood},
	volume = {343},
	issn = {0144-8617},
	url = {https://www.sciencedirect.com/science/article/pii/S014486172400660X},
	doi = {10.1016/j.carbpol.2024.122434},
	abstract = {Xylan is a fundamental structural polysaccharide in plant secondary cell walls and a valuable resource for biorefinery applications. Deciphering the molecular motifs of xylans that mediate their interaction with cellulose and lignin is fundamental to understand the structural integrity of plant cell walls and to design lignocellulosic materials. In the present study, we investigated the pattern of acetylation and glucuronidation substitution in hardwood glucuronoxylan (GX) extracted from aspen wood using subcritical water and alkaline conditions. Enzymatic digestions of GX with β-xylanases from glycosyl hydrolase (GH) families GH10, GH11 and GH30 generated xylo-oligosaccharides with controlled structures amenable for mass spectrometric glycan sequencing. We identified the occurrence of intramolecular motifs in aspen GX with block repeats of even glucuronidation (every 2 xylose units) and consecutive glucuronidation, which are unique features for hardwood xylans. The acetylation pattern of aspen GX shows major domains with evenly-spaced decorations, together with minor stretches of highly acetylated domains. These heterogenous patterns of GX can be correlated with its extractability and with its potential interaction with lignin and cellulose. Our study provides new insights into the molecular structure of xylan in hardwood species, which has fundamental implications for overcoming lignocellulose recalcitrance during biochemical conversion.},
	urldate = {2024-07-11},
	journal = {Carbohydrate Polymers},
	author = {Sivan, Pramod and Heinonen, Emilia and Escudero, Louis and Gandla, Madhavi Latha and Jiménez-Quero, Amparo and Jönsson, Leif J. and Mellerowicz, Ewa J. and Vilaplana, Francisco},
	month = nov,
	year = {2024},
	keywords = {Acetylation, Glucuronoxylan, Glycan sequencing, Hybrid aspen},
	pages = {122434},
}

Xylan is a fundamental structural polysaccharide in plant secondary cell walls and a valuable resource for biorefinery applications. Deciphering the molecular motifs of xylans that mediate their interaction with cellulose and lignin is fundamental to understand the structural integrity of plant cell walls and to design lignocellulosic materials. In the present study, we investigated the pattern of acetylation and glucuronidation substitution in hardwood glucuronoxylan (GX) extracted from aspen wood using subcritical water and alkaline conditions. Enzymatic digestions of GX with β-xylanases from glycosyl hydrolase (GH) families GH10, GH11 and GH30 generated xylo-oligosaccharides with controlled structures amenable for mass spectrometric glycan sequencing. We identified the occurrence of intramolecular motifs in aspen GX with block repeats of even glucuronidation (every 2 xylose units) and consecutive glucuronidation, which are unique features for hardwood xylans. The acetylation pattern of aspen GX shows major domains with evenly-spaced decorations, together with minor stretches of highly acetylated domains. These heterogenous patterns of GX can be correlated with its extractability and with its potential interaction with lignin and cellulose. Our study provides new insights into the molecular structure of xylan in hardwood species, which has fundamental implications for overcoming lignocellulose recalcitrance during biochemical conversion.

@article{khalfallah_ectomycorrhizal_2024,
	title = {“{Ectomycorrhizal} exploration type” could be a functional trait explaining the spatial distribution of tree symbiotic fungi as a function of forest humus forms},
	issn = {1432-1890},
	url = {https://doi.org/10.1007/s00572-024-01146-8},
	doi = {10.1007/s00572-024-01146-8},
	abstract = {In European forests, most tree species form symbioses with ectomycorrhizal (EM) and arbuscular mycorrhizal (AM) fungi. The EM fungi are classified into different morphological types based on the development and structure of their extraradical mycelium. These structures could be root extensions that help trees to acquire nutrients. However, the relationship between these morphological traits and functions involved in soil nutrient foraging is still under debate.},
	language = {en},
	urldate = {2024-05-10},
	journal = {Mycorrhiza},
	author = {Khalfallah, F and Bon, L and El Mazlouzi, M and Bakker, M.R and Fanin, N and Bellanger, R and Bernier, F and De Schrijver, A and Ducatillon, C and Fotelli, M.N and Gateble, G and Gundale, M.J and Larsson, M and Legout, A and Mason, W.L and Nordin, A and Smolander, A and Spyroglou, G and Vanguelova, E.I. and Vesterdal, L and Zeller, B and Augusto, L and Derrien, D and Buée, M},
	month = may,
	year = {2024},
}

In European forests, most tree species form symbioses with ectomycorrhizal (EM) and arbuscular mycorrhizal (AM) fungi. The EM fungi are classified into different morphological types based on the development and structure of their extraradical mycelium. These structures could be root extensions that help trees to acquire nutrients. However, the relationship between these morphological traits and functions involved in soil nutrient foraging is still under debate.

@article{long_comparative_2024,
	title = {Comparative metabolomics combined with genome sequencing provides insights into novel wolfberry-specific metabolites and their formation mechanisms},
	volume = {15},
	issn = {1664-462X},
	url = {https://www.frontiersin.org/journals/plant-science/articles/10.3389/fpls.2024.1392175/full},
	doi = {10.3389/fpls.2024.1392175},
	abstract = {Wolfberry (Lycium, of the family Solanaceae) has special nutritional benefits due to its valuable metabolites. Here, 16 wolfberry-specific metabolites were identified by comparing the metabolome of wolfberry with those of six species, including maize, rice, wheat, soybean, tomato and grape. The copy numbers of the riboflavin and phenyllactate degradation genes riboflavin kinase (RFK) and phenyllactate UDP-glycosyltransferase (UGT1) were lower in wolfberry than in other species, while the copy number of the phenyllactate synthesis gene hydroxyphenyl-pyruvate reductase (HPPR) was higher in wolfberry, suggesting that the copy number variation of these genes among species may be the main reason for the specific accumulation of riboflavin and phenyllactate in wolfberry. Moreover, the metabolome-based neighbor-joining tree revealed distinct clustering of monocots and dicots, suggesting that metabolites could reflect the evolutionary relationship among those species. Taken together, we identified 16 specific metabolites in wolfberry and provided new insight into the accumulation mechanism of species-specific metabolites at the genomic level.},
	language = {English},
	urldate = {2024-05-17},
	journal = {Frontiers in Plant Science},
	author = {Long, Qiyuan and Zhang, Changjian and Zhu, Hui and Zhou, Yutong and Liu, Shuo and Liu, Yanchen and Ma, Xuemin and An, Wei and Zhou, Jun and Zhao, Jianhua and Zhang, Yuanyuan and Jin, Cheng},
	month = apr,
	year = {2024},
	note = {Publisher: Frontiers},
	keywords = {Metabolome, Riboflavin, copy number variation, nutrition, phenyllactate},
}

Wolfberry (Lycium, of the family Solanaceae) has special nutritional benefits due to its valuable metabolites. Here, 16 wolfberry-specific metabolites were identified by comparing the metabolome of wolfberry with those of six species, including maize, rice, wheat, soybean, tomato and grape. The copy numbers of the riboflavin and phenyllactate degradation genes riboflavin kinase (RFK) and phenyllactate UDP-glycosyltransferase (UGT1) were lower in wolfberry than in other species, while the copy number of the phenyllactate synthesis gene hydroxyphenyl-pyruvate reductase (HPPR) was higher in wolfberry, suggesting that the copy number variation of these genes among species may be the main reason for the specific accumulation of riboflavin and phenyllactate in wolfberry. Moreover, the metabolome-based neighbor-joining tree revealed distinct clustering of monocots and dicots, suggesting that metabolites could reflect the evolutionary relationship among those species. Taken together, we identified 16 specific metabolites in wolfberry and provided new insight into the accumulation mechanism of species-specific metabolites at the genomic level.

@article{vittozzi_abi5_2024,
	title = {{ABI5} binding proteins: key players in coordinating plant growth and development},
	issn = {1360-1385},
	shorttitle = {{ABI5} binding proteins},
	url = {https://www.cell.com/trends/plant-science/abstract/S1360-1385(24)00065-7},
	doi = {10.1016/j.tplants.2024.03.009},
	abstract = {During the course of terrestrial evolution, plants have developed complex networks that involve the coordination of phytohormone signalling pathways in order to adapt to an ever-changing environment. Transcription factors coordinate these responses by engaging in different protein complexes and exerting both positive and negative effects. ABA INSENSITIVE 5 (ABI5) binding proteins (AFPs), which are closely related to NOVEL INTERACTOR OF JAZ (NINJA)-like proteins, are known for their fundamental role in plants’ morphological and physiological growth. Recent studies have shown that AFPs regulate several hormone-signalling pathways, including abscisic acid (ABA) and gibberellic acid (GA). Here, we review the genetic control of AFPs and their crosstalk with plant hormone signalling, and discuss the contributions of AFPs to plants’ growth and development.},
	language = {English},
	urldate = {2024-04-09},
	journal = {Trends in Plant Science},
	author = {Vittozzi, Ylenia and Krüger, Thorben and Majee, Adity and Née, Guillaume and Wenkel, Stephan},
	month = apr,
	year = {2024},
	pmid = {38584080},
	note = {Publisher: Elsevier},
	keywords = {AFP (ABI5 binding protein), abscisic acid, flowering regulation, microprotein, seed germination},
}

During the course of terrestrial evolution, plants have developed complex networks that involve the coordination of phytohormone signalling pathways in order to adapt to an ever-changing environment. Transcription factors coordinate these responses by engaging in different protein complexes and exerting both positive and negative effects. ABA INSENSITIVE 5 (ABI5) binding proteins (AFPs), which are closely related to NOVEL INTERACTOR OF JAZ (NINJA)-like proteins, are known for their fundamental role in plants’ morphological and physiological growth. Recent studies have shown that AFPs regulate several hormone-signalling pathways, including abscisic acid (ABA) and gibberellic acid (GA). Here, we review the genetic control of AFPs and their crosstalk with plant hormone signalling, and discuss the contributions of AFPs to plants’ growth and development.

@article{bruxaux_scots_2024,
	title = {Scots pine – panmixia and the elusive signal of genetic adaptation},
	volume = {243},
	copyright = {© 2024 The Authors. New Phytologist © 2024 New Phytologist Foundation},
	issn = {1469-8137},
	url = {https://onlinelibrary.wiley.com/doi/abs/10.1111/nph.19563},
	doi = {10.1111/nph.19563},
	abstract = {Scots pine is the foundation species of diverse forested ecosystems across Eurasia and displays remarkable ecological breadth, occurring in environments ranging from temperate rainforests to arid tundra margins. Such expansive distributions can be favored by various demographic and adaptive processes and the interactions between them. To understand the impact of neutral and selective forces on genetic structure in Scots pine, we conducted range-wide population genetic analyses on 2321 trees from 202 populations using genotyping-by-sequencing, reconstructed the recent demography of the species and examined signals of genetic adaptation. We found a high and uniform genetic diversity across the entire range (global FST 0.048), no increased genetic load in expanding populations and minor impact of the last glacial maximum on historical population sizes. Genetic-environmental associations identified only a handful of single-nucleotide polymorphisms significantly linked to environmental gradients. The results suggest that extensive gene flow is predominantly responsible for the observed genetic patterns in Scots pine. The apparent missing signal of genetic adaptation is likely attributed to the intricate genetic architecture controlling adaptation to multi-dimensional environments. The panmixia metapopulation of Scots pine offers a good study system for further exploration into how genetic adaptation and plasticity evolve under gene flow and changing environment.},
	language = {en},
	number = {3},
	urldate = {2024-07-11},
	journal = {New Phytologist},
	author = {Bruxaux, Jade and Zhao, Wei and Hall, David and Curtu, Alexandru Lucian and Androsiuk, Piotr and Drouzas, Andreas D. and Gailing, Oliver and Konrad, Heino and Sullivan, Alexis R. and Semerikov, Vladimir and Wang, Xiao-Ru},
	year = {2024},
	note = {\_eprint: https://onlinelibrary.wiley.com/doi/pdf/10.1111/nph.19563},
	keywords = {Pinus sylvestris, conifer, demography, gene flow, genetic diversity, genetic-environmental association, population structure},
	pages = {1231--1246},
}

Scots pine is the foundation species of diverse forested ecosystems across Eurasia and displays remarkable ecological breadth, occurring in environments ranging from temperate rainforests to arid tundra margins. Such expansive distributions can be favored by various demographic and adaptive processes and the interactions between them. To understand the impact of neutral and selective forces on genetic structure in Scots pine, we conducted range-wide population genetic analyses on 2321 trees from 202 populations using genotyping-by-sequencing, reconstructed the recent demography of the species and examined signals of genetic adaptation. We found a high and uniform genetic diversity across the entire range (global FST 0.048), no increased genetic load in expanding populations and minor impact of the last glacial maximum on historical population sizes. Genetic-environmental associations identified only a handful of single-nucleotide polymorphisms significantly linked to environmental gradients. The results suggest that extensive gene flow is predominantly responsible for the observed genetic patterns in Scots pine. The apparent missing signal of genetic adaptation is likely attributed to the intricate genetic architecture controlling adaptation to multi-dimensional environments. The panmixia metapopulation of Scots pine offers a good study system for further exploration into how genetic adaptation and plasticity evolve under gene flow and changing environment.

@article{abdel-fattah_growth-regulated_2024,
	title = {Growth-regulated co-occupancy of {Mediator} and {Lsm3} at intronic ribosomal protein genes},
	volume = {52},
	issn = {0305-1048},
	url = {https://doi.org/10.1093/nar/gkae266},
	doi = {10.1093/nar/gkae266},
	abstract = {Mediator is a well-known transcriptional co-regulator and serves as an adaptor between gene-specific regulatory proteins and RNA polymerase II. Studies on the chromatin-bound form of Mediator revealed interactions with additional protein complexes involved in various transcription-related processes, such as the Lsm2–8 complex that is part of the spliceosomal U6 small nuclear ribonucleoprotein complex. Here, we employ Chromatin Immunoprecipitation sequencing (ChIP-seq) of chromatin associated with the Lsm3 protein and the Med1 or Med15 Mediator subunits. We identify 86 genes co-occupied by both Lsm3 and Mediator, of which 73 were intron-containing ribosomal protein genes. In logarithmically growing cells, Mediator primarily binds to their promoter regions but also shows a second, less pronounced occupancy at their 3′-exons. During the late exponential phase, we observe a near-complete transition of Mediator from these promoters to a position in their 3′-ends, overlapping the Lsm3 binding sites ∼250 bp downstream of their last intron–exon boundaries. Using an unbiased RNA sequencing approach, we show that transition of Mediator from promoters to the last exon of these genes correlates to reduction of both their messenger RNA levels and splicing ratios, indicating that the Mediator and Lsm complexes cooperate to control growth-regulated expression of intron-containing ribosomal protein genes at the levels of transcription and splicing.},
	number = {11},
	urldate = {2024-07-01},
	journal = {Nucleic Acids Research},
	author = {Abdel-Fattah, Wael R and Carlsson, Mattias and Hu, Guo-Zhen and Singh, Ajeet and Vergara, Alexander and Aslam, Rameen and Ronne, Hans and Björklund, Stefan},
	month = jun,
	year = {2024},
	pages = {6220--6233},
}

Mediator is a well-known transcriptional co-regulator and serves as an adaptor between gene-specific regulatory proteins and RNA polymerase II. Studies on the chromatin-bound form of Mediator revealed interactions with additional protein complexes involved in various transcription-related processes, such as the Lsm2–8 complex that is part of the spliceosomal U6 small nuclear ribonucleoprotein complex. Here, we employ Chromatin Immunoprecipitation sequencing (ChIP-seq) of chromatin associated with the Lsm3 protein and the Med1 or Med15 Mediator subunits. We identify 86 genes co-occupied by both Lsm3 and Mediator, of which 73 were intron-containing ribosomal protein genes. In logarithmically growing cells, Mediator primarily binds to their promoter regions but also shows a second, less pronounced occupancy at their 3′-exons. During the late exponential phase, we observe a near-complete transition of Mediator from these promoters to a position in their 3′-ends, overlapping the Lsm3 binding sites ∼250 bp downstream of their last intron–exon boundaries. Using an unbiased RNA sequencing approach, we show that transition of Mediator from promoters to the last exon of these genes correlates to reduction of both their messenger RNA levels and splicing ratios, indicating that the Mediator and Lsm complexes cooperate to control growth-regulated expression of intron-containing ribosomal protein genes at the levels of transcription and splicing.

@article{lorrai_cell_2024,
	title = {Cell wall integrity modulates {HOOKLESS1} and {PHYTOCHROME} {INTERACTING} {FACTOR4} expression controlling apical hook formation},
	issn = {0032-0889},
	url = {https://doi.org/10.1093/plphys/kiae370},
	doi = {10.1093/plphys/kiae370},
	abstract = {Formation of the apical hook in etiolated dicot seedlings results from differential growth in the hypocotyl apex and is tightly controlled by environmental cues and hormones, among which auxin and gibberellins (GAs) play an important role. Cell expansion is tightly regulated by the cell wall, but whether and how feedback from this structure contributes to hook development is still unclear. Here, we show that etiolated seedlings of the Arabidopsis (Arabidopsis thaliana) quasimodo2-1 (qua2) mutant, defective in pectin biosynthesis, display severe defects in apical hook formation and maintenance, accompanied by loss of asymmetric auxin maxima and of differential cell expansion. Moreover, qua2 seedlings show reduced expression of HOOKLESS 1 (HLS1) and PHYTOCHROME INTERACTING FACTOR 4 (PIF4), which are positive regulators of hook formation. Treatment of wild-type seedlings with the cellulose inhibitor isoxaben (isx) also prevents hook development and represses HLS1 and PIF4 expression. Exogenous GAs, loss of DELLA proteins or HLS1 overexpression partially restore hook development in qua2 and isx-treated seedlings. Interestingly, increased agar concentration in the medium restores, both in qua2 and isx-treated seedlings, hook formation, asymmetric auxin maxima and PIF4 and HLS1 expression. Analysis of plants expressing a FRET-based GA sensor indicate that isx reduces accumulation of GAs in the apical hook region in a turgor-dependent manner. Lack of the cell wall integrity sensor THESEUS 1, which modulates turgor loss point, restores hook formation in qua2 and isx-treated seedlings. We propose that turgor-dependent signals link changes in cell wall integrity to the PIF4-HLS1 signalling module to control differential cell elongation during hook formation.},
	urldate = {2024-07-09},
	journal = {Plant Physiology},
	author = {Lorrai, Riccardo and Erguvan, Özer and Raggi, Sara and Jonsson, Kristoffer and Široká, Jitka and Tarkowská, Danuše and Novák, Ondřej and Griffiths, Jayne and Jones, Alexander M and Verger, Stéphane and Robert, Stéphanie and Ferrari, Simone},
	month = jul,
	year = {2024},
	pages = {kiae370},
}

Formation of the apical hook in etiolated dicot seedlings results from differential growth in the hypocotyl apex and is tightly controlled by environmental cues and hormones, among which auxin and gibberellins (GAs) play an important role. Cell expansion is tightly regulated by the cell wall, but whether and how feedback from this structure contributes to hook development is still unclear. Here, we show that etiolated seedlings of the Arabidopsis (Arabidopsis thaliana) quasimodo2-1 (qua2) mutant, defective in pectin biosynthesis, display severe defects in apical hook formation and maintenance, accompanied by loss of asymmetric auxin maxima and of differential cell expansion. Moreover, qua2 seedlings show reduced expression of HOOKLESS 1 (HLS1) and PHYTOCHROME INTERACTING FACTOR 4 (PIF4), which are positive regulators of hook formation. Treatment of wild-type seedlings with the cellulose inhibitor isoxaben (isx) also prevents hook development and represses HLS1 and PIF4 expression. Exogenous GAs, loss of DELLA proteins or HLS1 overexpression partially restore hook development in qua2 and isx-treated seedlings. Interestingly, increased agar concentration in the medium restores, both in qua2 and isx-treated seedlings, hook formation, asymmetric auxin maxima and PIF4 and HLS1 expression. Analysis of plants expressing a FRET-based GA sensor indicate that isx reduces accumulation of GAs in the apical hook region in a turgor-dependent manner. Lack of the cell wall integrity sensor THESEUS 1, which modulates turgor loss point, restores hook formation in qua2 and isx-treated seedlings. We propose that turgor-dependent signals link changes in cell wall integrity to the PIF4-HLS1 signalling module to control differential cell elongation during hook formation.

@article{strom_metabolomic_2024,
	title = {The {Metabolomic} {Profile} of {Microscopic} {Colitis} {Is} {Affected} by {Smoking} but {Not} {Histopathological} {Diagnosis}, {Clinical} {Course}, {Symptoms}, or {Treatment}},
	volume = {14},
	copyright = {http://creativecommons.org/licenses/by/3.0/},
	issn = {2218-1989},
	url = {https://www.mdpi.com/2218-1989/14/6/303},
	doi = {10.3390/metabo14060303},
	abstract = {Microscopic colitis (MC) is classified as collagenous colitis (CC) and lymphocytic colitis (LC). Genetic associations between CC and human leucocyte antigens (HLAs) have been found, with smoking being a predisposing external factor. Smoking has a great impact on metabolomics. The aim of this explorative study was to analyze global metabolomics in MC and to examine whether the metabolomic profile differed regarding the type and course of MC, the presence of IBS-like symptoms, treatment, and smoking habits. Of the 240 identified women with MC aged ≤73 years, 131 completed the study questionnaire; the Rome III questionnaire; and the Visual Analog Scale for Irritable Bowel Syndrome (VAS-IBS). Blood samples were analyzed by ultra-high-performance liquid chromatograph mass spectrometry (UHLC-MS/UHPLC-MSMS). The women, 63.1 (58.7–67.2) years old, were categorized based on CC (n = 76) and LC (n = 55); one episode or refractory MC; IBS-like symptoms or not; use of corticosteroids or not; and smoking habits. The only metabolomic differences found in the univariate model after adjustment for false discovery rate (FDR) were between smokers and non-smokers. Serotonin was markedly increased in smokers (p {\textless} 0.001). No clear patterns appeared when conducting a principal component analysis (PCA). No differences in the metabolomic profile were found depending on the type or clinical course of the disease, neither in the whole MC group nor in the subgroup analysis of CC.},
	language = {en},
	number = {6},
	urldate = {2024-07-01},
	journal = {Metabolites},
	author = {Ström, Axel and Stenlund, Hans and Ohlsson, Bodil},
	month = jun,
	year = {2024},
	note = {Number: 6
Publisher: Multidisciplinary Digital Publishing Institute},
	keywords = {collagenous colitis, lymphocytic colitis, metabolomics, microscopic colitis, smoking habits},
	pages = {303},
}

Microscopic colitis (MC) is classified as collagenous colitis (CC) and lymphocytic colitis (LC). Genetic associations between CC and human leucocyte antigens (HLAs) have been found, with smoking being a predisposing external factor. Smoking has a great impact on metabolomics. The aim of this explorative study was to analyze global metabolomics in MC and to examine whether the metabolomic profile differed regarding the type and course of MC, the presence of IBS-like symptoms, treatment, and smoking habits. Of the 240 identified women with MC aged ≤73 years, 131 completed the study questionnaire; the Rome III questionnaire; and the Visual Analog Scale for Irritable Bowel Syndrome (VAS-IBS). Blood samples were analyzed by ultra-high-performance liquid chromatograph mass spectrometry (UHLC-MS/UHPLC-MSMS). The women, 63.1 (58.7–67.2) years old, were categorized based on CC (n = 76) and LC (n = 55); one episode or refractory MC; IBS-like symptoms or not; use of corticosteroids or not; and smoking habits. The only metabolomic differences found in the univariate model after adjustment for false discovery rate (FDR) were between smokers and non-smokers. Serotonin was markedly increased in smokers (p \textless 0.001). No clear patterns appeared when conducting a principal component analysis (PCA). No differences in the metabolomic profile were found depending on the type or clinical course of the disease, neither in the whole MC group nor in the subgroup analysis of CC.

@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{dusi_involvement_2024,
	title = {Involvement of the tomato {BBX16} and {BBX17} {microProteins} in reproductive development},
	volume = {213},
	issn = {0981-9428},
	url = {https://www.sciencedirect.com/science/article/pii/S0981942824005412},
	doi = {10.1016/j.plaphy.2024.108873},
	abstract = {BBXs are B-Box zinc finger proteins that can act as transcription factors and regulators of protein complexes. Several BBX proteins play important roles in plant development. Two Arabidopsis thaliana microProteins belonging to the BBX family, named miP1a and miP1b, homotypically interact with and modulate the activity of other BBX proteins, including CONSTANS, which transcriptionally activates the florigen, FLOWERING LOCUS T. Arabidopsis plants overexpressing miP1a and miP1b showed delayed flowering. In tomato, the closest homologs of miP1a and miP1b are the microProteins SlBBX16 and SlBBX17. This study was aimed at investigating whether the constitutive expression of SlBBX16/17 in Arabidopsis and tomato impacted reproductive development. The heterologous expression of the two tomato microProteins in Arabidopsis caused a delay in the flowering transition; however, the effect was weaker than that observed when the native miP1a/b were overexpressed. In tomato, overexpression of SlBBX17 prolonged the flowering period; this effect was accompanied by downregulation of the flowering inhibitors Self Pruning (SP) and SP5G. SlBBX16 and SlBBX17 can hetero-oligomerize with TCMP-2, a cystine-knot peptide involved in flowering pattern regulation and early fruit development in tomato. The increased expression of both microProteins also caused alterations in tomato fruit development: we observed in the case of SlBBX17 a decrease in the number and size of ripe fruits as compared to WT plants, while for SlBBX16, a delay in fruit production up to the breaker stage. These effects were associated with changes in the expression of GA-responsive genes.},
	urldate = {2024-07-01},
	journal = {Plant Physiology and Biochemistry},
	author = {Dusi, Valentina and Pennisi, Federica and Fortini, Daniela and Atarés, Alejandro and Wenkel, Stephan and Molesini, Barbara and Pandolfini, Tiziana},
	month = aug,
	year = {2024},
	keywords = {BBX, Flowering time, Fruit development, Gibberellins, MicroProteins},
	pages = {108873},
}

BBXs are B-Box zinc finger proteins that can act as transcription factors and regulators of protein complexes. Several BBX proteins play important roles in plant development. Two Arabidopsis thaliana microProteins belonging to the BBX family, named miP1a and miP1b, homotypically interact with and modulate the activity of other BBX proteins, including CONSTANS, which transcriptionally activates the florigen, FLOWERING LOCUS T. Arabidopsis plants overexpressing miP1a and miP1b showed delayed flowering. In tomato, the closest homologs of miP1a and miP1b are the microProteins SlBBX16 and SlBBX17. This study was aimed at investigating whether the constitutive expression of SlBBX16/17 in Arabidopsis and tomato impacted reproductive development. The heterologous expression of the two tomato microProteins in Arabidopsis caused a delay in the flowering transition; however, the effect was weaker than that observed when the native miP1a/b were overexpressed. In tomato, overexpression of SlBBX17 prolonged the flowering period; this effect was accompanied by downregulation of the flowering inhibitors Self Pruning (SP) and SP5G. SlBBX16 and SlBBX17 can hetero-oligomerize with TCMP-2, a cystine-knot peptide involved in flowering pattern regulation and early fruit development in tomato. The increased expression of both microProteins also caused alterations in tomato fruit development: we observed in the case of SlBBX17 a decrease in the number and size of ripe fruits as compared to WT plants, while for SlBBX16, a delay in fruit production up to the breaker stage. These effects were associated with changes in the expression of GA-responsive genes.

@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},
	author = {Blaschek, Leonard and Serk, Henrik and Pesquet, Edouard},
	month = jun,
	year = {2024},
	note = {Publisher: American Chemical Society},
	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{hussein_cryoelectron_2024,
	title = {Cryo–electron microscopy reveals hydrogen positions and water networks in photosystem {II}},
	volume = {384},
	url = {https://www.science.org/doi/10.1126/science.adn6541},
	doi = {10.1126/science.adn6541},
	abstract = {Photosystem II starts the photosynthetic electron transport chain that converts solar energy into chemical energy and thus sustains life on Earth. It catalyzes two chemical reactions: water oxidation to molecular oxygen and plastoquinone reduction. Coupling of electron and proton transfer is crucial for efficiency; however, the molecular basis of these processes remains speculative owing to uncertain water binding sites and the lack of experimentally determined hydrogen positions. We thus collected high-resolution cryo–electron microscopy data of fully hydrated photosystem II from the thermophilic cyanobacterium Thermosynechococcus vestitus to a final resolution of 1.71 angstroms. The structure reveals several previously undetected partially occupied water binding sites and more than half of the hydrogen and proton positions. This clarifies the pathways of substrate water binding and plastoquinone B protonation.},
	number = {6702},
	urldate = {2024-06-26},
	journal = {Science},
	author = {Hussein, Rana and Graça, André and Forsman, Jack and Aydin, A. Orkun and Hall, Michael and Gaetcke, Julia and Chernev, Petko and Wendler, Petra and Dobbek, Holger and Messinger, Johannes and Zouni, Athina and Schröder, Wolfgang P.},
	month = jun,
	year = {2024},
	note = {Publisher: American Association for the Advancement of Science},
	pages = {1349--1355},
}

Photosystem II starts the photosynthetic electron transport chain that converts solar energy into chemical energy and thus sustains life on Earth. It catalyzes two chemical reactions: water oxidation to molecular oxygen and plastoquinone reduction. Coupling of electron and proton transfer is crucial for efficiency; however, the molecular basis of these processes remains speculative owing to uncertain water binding sites and the lack of experimentally determined hydrogen positions. We thus collected high-resolution cryo–electron microscopy data of fully hydrated photosystem II from the thermophilic cyanobacterium Thermosynechococcus vestitus to a final resolution of 1.71 angstroms. The structure reveals several previously undetected partially occupied water binding sites and more than half of the hydrogen and proton positions. This clarifies the pathways of substrate water binding and plastoquinone B protonation.

@article{mishra_overexpression_2024,
	title = {Overexpression of the plastidial pseudo-protease {AtFtsHi3} enhances drought tolerance while sustaining plant growth},
	volume = {176},
	issn = {1399-3054},
	url = {https://onlinelibrary.wiley.com/doi/abs/10.1111/ppl.14370},
	doi = {10.1111/ppl.14370},
	abstract = {With climate change, droughts are expected to be more frequent and severe, severely impacting plant biomass and quality. Here, we show that overexpressing the Arabidopsis gene AtFtsHi3 (FtsHi3OE) enhances drought-tolerant phenotypes without compromising plant growth. AtFtsHi3 encodes a chloroplast envelope pseudo-protease; knock-down mutants (ftshi3-1) are found to be drought tolerant but exhibit stunted growth. Altered AtFtsHi3 expression therefore leads to drought tolerance, while only diminished expression of this gene leads to growth retardation. To understand the underlying mechanisms of the enhanced drought tolerance, we compared the proteomes of ftshi3-1 and pFtsHi3-FtsHi3OE (pFtsHi3-OE) to wild-type plants under well-watered and drought conditions. Drought-related processes like osmotic stress, water transport, and abscisic acid response were enriched in pFtsHi3-OE and ftshi3-1 mutants following their enhanced drought response compared to wild-type. The knock-down mutant ftshi3-1 showed an increased abundance of HSP90, HSP93, and TIC110 proteins, hinting at a potential downstream role of AtFtsHi3 in chloroplast pre-protein import. Mathematical modeling was performed to understand how variation in the transcript abundance of AtFtsHi3 can, on the one hand, lead to drought tolerance in both overexpression and knock-down lines, yet, on the other hand, affect plant growth so differently. The results led us to hypothesize that AtFtsHi3 may form complexes with at least two other protease subunits, either as homo- or heteromeric structures. Enriched amounts of AtFtsH7/9, AtFtsH11, AtFtsH12, and AtFtsHi4 in ftshi3-1 suggest a possible compensation mechanism for these proteases in the hexamer.},
	language = {en},
	number = {3},
	urldate = {2024-06-10},
	journal = {Physiologia Plantarum},
	author = {Mishra, Laxmi S. and Cook, Sam D. and Kushwah, Sunita and Isaksson, Hanna and Straub, Isabella R. and Abele, Miriam and Mishra, Sanatkumar and Ludwig, Christina and Libby, Eric and Funk, Christiane},
	month = may,
	year = {2024},
	note = {\_eprint: https://onlinelibrary.wiley.com/doi/pdf/10.1111/ppl.14370},
	pages = {e14370},
}

With climate change, droughts are expected to be more frequent and severe, severely impacting plant biomass and quality. Here, we show that overexpressing the Arabidopsis gene AtFtsHi3 (FtsHi3OE) enhances drought-tolerant phenotypes without compromising plant growth. AtFtsHi3 encodes a chloroplast envelope pseudo-protease; knock-down mutants (ftshi3-1) are found to be drought tolerant but exhibit stunted growth. Altered AtFtsHi3 expression therefore leads to drought tolerance, while only diminished expression of this gene leads to growth retardation. To understand the underlying mechanisms of the enhanced drought tolerance, we compared the proteomes of ftshi3-1 and pFtsHi3-FtsHi3OE (pFtsHi3-OE) to wild-type plants under well-watered and drought conditions. Drought-related processes like osmotic stress, water transport, and abscisic acid response were enriched in pFtsHi3-OE and ftshi3-1 mutants following their enhanced drought response compared to wild-type. The knock-down mutant ftshi3-1 showed an increased abundance of HSP90, HSP93, and TIC110 proteins, hinting at a potential downstream role of AtFtsHi3 in chloroplast pre-protein import. Mathematical modeling was performed to understand how variation in the transcript abundance of AtFtsHi3 can, on the one hand, lead to drought tolerance in both overexpression and knock-down lines, yet, on the other hand, affect plant growth so differently. The results led us to hypothesize that AtFtsHi3 may form complexes with at least two other protease subunits, either as homo- or heteromeric structures. Enriched amounts of AtFtsH7/9, AtFtsH11, AtFtsH12, and AtFtsHi4 in ftshi3-1 suggest a possible compensation mechanism for these proteases in the hexamer.

@article{prasad_quantitative_2024,
	title = {Quantitative {Proteomics} for {Translational} {Pharmacology} and {Precision} {Medicine}: {State} of {The} {Art} and {Future} {Outlook}},
	copyright = {Copyright © 2024 American Society for Pharmacology and Experimental Therapeutics},
	issn = {0090-9556, 1521-009X},
	shorttitle = {Quantitative {Proteomics} for {Translational} {Pharmacology} and {Precision} {Medicine}},
	url = {https://dmd.aspetjournals.org/content/early/2024/05/31/dmd.124.001600},
	doi = {10.1124/dmd.124.001600},
	abstract = {Over the past 20 years, quantitative proteomics has contributed a wealth of protein expression data, which are currently used for a variety of systems pharmacology applications, as a complement or a surrogate for activity of the corresponding proteins. A symposium at the 25th North American ISSX meeting, in Boston, in September 2023, was held to explore current and emerging applications of quantitative proteomics in translational pharmacology and strategies for improved integration into model-informed drug development based on practical experience of each of the presenters. A summary of the talks and discussions is presented in this perspective alongside future outlooks that were outlined for future meetings.
Significance Statement This perspective explores current and emerging applications of quantitative proteomics in translational pharmacology and precision medicine, and outlines outlooks for improved integration into model-informed drug development.},
	language = {en},
	urldate = {2024-06-10},
	journal = {Drug Metabolism and Disposition},
	author = {Prasad, Bhagwat and Al-Majdoub, Zubida M. and Wegler, Christine and Rostami-Hodjegan, Amin and Achour, Brahim},
	month = jan,
	year = {2024},
	pmid = {38821856},
	note = {Publisher: American Society for Pharmacology and Experimental Therapeutics
Section: Minireview},
	keywords = {physiologically-based pharmacokinetic modeling/PBPK, proteomics, systems pharmacology},
}

Over the past 20 years, quantitative proteomics has contributed a wealth of protein expression data, which are currently used for a variety of systems pharmacology applications, as a complement or a surrogate for activity of the corresponding proteins. A symposium at the 25th North American ISSX meeting, in Boston, in September 2023, was held to explore current and emerging applications of quantitative proteomics in translational pharmacology and strategies for improved integration into model-informed drug development based on practical experience of each of the presenters. A summary of the talks and discussions is presented in this perspective alongside future outlooks that were outlined for future meetings. Significance Statement This perspective explores current and emerging applications of quantitative proteomics in translational pharmacology and precision medicine, and outlines outlooks for improved integration into model-informed drug development.

@article{chaudhari_modifying_2024,
	title = {Modifying lignin composition and xylan {O}-acetylation induces changes in cell wall composition, extractability, and digestibility},
	volume = {17},
	issn = {2731-3654},
	url = {https://doi.org/10.1186/s13068-024-02513-5},
	doi = {10.1186/s13068-024-02513-5},
	abstract = {Lignin and xylan are important determinants of cell wall structure and lignocellulosic biomass digestibility. Genetic manipulations that individually modify either lignin or xylan structure improve polysaccharide digestibility. However, the effects of their simultaneous modifications have not been explored in a similar context. Here, both individual and combinatorial modification in xylan and lignin was studied by analysing the effect on plant cell wall properties, biotic stress responses and integrity sensing.},
	number = {1},
	urldate = {2024-06-10},
	journal = {Biotechnology for Biofuels and Bioproducts},
	author = {Chaudhari, Aniket Anant and Sharma, Anant Mohan and Rastogi, Lavi and Dewangan, Bhagwat Prasad and Sharma, Raunak and Singh, Deepika and Sah, Rajan Kumar and Das, Shouvik and Bhattacharjee, Saikat and Mellerowicz, Ewa J. and Pawar, Prashant Anupama-Mohan},
	month = may,
	year = {2024},
	keywords = {Acetyl Xylan Esterase (AXE), G Lignin, Saccharification, Xylose release},
	pages = {73},
}

Lignin and xylan are important determinants of cell wall structure and lignocellulosic biomass digestibility. Genetic manipulations that individually modify either lignin or xylan structure improve polysaccharide digestibility. However, the effects of their simultaneous modifications have not been explored in a similar context. Here, both individual and combinatorial modification in xylan and lignin was studied by analysing the effect on plant cell wall properties, biotic stress responses and integrity sensing.

@article{schneider_effects_2024,
	title = {Effects of small-scale outplanting fertilization on conifer seedling growth and fungal community establishment},
	volume = {16},
	issn = {2666-7193},
	url = {https://www.sciencedirect.com/science/article/pii/S266671932400075X},
	doi = {10.1016/j.tfp.2024.100568},
	abstract = {Forestry in Sweden largely relies on planting genetically improved seedlings after clear-cutting, and high survival and early growth of planted seedlings is vital for stand establishment, economic viability, and carbon sequestration. Norway spruce (Picea abies) and Scots pine (Pinus sylvestris) are the two most important tree species in Swedish forest stands and both are associated with a variety of ectomycorrhizal fungi. While seedlings are generally not fertilized at outplanting, previous results have shown that fertilization with arginine phosphate can increase root growth and seedling survival. However, it is not clear how this affects fungal community composition on the roots of growing seedlings. In a planting experiment sampled after one and two growing seasons, we found that planting position had the largest effects both on seedling performance and on fungal community composition and provide insight into the early stages of fungal community succession on planted Norway spruce and Scots pine seedlings. Fungal taxa present on seedlings before planting persisted on seedling roots, while some degree of novel colonization by site indigenous taxa was observed. Fertilization modified the relative abundance of some fungal taxa but did not lead to significant changes in overall community composition. In terms of seedling performance, ammonium nitrate led to increased mortality while arginine phosphate improved root growth.},
	urldate = {2024-06-10},
	journal = {Trees, Forests and People},
	author = {Schneider, Andreas N. and Castro, David and Holmlund, Mattias and Näsholm, Torgny and Hurry, Vaughan and Street, Nathaniel R.},
	month = jun,
	year = {2024},
	keywords = {Ectomycorrhiza, Fertilization, Norway spruce, Rotation forestry, Scots pine, Seedling establishment},
	pages = {100568},
}

Forestry in Sweden largely relies on planting genetically improved seedlings after clear-cutting, and high survival and early growth of planted seedlings is vital for stand establishment, economic viability, and carbon sequestration. Norway spruce (Picea abies) and Scots pine (Pinus sylvestris) are the two most important tree species in Swedish forest stands and both are associated with a variety of ectomycorrhizal fungi. While seedlings are generally not fertilized at outplanting, previous results have shown that fertilization with arginine phosphate can increase root growth and seedling survival. However, it is not clear how this affects fungal community composition on the roots of growing seedlings. In a planting experiment sampled after one and two growing seasons, we found that planting position had the largest effects both on seedling performance and on fungal community composition and provide insight into the early stages of fungal community succession on planted Norway spruce and Scots pine seedlings. Fungal taxa present on seedlings before planting persisted on seedling roots, while some degree of novel colonization by site indigenous taxa was observed. Fertilization modified the relative abundance of some fungal taxa but did not lead to significant changes in overall community composition. In terms of seedling performance, ammonium nitrate led to increased mortality while arginine phosphate improved root growth.

@article{diao_development_2024,
	title = {Development of 51 {K} liquid-phased probe array for {Loblolly} and {Slash} pines and its application to {GWAS} of {Slash} pine breeding population},
	volume = {216},
	issn = {0926-6690},
	doi = {10.1016/j.indcrop.2024.118777},
	abstract = {Loblolly pine (Pinus taeda) and Slash pine (Pinus elliottii) are important economically and ecologically tree species worldwide. To implement genomic based breeding strategy, genotyping large number of samples is needed. However, huge and complex pines genome make it difficult to obtain abundant and cost-effectively markers. In this study, we designed a SNP array containing 51 K liquid-phased probes based on the published SNPs and probes of the two species, novel Slash pine-specific long-read transcript, and SNPs obtained from a double digest Restriction-Site Associated DNA sequencing (ddRADseq). We performed targeted capture sequencing using the developed SNP array on three pine species of Loblolly, Slash, and Caribbean pine (Pinus caribaea). The probe capture had an efficiency of 68.26\% on average. Principal Component Analysis (PCA), phylogenetic analysis, and genetic structure analysis of 28,670 SNPs genotyped for the three pine species demonstrated the transferability of the SNP array for the three pines. Furthermore, we genotyped 221 range-wide Slash pine genotypes, analyzed their genetic diversity and performed a genome-wide association study (GWAS). We identified 95 SNPs significantly associated with growth and wood quality traits of Slash pine. We have identified potential roles of the MYB2 and MYB46 transcription factors in regulating cell cycle and differentiation in Slash pine, while also suggesting that AP2/ERF and Glycosyl hydrolase may play significant roles in wood formation processes. This new SNP array can be widely applied in future molecular breeding research of conifers. © 2024 Elsevier B.V.},
	language = {English},
	journal = {Industrial Crops and Products},
	author = {Diao, S. and Ding, X. and Luan, Q. and Chen, Z.-Q. and Wu, H.X. and Li, X. and Zhang, Y. and Sun, J. and Wu, Y. and Zou, L.-H. and Jiang, J.},
	month = sep,
	year = {2024},
	keywords = {Candidate gene, Genetic variation, Genotyping by target sequencing, In-solution probe, SNPs},
}

Loblolly pine (Pinus taeda) and Slash pine (Pinus elliottii) are important economically and ecologically tree species worldwide. To implement genomic based breeding strategy, genotyping large number of samples is needed. However, huge and complex pines genome make it difficult to obtain abundant and cost-effectively markers. In this study, we designed a SNP array containing 51 K liquid-phased probes based on the published SNPs and probes of the two species, novel Slash pine-specific long-read transcript, and SNPs obtained from a double digest Restriction-Site Associated DNA sequencing (ddRADseq). We performed targeted capture sequencing using the developed SNP array on three pine species of Loblolly, Slash, and Caribbean pine (Pinus caribaea). The probe capture had an efficiency of 68.26% on average. Principal Component Analysis (PCA), phylogenetic analysis, and genetic structure analysis of 28,670 SNPs genotyped for the three pine species demonstrated the transferability of the SNP array for the three pines. Furthermore, we genotyped 221 range-wide Slash pine genotypes, analyzed their genetic diversity and performed a genome-wide association study (GWAS). We identified 95 SNPs significantly associated with growth and wood quality traits of Slash pine. We have identified potential roles of the MYB2 and MYB46 transcription factors in regulating cell cycle and differentiation in Slash pine, while also suggesting that AP2/ERF and Glycosyl hydrolase may play significant roles in wood formation processes. This new SNP array can be widely applied in future molecular breeding research of conifers. © 2024 Elsevier B.V.

@article{meena_antisense_2024,
	title = {Antisense transcription from stress-responsive transcription factors fine-tunes the cold response in {Arabidopsis}},
	issn = {1040-4651},
	url = {https://doi.org/10.1093/plcell/koae160},
	doi = {10.1093/plcell/koae160},
	abstract = {Transcription of antisense long noncoding RNAs (lncRNAs) occurs pervasively across eukaryotic genomes. Only a few antisense lncRNAs have been characterized and shown to control biological processes, albeit with idiosyncratic regulatory mechanisms. Thus, we largely lack knowledge about the general role of antisense transcription in eukaryotic organisms. Here, we characterized genes with antisense transcription initiating close to the Poly(A) signal (PAS genes) in Arabidopsis (Arabidopsis thaliana). We compared plant native elongation transcript sequencing (plaNET-seq) with RNA sequencing (RNA-seq) during short-term cold exposure and detected massive differences between the response in active transcription and steady-state levels of PAS gene-derived mRNAs. The cold-induced expression of transcription factors B-BOX DOMAIN PROTEIN28 (BBX28) and C2H2-TYPE ZINC FINGER FAMILY PROTEIN5 (ZAT5) was detected by plaNET-seq, while their steady-state level was only slightly altered due to high mRNA turnover. Knockdown of BBX28 and ZAT5 or of their respective antisense transcripts severely compromised plant freezing tolerance. Decreased antisense transcript expression levels resulted in a reduced cold response of BBX28 and ZAT5, revealing a positive regulatory role of both antisense transcripts. This study expands the known repertoire of noncoding transcripts. It highlights that native transcription approaches can complement steady state RNA techniques to identify biologically relevant players in stress responses.},
	urldate = {2024-05-28},
	journal = {The Plant Cell},
	author = {Meena, Shiv Kumar and Quevedo, Marti and Muniz Nardeli, Sarah and Verez, Clément and Bhat, Susheel Sagar and Zacharaki, Vasiliki and Kindgren, Peter},
	month = may,
	year = {2024},
	pages = {koae160},
}

Transcription of antisense long noncoding RNAs (lncRNAs) occurs pervasively across eukaryotic genomes. Only a few antisense lncRNAs have been characterized and shown to control biological processes, albeit with idiosyncratic regulatory mechanisms. Thus, we largely lack knowledge about the general role of antisense transcription in eukaryotic organisms. Here, we characterized genes with antisense transcription initiating close to the Poly(A) signal (PAS genes) in Arabidopsis (Arabidopsis thaliana). We compared plant native elongation transcript sequencing (plaNET-seq) with RNA sequencing (RNA-seq) during short-term cold exposure and detected massive differences between the response in active transcription and steady-state levels of PAS gene-derived mRNAs. The cold-induced expression of transcription factors B-BOX DOMAIN PROTEIN28 (BBX28) and C2H2-TYPE ZINC FINGER FAMILY PROTEIN5 (ZAT5) was detected by plaNET-seq, while their steady-state level was only slightly altered due to high mRNA turnover. Knockdown of BBX28 and ZAT5 or of their respective antisense transcripts severely compromised plant freezing tolerance. Decreased antisense transcript expression levels resulted in a reduced cold response of BBX28 and ZAT5, revealing a positive regulatory role of both antisense transcripts. This study expands the known repertoire of noncoding transcripts. It highlights that native transcription approaches can complement steady state RNA techniques to identify biologically relevant players in stress responses.

@article{yang_genomic_2024,
	title = {Genomic basis of the distinct biosynthesis of β-glucogallin, a biochemical marker for hydrolyzable tannin production, in three oak species},
	volume = {242},
	copyright = {© 2024 The Authors New Phytologist © 2024 New Phytologist Foundation},
	issn = {1469-8137},
	url = {https://onlinelibrary.wiley.com/doi/abs/10.1111/nph.19711},
	doi = {10.1111/nph.19711},
	abstract = {Hydrolyzable tannins (HTs), predominant polyphenols in oaks, are widely used in grape wine aging, feed additives, and human healthcare. However, the limited availability of a high-quality reference genome of oaks greatly hampered the recognition of the mechanism of HT biosynthesis. Here, high-quality reference genomes of three Asian oak species (Quercus variabilis, Quercus aliena, and Quercus dentata) that have different HT contents were generated. Multi-omics studies were carried out to identify key genes regulating HT biosynthesis. In vitro enzyme activity assay was also conducted. Dual-luciferase and yeast one-hybrid assays were used to reveal the transcriptional regulation. Our results revealed that β-glucogallin was a biochemical marker for HT production in the cupules of the three Asian oaks. UGT84A13 was confirmed as the key enzyme for β-glucogallin biosynthesis. The differential expression of UGT84A13, rather than enzyme activity, was the main reason for different β-glucogallin and HT accumulation. Notably, sequence variations in UGT84A13 promoters led to different trans-activating activities of WRKY32/59, explaining the different expression patterns of UGT84A13 among the three species. Our findings provide three high-quality new reference genomes for oak trees and give new insights into different transcriptional regulation for understanding β-glucogallin and HT biosynthesis in closely related oak species.},
	language = {en},
	number = {6},
	urldate = {2024-05-24},
	journal = {New Phytologist},
	author = {Yang, Qinsong and Li, Jinjin and Wang, Yan and Wang, Zefu and Pei, Ziqi and Street, Nathaniel R. and Bhalerao, Rishikesh P. and Yu, Zhaowei and Gao, Yuhao and Ni, Junbei and Jiao, Yang and Sun, Minghui and Yang, Xiong and Chen, Yixin and Liu, Puyuan and Wang, Jiaxi and Liu, Yong and Li, Guolei},
	year = {2024},
	note = {\_eprint: https://onlinelibrary.wiley.com/doi/pdf/10.1111/nph.19711},
	keywords = {UGT84A13, hydrolyzable tannin, oak, whole-genome sequencing, β-glucogallin},
	pages = {2702--2718},
}

Hydrolyzable tannins (HTs), predominant polyphenols in oaks, are widely used in grape wine aging, feed additives, and human healthcare. However, the limited availability of a high-quality reference genome of oaks greatly hampered the recognition of the mechanism of HT biosynthesis. Here, high-quality reference genomes of three Asian oak species (Quercus variabilis, Quercus aliena, and Quercus dentata) that have different HT contents were generated. Multi-omics studies were carried out to identify key genes regulating HT biosynthesis. In vitro enzyme activity assay was also conducted. Dual-luciferase and yeast one-hybrid assays were used to reveal the transcriptional regulation. Our results revealed that β-glucogallin was a biochemical marker for HT production in the cupules of the three Asian oaks. UGT84A13 was confirmed as the key enzyme for β-glucogallin biosynthesis. The differential expression of UGT84A13, rather than enzyme activity, was the main reason for different β-glucogallin and HT accumulation. Notably, sequence variations in UGT84A13 promoters led to different trans-activating activities of WRKY32/59, explaining the different expression patterns of UGT84A13 among the three species. Our findings provide three high-quality new reference genomes for oak trees and give new insights into different transcriptional regulation for understanding β-glucogallin and HT biosynthesis in closely related oak species.

@article{hoermayer_mechanical_2024,
	title = {Mechanical forces in plant tissue matrix orient cell divisions via microtubule stabilization},
	volume = {59},
	issn = {1534-5807},
	url = {https://www.sciencedirect.com/science/article/pii/S1534580724001771},
	doi = {10.1016/j.devcel.2024.03.009},
	abstract = {Plant morphogenesis relies exclusively on oriented cell expansion and division. Nonetheless, the mechanism(s) determining division plane orientation remain elusive. Here, we studied tissue healing after laser-assisted wounding in roots of Arabidopsis thaliana and uncovered how mechanical forces stabilize and reorient the microtubule cytoskeleton for the orientation of cell division. We identified that root tissue functions as an interconnected cell matrix, with a radial gradient of tissue extendibility causing predictable tissue deformation after wounding. This deformation causes instant redirection of expansion in the surrounding cells and reorientation of microtubule arrays, ultimately predicting cell division orientation. Microtubules are destabilized under low tension, whereas stretching of cells, either through wounding or external aspiration, immediately induces their polymerization. The higher microtubule abundance in the stretched cell parts leads to the reorientation of microtubule arrays and, ultimately, informs cell division planes. This provides a long-sought mechanism for flexible re-arrangement of cell divisions by mechanical forces for tissue reconstruction and plant architecture.},
	number = {10},
	urldate = {2024-05-24},
	journal = {Developmental Cell},
	author = {Hoermayer, Lukas and Montesinos, Juan Carlos and Trozzi, Nicola and Spona, Leonhard and Yoshida, Saiko and Marhava, Petra and Caballero-Mancebo, Silvia and Benková, Eva and Heisenberg, Carl-Philip and Dagdas, Yasin and Majda, Mateusz and Friml, Jiří},
	month = may,
	year = {2024},
	keywords = {ablation, cell division, cell division plane, cell expansion, mechanical forces, microscopy, microtubules, plant development},
	pages = {1333--1344.e4},
}

Plant morphogenesis relies exclusively on oriented cell expansion and division. Nonetheless, the mechanism(s) determining division plane orientation remain elusive. Here, we studied tissue healing after laser-assisted wounding in roots of Arabidopsis thaliana and uncovered how mechanical forces stabilize and reorient the microtubule cytoskeleton for the orientation of cell division. We identified that root tissue functions as an interconnected cell matrix, with a radial gradient of tissue extendibility causing predictable tissue deformation after wounding. This deformation causes instant redirection of expansion in the surrounding cells and reorientation of microtubule arrays, ultimately predicting cell division orientation. Microtubules are destabilized under low tension, whereas stretching of cells, either through wounding or external aspiration, immediately induces their polymerization. The higher microtubule abundance in the stretched cell parts leads to the reorientation of microtubule arrays and, ultimately, informs cell division planes. This provides a long-sought mechanism for flexible re-arrangement of cell divisions by mechanical forces for tissue reconstruction and plant architecture.

@article{kankaanpaa_extracellular_2024,
	title = {Extracellular vesicles of {Norway} spruce contain precursors and enzymes for lignin formation and salicylic acid},
	issn = {0032-0889},
	url = {https://doi.org/10.1093/plphys/kiae287},
	doi = {10.1093/plphys/kiae287},
	abstract = {Lignin is a phenolic polymer in plants that rigidifies the cell walls of water-conducting tracheary elements and support-providing fibers and stone cells. Different mechanisms have been suggested for the transport of lignin precursors to the site of lignification in the cell wall. Extracellular vesicle (EV)-enriched samples isolated from a lignin-forming cell suspension culture of Norway spruce (Picea abies L. Karst.) contained both phenolic metabolites and enzymes related to lignin biosynthesis. Metabolomic analysis revealed mono-, di- and oligolignols in the EV isolates, as well as carbohydrates and amino acids. In addition, salicylic acid (SA) and some proteins involved in SA signaling were detected in the EV-enriched samples. A proteomic analysis detected several laccases, peroxidases, β-glucosidases, putative dirigent proteins, and cell wall-modifying enzymes such as glycosyl hydrolases, transglucosylase/hydrolases, and expansins in EVs. Our findings suggest that EVs are involved in transporting enzymes required for lignin polymerization in Norway spruce, and that radical coupling of monolignols can occur in these vesicles.},
	urldate = {2024-05-24},
	journal = {Plant Physiology},
	author = {Kankaanpää, Santeri and Väisänen, Enni and Goeminne, Geert and Soliymani, Rabah and Desmet, Sandrien and Samoylenko, Anatoliy and Vainio, Seppo and Wingsle, Gunnar and Boerjan, Wout and Vanholme, Ruben and Kärkönen, Anna},
	month = may,
	year = {2024},
	pages = {kiae287},
}

Lignin is a phenolic polymer in plants that rigidifies the cell walls of water-conducting tracheary elements and support-providing fibers and stone cells. Different mechanisms have been suggested for the transport of lignin precursors to the site of lignification in the cell wall. Extracellular vesicle (EV)-enriched samples isolated from a lignin-forming cell suspension culture of Norway spruce (Picea abies L. Karst.) contained both phenolic metabolites and enzymes related to lignin biosynthesis. Metabolomic analysis revealed mono-, di- and oligolignols in the EV isolates, as well as carbohydrates and amino acids. In addition, salicylic acid (SA) and some proteins involved in SA signaling were detected in the EV-enriched samples. A proteomic analysis detected several laccases, peroxidases, β-glucosidases, putative dirigent proteins, and cell wall-modifying enzymes such as glycosyl hydrolases, transglucosylase/hydrolases, and expansins in EVs. Our findings suggest that EVs are involved in transporting enzymes required for lignin polymerization in Norway spruce, and that radical coupling of monolignols can occur in these vesicles.

@article{foresi_tiny_2024,
	title = {The tiny giant of the sea, \textit{{Ostreococcus}'s} unique adaptations},
	volume = {211},
	issn = {0981-9428},
	url = {https://www.sciencedirect.com/science/article/pii/S0981942824003292},
	doi = {10.1016/j.plaphy.2024.108661},
	abstract = {Ostreococcus spp. are unicellular organisms with one of the simplest cellular organizations. The sequencing of the genomes of different Ostreococcus species has reinforced this status since Ostreococcus tauri has one most compact nuclear genomes among eukaryotic organisms. Despite this, it has retained a number of genes, setting it apart from other organisms with similar small genomes. Ostreococcus spp. feature a substantial number of selenocysteine-containing proteins, which, due to their higher catalytic activity compared to their selenium-lacking counterparts, may require a reduced quantity of proteins. Notably, O. tauri encodes several ammonium transporter genes, that may provide it with a competitive edge for acquiring nitrogen (N). This characteristic makes it an intriguing model for studying the efficient use of N in eukaryotes. Under conditions of low N availability, O. tauri utilizes N from abundant proteins or amino acids, such as L-arginine, similar to higher plants. However, the presence of a nitric oxide synthase (L-arg substrate) sheds light on a new metabolic pathway for L-arg in algae. The metabolic adaptations of O. tauri to day and night cycles offer valuable insights into carbon and iron metabolic configuration. O. tauri has evolved novel strategies to optimize iron uptake, lacking the classic components of the iron absorption mechanism. Overall, the cellular and genetic characteristics of Ostreococcus contribute to its evolutionary success, making it an excellent model for studying the physiological and genetic aspects of how green algae have adapted to the marine environment. Furthermore, given its potential for lipid accumulation and its marine habitat, it may represent a promising avenue for third-generation biofuels.},
	urldate = {2024-05-17},
	journal = {Plant Physiology and Biochemistry},
	author = {Foresi, Noelia and De Marco, María Agustina and Del Castello, Fiorella and Ramirez, Leonor and Nejamkin, Andres and Calo, Gonzalo and Grimsley, Nigel and Correa-Aragunde, Natalia and Martínez-Noël, Giselle M. A.},
	month = jun,
	year = {2024},
	keywords = {Alga, Iron, Lipids-starch, Mamiellales, Mamiellophyceae, Nitrogen, Picoeukaryote, Picophytoplankton},
	pages = {108661},
}

Ostreococcus spp. are unicellular organisms with one of the simplest cellular organizations. The sequencing of the genomes of different Ostreococcus species has reinforced this status since Ostreococcus tauri has one most compact nuclear genomes among eukaryotic organisms. Despite this, it has retained a number of genes, setting it apart from other organisms with similar small genomes. Ostreococcus spp. feature a substantial number of selenocysteine-containing proteins, which, due to their higher catalytic activity compared to their selenium-lacking counterparts, may require a reduced quantity of proteins. Notably, O. tauri encodes several ammonium transporter genes, that may provide it with a competitive edge for acquiring nitrogen (N). This characteristic makes it an intriguing model for studying the efficient use of N in eukaryotes. Under conditions of low N availability, O. tauri utilizes N from abundant proteins or amino acids, such as L-arginine, similar to higher plants. However, the presence of a nitric oxide synthase (L-arg substrate) sheds light on a new metabolic pathway for L-arg in algae. The metabolic adaptations of O. tauri to day and night cycles offer valuable insights into carbon and iron metabolic configuration. O. tauri has evolved novel strategies to optimize iron uptake, lacking the classic components of the iron absorption mechanism. Overall, the cellular and genetic characteristics of Ostreococcus contribute to its evolutionary success, making it an excellent model for studying the physiological and genetic aspects of how green algae have adapted to the marine environment. Furthermore, given its potential for lipid accumulation and its marine habitat, it may represent a promising avenue for third-generation biofuels.

@article{larsson_diminishing_2024,
	title = {Diminishing legacy effects from forest fertilization on stand structure, vegetation community, and soil function},
	volume = {563},
	issn = {0378-1127},
	url = {https://www.sciencedirect.com/science/article/pii/S0378112724002792},
	doi = {10.1016/j.foreco.2024.121967},
	abstract = {While there is consensus that fertilization with nitrogen (N) is a cost-effective way of increasing both forest biomass yield and timber harvest profitability, the strength and longevity of legacy effects are debated. To quantify legacy effects of past fertilization, we analysed 21 mixed Pinus sylvesteris and Picea abies stands. The stands, on average 23 years old at the time of this study, were either unfertilized (n=7), fertilized with 150 kg N ha−1 once 36 years ago (n=7), or twice, 45 and 36 years ago, respectively (n=7), during the previous stand rotation. We performed measurements on soil N mineralisation and N availability, forest growth, ground vegetation community composition, soil and vegetation C/N ratios and soil C and N stocks, many of which responded to legacy N fertilization earlier in stand development. Our results show that the legacy effects of fertilization during the previous stand rotation have diminished through time, indicating an eventual convergence of stand properties. Specifically, all significant effects present in the previous measurement period (over a decade ago), were weaker or completely absent in the current study (i.e. 36 years after fertilization and 23 years after initiation of the new stands). None-the-less, this indicates a longer legacy effect of N fertilization than what is normally considered and suggests that care should be taken to mitigate unwanted, long-term effects when utilizing N addition to promote tree growth in boreal forests.},
	urldate = {2024-05-15},
	journal = {Forest Ecology and Management},
	author = {Larsson, Marcus and Strengbom, Joachim and Gundale, Michael J. and Nordin, Annika},
	month = jul,
	year = {2024},
	keywords = {Forest fertilization, Forest growth, Ion-exchange resin, Mineralization, Soil organic carbon, Vegetation community composition},
	pages = {121967},
}

While there is consensus that fertilization with nitrogen (N) is a cost-effective way of increasing both forest biomass yield and timber harvest profitability, the strength and longevity of legacy effects are debated. To quantify legacy effects of past fertilization, we analysed 21 mixed Pinus sylvesteris and Picea abies stands. The stands, on average 23 years old at the time of this study, were either unfertilized (n=7), fertilized with 150 kg N ha−1 once 36 years ago (n=7), or twice, 45 and 36 years ago, respectively (n=7), during the previous stand rotation. We performed measurements on soil N mineralisation and N availability, forest growth, ground vegetation community composition, soil and vegetation C/N ratios and soil C and N stocks, many of which responded to legacy N fertilization earlier in stand development. Our results show that the legacy effects of fertilization during the previous stand rotation have diminished through time, indicating an eventual convergence of stand properties. Specifically, all significant effects present in the previous measurement period (over a decade ago), were weaker or completely absent in the current study (i.e. 36 years after fertilization and 23 years after initiation of the new stands). None-the-less, this indicates a longer legacy effect of N fertilization than what is normally considered and suggests that care should be taken to mitigate unwanted, long-term effects when utilizing N addition to promote tree growth in boreal forests.

@article{haggstrom_effects_2024,
	title = {Effects of {Planting} {Position}, {Seedling} {Size}, and {Organic} {Nitrogen} {Fertilization} on the {Establishment} of {Scots} {Pine} ({Pinus} sylvestris {L}.) and {Norway} {Spruce} ({Picea} abies ({L}.) {Karst}) {Seedlings}},
	volume = {15},
	copyright = {http://creativecommons.org/licenses/by/3.0/},
	issn = {1999-4907},
	url = {https://www.mdpi.com/1999-4907/15/4/703},
	doi = {10.3390/f15040703},
	abstract = {The forest regeneration phase in Sweden commonly involves mechanical soil preparation followed by the planting of Scots pine (Pinus sylvestris L.) or Norway spruce (Picea abies (L.) Karst) seedlings. The prepared soil offers planting positions with different properties, including reduced damage by pine weevils (Hylobius abietis L.). Nitrogen fertilization can be applied at the time of planting to aid establishment of the seedlings. In this study, we compared the effects of different planting positions, organic nitrogen fertilization, and different seedling sizes on the early survival and growth of Scots pine and Norway spruce seedlings. The main planting positions were capped mound, hinge, and mineral soil. Seedlings planted close to organic material were categorized as being in “low-quality positions”, since proximity to organic material increases pine weevil attraction. Higher mortality rates related to pine weevil damage were recorded for the seedlings planted in the low-quality positions, regardless of seedling size or N fertilization. Pine weevil attack rates increased with increasing seedling size. Growth was, in general, lowest in the mineral soil positions. The effect of organic N fertilization on growth was positive for the spruce regardless of the planting position or seedling size, while it depended on the planting position and seedling size for the pine, indicating that the effects of organic N fertilization depend on the seedling species, seedling size, and planting position.},
	language = {en},
	number = {4},
	urldate = {2024-05-10},
	journal = {Forests},
	author = {Häggström, Bodil and Hajek, Jörgen and Nordin, Annika and Öhlund, Jonas},
	month = apr,
	year = {2024},
	note = {Number: 4
Publisher: Multidisciplinary Digital Publishing Institute},
	keywords = {Norway spruce, Scots pine, forest regeneration, organic N fertilization, pine weevil, planting position, seedling size},
	pages = {703},
}

The forest regeneration phase in Sweden commonly involves mechanical soil preparation followed by the planting of Scots pine (Pinus sylvestris L.) or Norway spruce (Picea abies (L.) Karst) seedlings. The prepared soil offers planting positions with different properties, including reduced damage by pine weevils (Hylobius abietis L.). Nitrogen fertilization can be applied at the time of planting to aid establishment of the seedlings. In this study, we compared the effects of different planting positions, organic nitrogen fertilization, and different seedling sizes on the early survival and growth of Scots pine and Norway spruce seedlings. The main planting positions were capped mound, hinge, and mineral soil. Seedlings planted close to organic material were categorized as being in “low-quality positions”, since proximity to organic material increases pine weevil attraction. Higher mortality rates related to pine weevil damage were recorded for the seedlings planted in the low-quality positions, regardless of seedling size or N fertilization. Pine weevil attack rates increased with increasing seedling size. Growth was, in general, lowest in the mineral soil positions. The effect of organic N fertilization on growth was positive for the spruce regardless of the planting position or seedling size, while it depended on the planting position and seedling size for the pine, indicating that the effects of organic N fertilization depend on the seedling species, seedling size, and planting position.

@article{raebild_polyploidy_2024,
	title = {Polyploidy – {A} tool in adapting trees to future climate changes? {A} review of polyploidy in trees},
	volume = {560},
	issn = {0378-1127},
	shorttitle = {Polyploidy – {A} tool in adapting trees to future climate changes?},
	url = {https://www.sciencedirect.com/science/article/pii/S0378112724000793},
	doi = {10.1016/j.foreco.2024.121767},
	abstract = {Polyploidy, or genome doubling, has occurred repeatedly through plant evolution. While polyploid plants are used extensively in agriculture and horticulture, they have so far found limited use in forestry. Here we review the potentials of polyploid trees under climate change, and investigate if there is support for increased use. We find that polyploid trees like other plants have consistent increases in cell sizes compared to diploids, and that leaf-area based rates of photosynthesis tend to increase with increasing levels of ploidy. While no particular trend could be discerned in terms of biomass between trees of different ploidy levels, physiology is affected by polyploidization and several studies point towards a high potential for polyploid trees to adapt to drought stress. The ploidy level of most tree species is unknown, and analysis of geographical patterns in frequencies of polyploid trees are inconclusive. Artificial polyploid trees are often created by colchicine and in a few cases these have been successfully applied in forestry, but the effects of induced polyploidization in many economically important tree species remains untested. Polyploids would also be increasingly useful in tree breeding programs, to create synthetic hybrids or sterile triploids that could control unwanted spreading of germplasm in nature. In conclusion, this review suggests that polyploid trees may be superior under climate change in some cases, but that the potential of polyploids is not yet fully known and should be evaluated on a case-to-case basis for different tree species.},
	urldate = {2024-05-10},
	journal = {Forest Ecology and Management},
	author = {Ræbild, Anders and Anamthawat-Jónsson, Kesara and Egertsdotter, Ulrika and Immanen, Juha and Jensen, Anna Monrad and Koutouleas, Athina and Martens, Helle Jakobe and Nieminen, Kaisa and Olofsson, Jill Katharina and Röper, Anna-Catharina and Salojärvi, Jarkko and Strömvik, Martina and Vatanparast, Mohammad and Vivian-Smith, Adam},
	month = may,
	year = {2024},
	keywords = {Adaptation, Ecophysiology, Fitness, Forestry, Tree breeding, Whole genome duplication (WGD)},
	pages = {121767},
}

Polyploidy, or genome doubling, has occurred repeatedly through plant evolution. While polyploid plants are used extensively in agriculture and horticulture, they have so far found limited use in forestry. Here we review the potentials of polyploid trees under climate change, and investigate if there is support for increased use. We find that polyploid trees like other plants have consistent increases in cell sizes compared to diploids, and that leaf-area based rates of photosynthesis tend to increase with increasing levels of ploidy. While no particular trend could be discerned in terms of biomass between trees of different ploidy levels, physiology is affected by polyploidization and several studies point towards a high potential for polyploid trees to adapt to drought stress. The ploidy level of most tree species is unknown, and analysis of geographical patterns in frequencies of polyploid trees are inconclusive. Artificial polyploid trees are often created by colchicine and in a few cases these have been successfully applied in forestry, but the effects of induced polyploidization in many economically important tree species remains untested. Polyploids would also be increasingly useful in tree breeding programs, to create synthetic hybrids or sterile triploids that could control unwanted spreading of germplasm in nature. In conclusion, this review suggests that polyploid trees may be superior under climate change in some cases, but that the potential of polyploids is not yet fully known and should be evaluated on a case-to-case basis for different tree species.

@article{shi_super-pangenome_2024,
	title = {The super-pangenome of {Populus} unveils genomic facets for its adaptation and diversification in widespread forest trees},
	volume = {17},
	issn = {1674-2052},
	url = {https://www.cell.com/molecular-plant/abstract/S1674-2052(24)00082-0},
	doi = {10.1016/j.molp.2024.03.009},
	abstract = {{\textless}h2{\textgreater}Abstract{\textless}/h2{\textgreater}{\textless}p{\textgreater}Understanding the underlying mechanisms and links between genome evolution and adaptive innovations stands as a key goal in evolutionary studies. Poplars, among the world's most widely distributed and cultivated trees, exhibit extensive phenotypic diversity and environmental adaptability. In this study, we present a genus-level super-pangenome comprising 19 \textit{Populus} genomes, revealing the likely pivotal role of private genes in facilitating local environmental and climate adaptation. Through the integration of pangenomes with transcriptomes, methylomes, and chromatin accessibility mapping, we unveil that the evolutionary trajectories of pangenes and duplicated genes are closely linked to local genomic landscapes of regulatory and epigenetic architectures, notably CG methylation in gene-body regions. Further comparative genomic analyses have enabled the identification of 142 202 structural variants across species that intersect with a significant number of genes and contribute substantially to both phenotypic and adaptive divergence. We have experimentally validated a ∼180-bp presence/absence variant affecting the expression of the \textit{CUC2} gene, crucial for leaf serration formation. Finally, we developed a user-friendly web-based tool encompassing the multi-omics resources associated with the \textit{Populus} super-pangenome (http://www.populus-superpangenome.com). Together, the present pioneering super-pangenome resource in forest trees not only aids in the advancement of breeding efforts of this globally important tree genus but also offers valuable insights into potential avenues for comprehending tree biology.{\textless}/p{\textgreater}},
	language = {English},
	number = {5},
	urldate = {2024-05-10},
	journal = {Molecular Plant},
	author = {Shi, Tingting and Zhang, Xinxin and Hou, Yukang and Jia, Changfu and Dan, Xuming and Zhang, Yulin and Jiang, Yuanzhong and Lai, Qiang and Feng, Jiajun and Feng, Jianju and Ma, Tao and Wu, Jiali and Liu, Shuyu and Zhang, Lei and Long, Zhiqin and Chen, Liyang and Street, Nathaniel R. and Ingvarsson, Pär K. and Liu, Jianquan and Yin, Tongming and Wang, Jing},
	month = may,
	year = {2024},
	pmid = {38486452},
	note = {Publisher: Elsevier},
	keywords = {genome evolution, pan-genomes, structural variation, whole genome duplication},
	pages = {725--746},
}

\textlessh2\textgreaterAbstract\textless/h2\textgreater\textlessp\textgreaterUnderstanding the underlying mechanisms and links between genome evolution and adaptive innovations stands as a key goal in evolutionary studies. Poplars, among the world's most widely distributed and cultivated trees, exhibit extensive phenotypic diversity and environmental adaptability. In this study, we present a genus-level super-pangenome comprising 19 Populus genomes, revealing the likely pivotal role of private genes in facilitating local environmental and climate adaptation. Through the integration of pangenomes with transcriptomes, methylomes, and chromatin accessibility mapping, we unveil that the evolutionary trajectories of pangenes and duplicated genes are closely linked to local genomic landscapes of regulatory and epigenetic architectures, notably CG methylation in gene-body regions. Further comparative genomic analyses have enabled the identification of 142 202 structural variants across species that intersect with a significant number of genes and contribute substantially to both phenotypic and adaptive divergence. We have experimentally validated a ∼180-bp presence/absence variant affecting the expression of the CUC2 gene, crucial for leaf serration formation. Finally, we developed a user-friendly web-based tool encompassing the multi-omics resources associated with the Populus super-pangenome (http://www.populus-superpangenome.com). Together, the present pioneering super-pangenome resource in forest trees not only aids in the advancement of breeding efforts of this globally important tree genus but also offers valuable insights into potential avenues for comprehending tree biology.\textless/p\textgreater

@article{zhao_evolutionary_2024,
	title = {Evolutionary radiation of the {Eurasian} {Pinus} species under pervasive gene flow},
	volume = {242},
	copyright = {© 2024 The Authors. New Phytologist © 2024 New Phytologist Foundation},
	issn = {1469-8137},
	url = {https://onlinelibrary.wiley.com/doi/abs/10.1111/nph.19694},
	doi = {10.1111/nph.19694},
	abstract = {Evolutionary radiation, a pivotal aspect of macroevolution, offers valuable insights into evolutionary processes. The genus Pinus is the largest genus in conifers with c. 90\% of the extant species emerged in the Miocene, which signifies a case of rapid diversification. Despite this remarkable history, our understanding of the mechanisms driving radiation within this expansive genus has remained limited. Using exome capture sequencing and a fossil-calibrated phylogeny, we investigated the divergence history, niche diversification, and introgression among 13 closely related Eurasian species spanning climate zones from the tropics to the boreal Arctic. We detected complex introgression among lineages in subsection Pinus at all stages of the phylogeny. Despite this widespread gene exchange, each species maintained its genetic identity and showed clear niche differentiation. Demographic analysis unveiled distinct population histories among these species, which further influenced the nucleotide diversity and efficacy of purifying and positive selection in each species. Our findings suggest that radiation in the Eurasian pines was likely fueled by interspecific recombination and further reinforced by their adaptation to distinct environments. Our study highlights the constraints and opportunities for evolutionary change, and the expectations of future adaptation in response to environmental changes in different lineages.},
	language = {en},
	number = {5},
	urldate = {2024-05-10},
	journal = {New Phytologist},
	author = {Zhao, Wei and Gao, Jie and Hall, David and Andersson, Bea Angelica and Bruxaux, Jade and Tomlinson, Kyle W. and Drouzas, Andreas D. and Suyama, Yoshihisa and Wang, Xiao-Ru},
	year = {2024},
	note = {\_eprint: https://onlinelibrary.wiley.com/doi/pdf/10.1111/nph.19694},
	keywords = {Pinus evolution, demographic history, divergent adaptation, ecological gradients, introgression, phylogeny, selection},
	pages = {2353--2368},
}

Evolutionary radiation, a pivotal aspect of macroevolution, offers valuable insights into evolutionary processes. The genus Pinus is the largest genus in conifers with c. 90% of the extant species emerged in the Miocene, which signifies a case of rapid diversification. Despite this remarkable history, our understanding of the mechanisms driving radiation within this expansive genus has remained limited. Using exome capture sequencing and a fossil-calibrated phylogeny, we investigated the divergence history, niche diversification, and introgression among 13 closely related Eurasian species spanning climate zones from the tropics to the boreal Arctic. We detected complex introgression among lineages in subsection Pinus at all stages of the phylogeny. Despite this widespread gene exchange, each species maintained its genetic identity and showed clear niche differentiation. Demographic analysis unveiled distinct population histories among these species, which further influenced the nucleotide diversity and efficacy of purifying and positive selection in each species. Our findings suggest that radiation in the Eurasian pines was likely fueled by interspecific recombination and further reinforced by their adaptation to distinct environments. Our study highlights the constraints and opportunities for evolutionary change, and the expectations of future adaptation in response to environmental changes in different lineages.

@article{bekele_methane_2024,
	title = {Methane production from locally available ruminant feedstuffs in {Ethiopia} – {An} \textit{in vitro} study},
	volume = {312},
	issn = {0377-8401},
	url = {https://www.sciencedirect.com/science/article/pii/S0377840124001056},
	doi = {10.1016/j.anifeedsci.2024.115977},
	abstract = {Achieving optimal nutrient composition in locally sourced ruminant feeds is important, but can be challenging in resource-limited production systems. For example, improving the composition of available local feed resources is a key obstacle to efficiently mitigating enteric methane (CH4) emissions in ruminants. This study characterized the nutritional content and in vitro methane (CH4) yield of ruminant feedstuffs accessible in Ethiopia. A survey of 60 experienced farmers in two representative districts in Amhara region, Ethiopia, provided 33 feed samples, which were classified into four ruminant feed categories: Grasses (n=10); indigenous plants (trees, shrubs, herbaceous plants) (n=13); crop residues (n=5); and agro-industrial by-products (n=5). Nutritional composition was assessed by proximate and detergent methods. Methane yield (g CH4/kg feed dry matter (DM)) and total gas yield (L/kg DM) were evaluated using a fully automated in vitro gas production system. A colorimetric assay was conducted to measure condensed tannin content (CT, mg/g) in relevant feeds. Lower crude protein (CP) values were observed for the grass (mean 65.2 g/kg DM) and crop residues (mean 54.5 g/kg DM) categories. Agro-industrial by-products had the highest CP (mean 260 g/kg DM), while indigenous plants exhibited intermediate levels (163 g/kg DM). There was significant variation in CH4 yield (P{\textless}0.01) between grasses (12.4–24.7 g/kg DM) indigenous plants (1.8–19.3 g/kg DM), and agro-industrial by-products (8.1–26.9 g/kg DM). The indigenous plant Trifolium acaule gave the lowest in vitro CH4 yield (1.8 g/kg DM). A positive relationship was observed between in vitro dry matter digestibility (IVDMD), CH4, and total gas yield. Percentage of CH4 in total gas production varied with feed category (grasses 14.5–19.6\%; indigenous plants 3.1–16.9\%; crop residues 15.8–20.6\%; agro-industrial by-products 12.8–18.7\%), and within category, e.g., Trifolium acaule (3.1\%), Acacia nilotica L. (7.1\%), Ziziphus spina-christi (9.9\%), brewer’s spent grains (BSG) (12.8\%), local liquor (areki) residues (14.1\%), and local beer (tella) residues (15.1\%). A negative relationship was observed between CT content and in vitro CH4 yield, with a stronger (P{\textless}0.05) correlation for soluble CTs (R2 = 0.46) than cell-bound CTs (R2 = 0.25) and total CTs (R2 = 0.29). Based on methanogenic properties and effects of CTs on in vitro CH4 yield, indigenous plants should be prioritized in ruminant rations in Ethiopia. Making nutritional composition and CH4 data publicly available could help develop environmentally sound, cost-effective rations for ruminant livestock, benefiting local farmers and leading to more sustainable and efficient livestock production in Ethiopia.},
	urldate = {2024-05-06},
	journal = {Animal Feed Science and Technology},
	author = {Bekele, Wondimagegne and Huhtanen, Pekka and Zegeye, Abiy and Simachew, Addis and Siddique, Abu Bakar and Albrectsen, Benedicte Riber and Ramin, Mohammad},
	month = jun,
	year = {2024},
	keywords = {CH, CH gas percentage, Local feeds, condensed tannins, dry matter digestibility},
	pages = {115977},
}

Achieving optimal nutrient composition in locally sourced ruminant feeds is important, but can be challenging in resource-limited production systems. For example, improving the composition of available local feed resources is a key obstacle to efficiently mitigating enteric methane (CH4) emissions in ruminants. This study characterized the nutritional content and in vitro methane (CH4) yield of ruminant feedstuffs accessible in Ethiopia. A survey of 60 experienced farmers in two representative districts in Amhara region, Ethiopia, provided 33 feed samples, which were classified into four ruminant feed categories: Grasses (n=10); indigenous plants (trees, shrubs, herbaceous plants) (n=13); crop residues (n=5); and agro-industrial by-products (n=5). Nutritional composition was assessed by proximate and detergent methods. Methane yield (g CH4/kg feed dry matter (DM)) and total gas yield (L/kg DM) were evaluated using a fully automated in vitro gas production system. A colorimetric assay was conducted to measure condensed tannin content (CT, mg/g) in relevant feeds. Lower crude protein (CP) values were observed for the grass (mean 65.2 g/kg DM) and crop residues (mean 54.5 g/kg DM) categories. Agro-industrial by-products had the highest CP (mean 260 g/kg DM), while indigenous plants exhibited intermediate levels (163 g/kg DM). There was significant variation in CH4 yield (P\textless0.01) between grasses (12.4–24.7 g/kg DM) indigenous plants (1.8–19.3 g/kg DM), and agro-industrial by-products (8.1–26.9 g/kg DM). The indigenous plant Trifolium acaule gave the lowest in vitro CH4 yield (1.8 g/kg DM). A positive relationship was observed between in vitro dry matter digestibility (IVDMD), CH4, and total gas yield. Percentage of CH4 in total gas production varied with feed category (grasses 14.5–19.6%; indigenous plants 3.1–16.9%; crop residues 15.8–20.6%; agro-industrial by-products 12.8–18.7%), and within category, e.g., Trifolium acaule (3.1%), Acacia nilotica L. (7.1%), Ziziphus spina-christi (9.9%), brewer’s spent grains (BSG) (12.8%), local liquor (areki) residues (14.1%), and local beer (tella) residues (15.1%). A negative relationship was observed between CT content and in vitro CH4 yield, with a stronger (P\textless0.05) correlation for soluble CTs (R2 = 0.46) than cell-bound CTs (R2 = 0.25) and total CTs (R2 = 0.29). Based on methanogenic properties and effects of CTs on in vitro CH4 yield, indigenous plants should be prioritized in ruminant rations in Ethiopia. Making nutritional composition and CH4 data publicly available could help develop environmentally sound, cost-effective rations for ruminant livestock, benefiting local farmers and leading to more sustainable and efficient livestock production in Ethiopia.

@article{shi_high-quality_2024,
	title = {High-quality genome assembly enables prediction of allele-specific gene expression in hybrid poplar},
	volume = {195},
	issn = {0032-0889},
	url = {https://doi.org/10.1093/plphys/kiae078},
	doi = {10.1093/plphys/kiae078},
	abstract = {Poplar (Populus) is a well-established model system for tree genomics and molecular breeding, and hybrid poplar is widely used in forest plantations. However, distinguishing its diploid homologous chromosomes is difficult, complicating advanced functional studies on specific alleles. In this study, we applied a trio-binning design and PacBio high-fidelity long-read sequencing to obtain haplotype-phased telomere-to-telomere genome assemblies for the 2 parents of the well-studied F1 hybrid “84K” (Populus alba × Populus tremula var. glandulosa). Almost all chromosomes, including the telomeres and centromeres, were completely assembled for each haplotype subgenome apart from 2 small gaps on one chromosome. By incorporating information from these haplotype assemblies and extensive RNA-seq data, we analyzed gene expression patterns between the 2 subgenomes and alleles. Transcription bias at the subgenome level was not uncovered, but extensive-expression differences were detected between alleles. We developed machine-learning (ML) models to predict allele-specific expression (ASE) with high accuracy and identified underlying genome features most highly influencing ASE. One of our models with 15 predictor variables achieved 77\% accuracy on the training set and 74\% accuracy on the testing set. ML models identified gene body CHG methylation, sequence divergence, and transposon occupancy both upstream and downstream of alleles as important factors for ASE. Our haplotype-phased genome assemblies and ML strategy highlight an avenue for functional studies in Populus and provide additional tools for studying ASE and heterosis in hybrids.},
	number = {1},
	urldate = {2024-05-03},
	journal = {Plant Physiology},
	author = {Shi, Tian-Le and Jia, Kai-Hua and Bao, Yu-Tao and Nie, Shuai and Tian, Xue-Chan and Yan, Xue-Mei and Chen, Zhao-Yang and Li, Zhi-Chao and Zhao, Shi-Wei and Ma, Hai-Yao and Zhao, Ye and Li, Xiang and Zhang, Ren-Gang and Guo, Jing and Zhao, Wei and El-Kassaby, Yousry Aly and Müller, Niels and Van de Peer, Yves and Wang, Xiao-Ru and Street, Nathaniel Robert and Porth, Ilga and An, Xinmin and Mao, Jian-Feng},
	month = may,
	year = {2024},
	pages = {652--670},
}

Poplar (Populus) is a well-established model system for tree genomics and molecular breeding, and hybrid poplar is widely used in forest plantations. However, distinguishing its diploid homologous chromosomes is difficult, complicating advanced functional studies on specific alleles. In this study, we applied a trio-binning design and PacBio high-fidelity long-read sequencing to obtain haplotype-phased telomere-to-telomere genome assemblies for the 2 parents of the well-studied F1 hybrid “84K” (Populus alba × Populus tremula var. glandulosa). Almost all chromosomes, including the telomeres and centromeres, were completely assembled for each haplotype subgenome apart from 2 small gaps on one chromosome. By incorporating information from these haplotype assemblies and extensive RNA-seq data, we analyzed gene expression patterns between the 2 subgenomes and alleles. Transcription bias at the subgenome level was not uncovered, but extensive-expression differences were detected between alleles. We developed machine-learning (ML) models to predict allele-specific expression (ASE) with high accuracy and identified underlying genome features most highly influencing ASE. One of our models with 15 predictor variables achieved 77% accuracy on the training set and 74% accuracy on the testing set. ML models identified gene body CHG methylation, sequence divergence, and transposon occupancy both upstream and downstream of alleles as important factors for ASE. Our haplotype-phased genome assemblies and ML strategy highlight an avenue for functional studies in Populus and provide additional tools for studying ASE and heterosis in hybrids.

@article{wang_slnac3_2024,
	title = {{SlNAC3} suppresses cold tolerance in tomatoes by enhancing ethylene biosynthesis},
	copyright = {© 2024 John Wiley \& Sons Ltd.},
	issn = {1365-3040},
	url = {https://onlinelibrary.wiley.com/doi/abs/10.1111/pce.14933},
	doi = {10.1111/pce.14933},
	abstract = {Low temperature stress poses a significant challenge to the productivity of horticultural crops. The dynamic expression of cold-responsive genes plays a crucial role in plant cold tolerance. While NAC transcription factors have been extensively studied in plant growth and development, their involvement in regulating plant cold tolerance remains poorly understood. In this study, we focused on the identification and characterisation of SlNAC3 as the most rapid and robust responsive gene in tomato under low temperature conditions. Manipulating SlNAC3 through overexpression or silencing resulted in reduced or enhanced cold tolerance, respectively. Surprisingly, we discovered a negative correlation between the expression of CBF and cold tolerance in the SlNAC3 transgenic lines. These findings suggest that SlNAC3 regulates tomato cold tolerance likely through a CBF-independent pathway. Furthermore, we conducted additional investigations to identify the molecular mechanisms underlying SINAC3-mediated cold tolerance in tomatoes. Our results revealed that SlNAC3 controls the transcription of ethylene biosynthetic genes, thereby bursting ethylene release in response to cold stress. Indeed, the silencing of these genes led to an augmentation in cold tolerance. This discovery provides valuable insights into the regulatory pathways involved in ethylene-mediated cold tolerance in tomatoes, offering potential strategies for developing innovative approaches to enhance cold stress resilience in this economically important crop species.},
	language = {en},
	urldate = {2024-05-03},
	journal = {Plant, Cell \& Environment},
	author = {Wang, Tao and Ma, Xuemin and Chen, Ying and Wang, Cuicui and Xia, Zhenxiao and Liu, Zixi and Gao, Lihong and Zhang, Wenna},
	month = may,
	year = {2024},
	note = {\_eprint: https://onlinelibrary.wiley.com/doi/pdf/10.1111/pce.14933},
	keywords = {NAC transcription factor, cold response},
}

Low temperature stress poses a significant challenge to the productivity of horticultural crops. The dynamic expression of cold-responsive genes plays a crucial role in plant cold tolerance. While NAC transcription factors have been extensively studied in plant growth and development, their involvement in regulating plant cold tolerance remains poorly understood. In this study, we focused on the identification and characterisation of SlNAC3 as the most rapid and robust responsive gene in tomato under low temperature conditions. Manipulating SlNAC3 through overexpression or silencing resulted in reduced or enhanced cold tolerance, respectively. Surprisingly, we discovered a negative correlation between the expression of CBF and cold tolerance in the SlNAC3 transgenic lines. These findings suggest that SlNAC3 regulates tomato cold tolerance likely through a CBF-independent pathway. Furthermore, we conducted additional investigations to identify the molecular mechanisms underlying SINAC3-mediated cold tolerance in tomatoes. Our results revealed that SlNAC3 controls the transcription of ethylene biosynthetic genes, thereby bursting ethylene release in response to cold stress. Indeed, the silencing of these genes led to an augmentation in cold tolerance. This discovery provides valuable insights into the regulatory pathways involved in ethylene-mediated cold tolerance in tomatoes, offering potential strategies for developing innovative approaches to enhance cold stress resilience in this economically important crop species.

@article{mishra_adventitious_2024,
	title = {Adventitious rooting in response to long-term cold: a possible mechanism of clonal growth in alpine perennials},
	volume = {15},
	issn = {1664-462X},
	shorttitle = {Adventitious rooting in response to long-term cold},
	url = {https://www.frontiersin.org/journals/plant-science/articles/10.3389/fpls.2024.1352830/full},
	doi = {10.3389/fpls.2024.1352830},
	abstract = {{\textless}p{\textgreater}Arctic alpine species experience extended periods of cold and unpredictable conditions during flowering. Thus, often, alpine plants use both sexual and asexual means of reproduction to maximize fitness and ensure reproductive success. We used the arctic alpine perennial {\textless}italic{\textgreater}Arabis alpina{\textless}/italic{\textgreater} to explore the role of prolonged cold exposure on adventitious rooting. We exposed plants to 4°C for different durations and scored the presence of adventitious roots on the main stem and axillary branches. Our physiological studies demonstrated the presence of adventitious roots after 21 weeks at 4°C saturating the effect of cold on this process. Notably, adventitious roots on the main stem developing in specific internodes allowed us to identify the gene regulatory network involved in the formation of adventitious roots in cold using transcriptomics. These data and histological studies indicated that adventitious roots in {\textless}italic{\textgreater}A. alpina{\textless}/italic{\textgreater} stems initiate during cold exposure and emerge after plants experience growth promoting conditions. While the initiation of adventitious root was not associated with changes of {\textless}italic{\textgreater}DR5{\textless}/italic{\textgreater} auxin response and free endogenous auxin level in the stems, the emergence of the adventitious root primordia was. Using the transcriptomic data, we discerned the sequential hormone responses occurring in various stages of adventitious root formation and identified supplementary pathways putatively involved in adventitious root emergence, such as glucosinolate metabolism. Together, our results highlight the role of low temperature during clonal growth in alpine plants and provide insights on the molecular mechanisms involved at distinct stages of adventitious rooting.{\textless}/p{\textgreater}},
	language = {English},
	urldate = {2024-05-03},
	journal = {Frontiers in Plant Science},
	author = {Mishra, Priyanka and Roggen, Adrian and Ljung, Karin and Albani, Maria C. and Vayssières, Alice},
	month = apr,
	year = {2024},
	note = {Publisher: Frontiers},
	keywords = {Adventitious root, Arabis alpina, Clonal propagation, Transcriptome, alpine, extended cold exposure, phytohormones},
}

\textlessp\textgreaterArctic alpine species experience extended periods of cold and unpredictable conditions during flowering. Thus, often, alpine plants use both sexual and asexual means of reproduction to maximize fitness and ensure reproductive success. We used the arctic alpine perennial \textlessitalic\textgreaterArabis alpina\textless/italic\textgreater to explore the role of prolonged cold exposure on adventitious rooting. We exposed plants to 4°C for different durations and scored the presence of adventitious roots on the main stem and axillary branches. Our physiological studies demonstrated the presence of adventitious roots after 21 weeks at 4°C saturating the effect of cold on this process. Notably, adventitious roots on the main stem developing in specific internodes allowed us to identify the gene regulatory network involved in the formation of adventitious roots in cold using transcriptomics. These data and histological studies indicated that adventitious roots in \textlessitalic\textgreaterA. alpina\textless/italic\textgreater stems initiate during cold exposure and emerge after plants experience growth promoting conditions. While the initiation of adventitious root was not associated with changes of \textlessitalic\textgreaterDR5\textless/italic\textgreater auxin response and free endogenous auxin level in the stems, the emergence of the adventitious root primordia was. Using the transcriptomic data, we discerned the sequential hormone responses occurring in various stages of adventitious root formation and identified supplementary pathways putatively involved in adventitious root emergence, such as glucosinolate metabolism. Together, our results highlight the role of low temperature during clonal growth in alpine plants and provide insights on the molecular mechanisms involved at distinct stages of adventitious rooting.\textless/p\textgreater

@article{ding_molecular_2024,
	title = {Molecular {Advances} of {Bud} {Dormancy} in {Trees}},
	issn = {0022-0957},
	url = {https://doi.org/10.1093/jxb/erae183},
	doi = {10.1093/jxb/erae183},
	abstract = {Seasonal bud dormancy in perennial woody plants is a crucial and intricate process that is vital for the survival and development of plants. Over the past few decades, significant advancements have been made in understanding many features of bud dormancy, particularly in model species, where certain molecular mechanisms underlying this process have been elucidated. In this review, we provide an overview of recent molecular progress in understanding bud dormancy in trees, with a specific emphasis on the integration of common signaling and molecular mechanisms identified across different tree species. Additionally, we address some challenges that have emerged in the in-depth understanding of bud dormancy and offer insights for future studies.},
	urldate = {2024-04-29},
	journal = {Journal of Experimental Botany},
	author = {Ding, Jihua and Wang, Kejing and Pandey, Shashank and Perales, Mariano and Allona, Isabel and Khan, Md Rezaul Islam and Busov, Victor B and Bhalerao, Rishikesh P},
	month = apr,
	year = {2024},
	pages = {erae183},
}

Seasonal bud dormancy in perennial woody plants is a crucial and intricate process that is vital for the survival and development of plants. Over the past few decades, significant advancements have been made in understanding many features of bud dormancy, particularly in model species, where certain molecular mechanisms underlying this process have been elucidated. In this review, we provide an overview of recent molecular progress in understanding bud dormancy in trees, with a specific emphasis on the integration of common signaling and molecular mechanisms identified across different tree species. Additionally, we address some challenges that have emerged in the in-depth understanding of bud dormancy and offer insights for 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},
	shorttitle = {{ChloroSpec}},
	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 = {2024-04-29},
	journal = {Physiologia Plantarum},
	author = {Nanda, Sanchali and Shutova, Tatyana and Cainzos, Maximiliano and Bag, Pushan and Jansson, Stefan and Holzwarth, Alfred R.},
	month = apr,
	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{tian_plant-lncpipe_2024,
	title = {Plant-{LncPipe}: a computational pipeline providing significant improvement in plant {lncRNA} identification},
	volume = {11},
	issn = {2662-6810},
	shorttitle = {Plant-{LncPipe}},
	url = {https://doi.org/10.1093/hr/uhae041},
	doi = {10.1093/hr/uhae041},
	abstract = {Long non-coding RNAs (lncRNAs) play essential roles in various biological processes, such as chromatin remodeling, post-transcriptional regulation, and epigenetic modifications. Despite their critical functions in regulating plant growth, root development, and seed dormancy, the identification of plant lncRNAs remains a challenge due to the scarcity of specific and extensively tested identification methods. Most mainstream machine learning-based methods used for plant lncRNA identification were initially developed using human or other animal datasets, and their accuracy and effectiveness in predicting plant lncRNAs have not been fully evaluated or exploited. To overcome this limitation, we retrained several models, including CPAT, PLEK, and LncFinder, using plant datasets and compared their performance with mainstream lncRNA prediction tools such as CPC2, CNCI, RNAplonc, and LncADeep. Retraining these models significantly improved their performance, and two of the retrained models, LncFinder-plant and CPAT-plant, alongside their ensemble, emerged as the most suitable tools for plant lncRNA identification. This underscores the importance of model retraining in tackling the challenges associated with plant lncRNA identification. Finally, we developed a pipeline (Plant-LncPipe) that incorporates an ensemble of the two best-performing models and covers the entire data analysis process, including reads mapping, transcript assembly, lncRNA identification, classification, and origin, for the efficient identification of lncRNAs in plants. The pipeline, Plant-LncPipe, is available at: https://github.com/xuechantian/Plant-LncRNA-pipline.},
	number = {4},
	urldate = {2024-04-29},
	journal = {Horticulture Research},
	author = {Tian, Xue-Chan and Chen, Zhao-Yang and Nie, Shuai and Shi, Tian-Le and Yan, Xue-Mei and Bao, Yu-Tao and Li, Zhi-Chao and Ma, Hai-Yao and Jia, Kai-Hua and Zhao, Wei and Mao, Jian-Feng},
	month = apr,
	year = {2024},
	pages = {uhae041},
}

Long non-coding RNAs (lncRNAs) play essential roles in various biological processes, such as chromatin remodeling, post-transcriptional regulation, and epigenetic modifications. Despite their critical functions in regulating plant growth, root development, and seed dormancy, the identification of plant lncRNAs remains a challenge due to the scarcity of specific and extensively tested identification methods. Most mainstream machine learning-based methods used for plant lncRNA identification were initially developed using human or other animal datasets, and their accuracy and effectiveness in predicting plant lncRNAs have not been fully evaluated or exploited. To overcome this limitation, we retrained several models, including CPAT, PLEK, and LncFinder, using plant datasets and compared their performance with mainstream lncRNA prediction tools such as CPC2, CNCI, RNAplonc, and LncADeep. Retraining these models significantly improved their performance, and two of the retrained models, LncFinder-plant and CPAT-plant, alongside their ensemble, emerged as the most suitable tools for plant lncRNA identification. This underscores the importance of model retraining in tackling the challenges associated with plant lncRNA identification. Finally, we developed a pipeline (Plant-LncPipe) that incorporates an ensemble of the two best-performing models and covers the entire data analysis process, including reads mapping, transcript assembly, lncRNA identification, classification, and origin, for the efficient identification of lncRNAs in plants. The pipeline, Plant-LncPipe, is available at: https://github.com/xuechantian/Plant-LncRNA-pipline.

@article{sandell_genomic_2024,
	title = {Genomic basis of seed colour in quinoa inferred from variant patterns using extreme gradient boosting},
	volume = {22},
	copyright = {© 2023 The Authors. Plant Biotechnology Journal published by Society for Experimental Biology and The Association of Applied Biologists and John Wiley \& Sons Ltd.},
	issn = {1467-7652},
	url = {https://onlinelibrary.wiley.com/doi/abs/10.1111/pbi.14267},
	doi = {10.1111/pbi.14267},
	abstract = {Quinoa is an agriculturally important crop species originally domesticated in the Andes of central South America. One of its most important phenotypic traits is seed colour. Seed colour variation is determined by contrasting abundance of betalains, a class of strong antioxidant and free radicals scavenging colour pigments only found in plants of the order Caryophyllales. However, the genetic basis for these pigments in seeds remains to be identified. Here we demonstrate the application of machine learning (extreme gradient boosting) to identify genetic variants predictive of seed colour. We show that extreme gradient boosting outperforms the classical genome-wide association approach. We provide re-sequencing and phenotypic data for 156 South American quinoa accessions and identify candidate genes potentially controlling betalain content in quinoa seeds. Genes identified include novel cytochrome P450 genes and known members of the betalain synthesis pathway, as well as genes annotated as being involved in seed development. Our work showcases the power of modern machine learning methods to extract biologically meaningful information from large sequencing data sets.},
	language = {en},
	number = {5},
	urldate = {2024-04-19},
	journal = {Plant Biotechnology Journal},
	author = {Sandell, Felix L. and Holzweber, Thomas and Street, Nathaniel R. and Dohm, Juliane C. and Himmelbauer, Heinz},
	year = {2024},
	note = {\_eprint: https://onlinelibrary.wiley.com/doi/pdf/10.1111/pbi.14267},
	keywords = {betalain synthesis pathway, genome sequencing, genotype-phenotype relationships, machine learning, quinoa, seed colour},
	pages = {1312--1324},
}

Quinoa is an agriculturally important crop species originally domesticated in the Andes of central South America. One of its most important phenotypic traits is seed colour. Seed colour variation is determined by contrasting abundance of betalains, a class of strong antioxidant and free radicals scavenging colour pigments only found in plants of the order Caryophyllales. However, the genetic basis for these pigments in seeds remains to be identified. Here we demonstrate the application of machine learning (extreme gradient boosting) to identify genetic variants predictive of seed colour. We show that extreme gradient boosting outperforms the classical genome-wide association approach. We provide re-sequencing and phenotypic data for 156 South American quinoa accessions and identify candidate genes potentially controlling betalain content in quinoa seeds. Genes identified include novel cytochrome P450 genes and known members of the betalain synthesis pathway, as well as genes annotated as being involved in seed development. Our work showcases the power of modern machine learning methods to extract biologically meaningful information from large sequencing data sets.

@article{lathe_nks1elmo4_2024,
	title = {{NKS1}/{ELMO4} is an integral protein of a pectin synthesis protein complex and maintains {Golgi} morphology and cell adhesion in {Arabidopsis}},
	volume = {121},
	url = {https://www.pnas.org/doi/10.1073/pnas.2321759121},
	doi = {10.1073/pnas.2321759121},
	abstract = {Adjacent plant cells are connected by specialized cell wall regions, called middle lamellae, which influence critical agricultural characteristics, including fruit ripening and organ abscission. Middle lamellae are enriched in pectin polysaccharides, specifically homogalacturonan (HG). Here, we identify a plant-specific Arabidopsis DUF1068 protein, called NKS1/ELMO4, that is required for middle lamellae integrity and cell adhesion. NKS1 localizes to the Golgi apparatus and loss of NKS1 results in changes to Golgi structure and function. The nks1 mutants also display HG deficient phenotypes, including reduced seedling growth, changes to cell wall composition, and tissue integrity defects. These phenotypes are comparable to qua1 and qua2 mutants, which are defective in HG biosynthesis. Notably, genetic interactions indicate that NKS1 and the QUAs work in a common pathway. Protein interaction analyses and modeling corroborate that they work together in a stable protein complex with other pectin-related proteins. We propose that NKS1 is an integral part of a large pectin synthesis protein complex and that proper function of this complex is important to support Golgi structure and function.},
	number = {15},
	urldate = {2024-04-12},
	journal = {Proceedings of the National Academy of Sciences},
	author = {Lathe, Rahul S. and McFarlane, Heather E. and Kesten, Christopher and Wang, Liu and Khan, Ghazanfar Abbas and Ebert, Berit and Ramírez-Rodríguez, Eduardo Antonio and Zheng, Shuai and Noord, Niels and Frandsen, Kristian and Bhalerao, Rishikesh P. and Persson, Staffan},
	month = apr,
	year = {2024},
	note = {Publisher: Proceedings of the National Academy of Sciences},
	pages = {e2321759121},
}

Adjacent plant cells are connected by specialized cell wall regions, called middle lamellae, which influence critical agricultural characteristics, including fruit ripening and organ abscission. Middle lamellae are enriched in pectin polysaccharides, specifically homogalacturonan (HG). Here, we identify a plant-specific Arabidopsis DUF1068 protein, called NKS1/ELMO4, that is required for middle lamellae integrity and cell adhesion. NKS1 localizes to the Golgi apparatus and loss of NKS1 results in changes to Golgi structure and function. The nks1 mutants also display HG deficient phenotypes, including reduced seedling growth, changes to cell wall composition, and tissue integrity defects. These phenotypes are comparable to qua1 and qua2 mutants, which are defective in HG biosynthesis. Notably, genetic interactions indicate that NKS1 and the QUAs work in a common pathway. Protein interaction analyses and modeling corroborate that they work together in a stable protein complex with other pectin-related proteins. We propose that NKS1 is an integral part of a large pectin synthesis protein complex and that proper function of this complex is important to support Golgi structure and function.

@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},
	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
Publisher: Multidisciplinary Digital Publishing Institute},
	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{kleczkowski_multiple_2024,
	title = {Multiple {Roles} of {Glycerate} {Kinase}—{From} {Photorespiration} to {Gluconeogenesis}, {C4} {Metabolism}, and {Plant} {Immunity}},
	volume = {25},
	copyright = {http://creativecommons.org/licenses/by/3.0/},
	issn = {1422-0067},
	url = {https://www.mdpi.com/1422-0067/25/6/3258},
	doi = {10.3390/ijms25063258},
	abstract = {Plant glycerate kinase (GK) was previously considered an exclusively chloroplastic enzyme of the glycolate pathway (photorespiration), and its sole predicted role was to return most of the glycolate-derived carbon (as glycerate) to the Calvin cycle. However, recent discovery of cytosolic GK revealed metabolic links for glycerate to other processes. Although GK was initially proposed as being solely regulated by substrate availability, subsequent discoveries of its redox regulation and the light involvement in the production of chloroplastic and cytosolic GK isoforms have indicated a more refined regulation of the pathways of glycerate conversion. Here, we re-evaluate the importance of GK and emphasize its multifaceted role in plants. Thus, GK can be a major player in several branches of primary metabolism, including the glycolate pathway, gluconeogenesis, glycolysis, and C4 metabolism. In addition, recently, the chloroplastic (but not cytosolic) GK isoform was implicated as part of a light-dependent plant immune response to pathogen attack. The origins of glycerate are also discussed here; it is produced in several cell compartments and undergoes huge fluctuations depending on light/dark conditions. The recent discovery of the vacuolar glycerate transporter adds yet another layer to our understanding of glycerate transport/metabolism and that of other two- and three-carbon metabolites.},
	language = {en},
	number = {6},
	urldate = {2024-04-02},
	journal = {International Journal of Molecular Sciences},
	author = {Kleczkowski, Leszek A. and Igamberdiev, Abir U.},
	month = mar,
	year = {2024},
	note = {Number: 6
Publisher: Multidisciplinary Digital Publishing Institute},
	keywords = {\textit{Phytophthora infestans}, C$_{\textrm{4}}$ photosynthesis, gluconeogenesis, glycerate metabolism, glycolate pathway, sucrose synthesis},
	pages = {3258},
}

Plant glycerate kinase (GK) was previously considered an exclusively chloroplastic enzyme of the glycolate pathway (photorespiration), and its sole predicted role was to return most of the glycolate-derived carbon (as glycerate) to the Calvin cycle. However, recent discovery of cytosolic GK revealed metabolic links for glycerate to other processes. Although GK was initially proposed as being solely regulated by substrate availability, subsequent discoveries of its redox regulation and the light involvement in the production of chloroplastic and cytosolic GK isoforms have indicated a more refined regulation of the pathways of glycerate conversion. Here, we re-evaluate the importance of GK and emphasize its multifaceted role in plants. Thus, GK can be a major player in several branches of primary metabolism, including the glycolate pathway, gluconeogenesis, glycolysis, and C4 metabolism. In addition, recently, the chloroplastic (but not cytosolic) GK isoform was implicated as part of a light-dependent plant immune response to pathogen attack. The origins of glycerate are also discussed here; it is produced in several cell compartments and undergoes huge fluctuations depending on light/dark conditions. The recent discovery of the vacuolar glycerate transporter adds yet another layer to our understanding of glycerate transport/metabolism and that of other two- and three-carbon metabolites.

@article{aguida_seeing_2024,
	title = {‘{Seeing}’ the electromagnetic spectrum: spotlight on the cryptochrome photocycle},
	volume = {15},
	issn = {1664-462X},
	shorttitle = {‘{Seeing}’ the electromagnetic spectrum},
	url = {https://www.frontiersin.org/journals/plant-science/articles/10.3389/fpls.2024.1340304},
	doi = {10.3389/fpls.2024.1340304},
	abstract = {Cryptochromes are widely dispersed flavoprotein photoreceptors that regulate numerous developmental responses to light in plants, as well as to stress and entrainment of the circadian clock in animals and humans. All cryptochromes are closely related to an ancient family of light-absorbing flavoenzymes known as photolyases, which use light as an energy source for DNA repair but themselves have no light sensing role. Here we review the means by which plant cryptochromes acquired a light sensing function. This transition involved subtle changes within the flavin binding pocket which gave rise to a visual photocycle consisting of light-inducible and dark-reversible flavin redox state transitions. In this photocycle, light first triggers flavin reduction from an initial dark-adapted resting state (FADox). The reduced state is the biologically active or ‘lit’ state, correlating with biological activity. Subsequently, the photoreduced flavin reoxidises back to the dark adapted or ‘resting’ state. Because the rate of reoxidation determines the lifetime of the signaling state, it significantly modulates biological activity. As a consequence of this redox photocycle Crys respond to both the wavelength and the intensity of light, but are in addition regulated by factors such as temperature, oxygen concentration, and cellular metabolites that alter rates of flavin reoxidation even independently of light. Mechanistically, flavin reduction is correlated with conformational change in the protein, which is thought to mediate biological activity through interaction with biological signaling partners. In addition, a second, entirely independent signaling mechanism arises from the cryptochrome photocycle in the form of reactive oxygen species (ROS). These are synthesized during flavin reoxidation, are known mediators of biotic and abiotic stress responses, and have been linked to Cry biological activity in plants and animals. Additional special properties arising from the cryptochrome photocycle include responsivity to electromagnetic fields and their applications in optogenetics. Finally, innovations in methodology such as the use of Nitrogen Vacancy (NV) diamond centers to follow cryptochrome magnetic field sensitivity in vivo are discussed, as well as the potential for a whole new technology of ‘magneto-genetics’ for future applications in synthetic biology and medicine.},
	urldate = {2024-03-22},
	journal = {Frontiers in Plant Science},
	author = {Aguida, Blanche and Babo, Jonathan and Baouz, Soria and Jourdan, Nathalie and Procopio, Maria and El-Esawi, Mohamed A. and Engle, Dorothy and Mills, Stephen and Wenkel, Stephan and Huck, Alexander and Berg-Sørensen, Kirstine and Kampranis, Sotirios C. and Link, Justin and Ahmad, Margaret},
	month = mar,
	year = {2024},
	keywords = {⛔ No DOI found},
}

Cryptochromes are widely dispersed flavoprotein photoreceptors that regulate numerous developmental responses to light in plants, as well as to stress and entrainment of the circadian clock in animals and humans. All cryptochromes are closely related to an ancient family of light-absorbing flavoenzymes known as photolyases, which use light as an energy source for DNA repair but themselves have no light sensing role. Here we review the means by which plant cryptochromes acquired a light sensing function. This transition involved subtle changes within the flavin binding pocket which gave rise to a visual photocycle consisting of light-inducible and dark-reversible flavin redox state transitions. In this photocycle, light first triggers flavin reduction from an initial dark-adapted resting state (FADox). The reduced state is the biologically active or ‘lit’ state, correlating with biological activity. Subsequently, the photoreduced flavin reoxidises back to the dark adapted or ‘resting’ state. Because the rate of reoxidation determines the lifetime of the signaling state, it significantly modulates biological activity. As a consequence of this redox photocycle Crys respond to both the wavelength and the intensity of light, but are in addition regulated by factors such as temperature, oxygen concentration, and cellular metabolites that alter rates of flavin reoxidation even independently of light. Mechanistically, flavin reduction is correlated with conformational change in the protein, which is thought to mediate biological activity through interaction with biological signaling partners. In addition, a second, entirely independent signaling mechanism arises from the cryptochrome photocycle in the form of reactive oxygen species (ROS). These are synthesized during flavin reoxidation, are known mediators of biotic and abiotic stress responses, and have been linked to Cry biological activity in plants and animals. Additional special properties arising from the cryptochrome photocycle include responsivity to electromagnetic fields and their applications in optogenetics. Finally, innovations in methodology such as the use of Nitrogen Vacancy (NV) diamond centers to follow cryptochrome magnetic field sensitivity in vivo are discussed, as well as the potential for a whole new technology of ‘magneto-genetics’ for future applications in synthetic biology and medicine.

@article{climent_trade-offs_2024,
	title = {Trade-offs and {Trait} {Integration} in {Tree} {Phenotypes}: {Consequences} for the {Sustainable} {Use} of {Genetic} {Resources}},
	issn = {2198-6436},
	shorttitle = {Trade-offs and {Trait} {Integration} in {Tree} {Phenotypes}},
	url = {https://doi.org/10.1007/s40725-024-00217-5},
	doi = {10.1007/s40725-024-00217-5},
	abstract = {In this review, we synthesise current knowledge on trade-offs among traits in key fitness dimensions and identify major research gaps with the intention of laying the groundwork for a rapid advance in tree breeding for multiple objectives as a key contribution to the sustainability of planted forests in the future.},
	language = {en},
	urldate = {2024-04-02},
	journal = {Current Forestry Reports},
	author = {Climent, Jose and Alía, Ricardo and Karkkainen, Katri and Bastien, Catherine and Benito-Garzon, Marta and Bouffier, Laurent and De Dato, Giovanbattista and Delzon, Sylvain and Dowkiw, Arnaud and Elvira-Recuenco, Margarita and Grivet, Delphine and González-Martínez, Santiago C. and Hayatgheibi, Haleh and Kujala, Sonja and Leplé, Jean-Charles and Martín-Sanz, Ruth C. and de Miguel, Marina and Monteverdi, M. Cristina and Mutke, Sven and Plomion, Christophe and Ramírez-Valiente, José Alberto and Sanchez, Leopoldo and Solé-Medina, Aida and Soularue, Jean-Paul and Steffenrem, Arne and Teani, Angela and Westin, Johan and Whittet, Richard and Wu, Harry and Zas, Rafael and Cavers, Stephen},
	month = mar,
	year = {2024},
	keywords = {Breeding, Forest trees, Global change, Phenotypic integration, Resilience, Trade-offs},
}

In this review, we synthesise current knowledge on trade-offs among traits in key fitness dimensions and identify major research gaps with the intention of laying the groundwork for a rapid advance in tree breeding for multiple objectives as a key contribution to the sustainability of planted forests in the future.

@article{blomberg_pseudomonas_2024,
	title = {Pseudomonas syringae infectivity correlates to altered transcript and metabolite levels of {Arabidopsis} mediator mutants},
	volume = {14},
	copyright = {2024 The Author(s)},
	issn = {2045-2322},
	url = {https://www.nature.com/articles/s41598-024-57192-x},
	doi = {10.1038/s41598-024-57192-x},
	abstract = {Rapid metabolic responses to pathogens are essential for plant survival and depend on numerous transcription factors. Mediator is the major transcriptional co-regulator for integration and transmission of signals from transcriptional regulators to RNA polymerase II. Using four Arabidopsis Mediator mutants, med16, med18, med25 and cdk8, we studied how differences in regulation of their transcript and metabolite levels correlate to their responses to Pseudomonas syringae infection. We found that med16 and cdk8 were susceptible, while med25 showed increased resistance. Glucosinolate, phytoalexin and carbohydrate levels were reduced already before infection in med16 and cdk8, but increased in med25, which also displayed increased benzenoids levels. Early after infection, wild type plants showed reduced glucosinolate and nucleoside levels, but increases in amino acids, benzenoids, oxylipins and the phytoalexin camalexin. The Mediator mutants showed altered levels of these metabolites and in regulation of genes encoding key enzymes for their metabolism. At later stage, mutants displayed defective levels of specific amino acids, carbohydrates, lipids and jasmonates which correlated to their infection response phenotypes. Our results reveal that MED16, MED25 and CDK8 are required for a proper, coordinated transcriptional response of genes which encode enzymes involved in important metabolic pathways for Arabidopsis responses to Pseudomonas syringae infections.},
	language = {en},
	number = {1},
	urldate = {2024-04-02},
	journal = {Scientific Reports},
	author = {Blomberg, Jeanette and Tasselius, Viktor and Vergara, Alexander and Karamat, Fazeelat and Imran, Qari Muhammad and Strand, Åsa and Rosvall, Martin and Björklund, Stefan},
	month = mar,
	year = {2024},
	note = {Publisher: Nature Publishing Group},
	keywords = {Plant cell biology, Plant immunity, Plant molecular biology, Plant physiology, Plant sciences, Plant stress responses, Secondary metabolism, Transcriptional regulatory elements, Transcriptomics},
	pages = {6771},
}

Rapid metabolic responses to pathogens are essential for plant survival and depend on numerous transcription factors. Mediator is the major transcriptional co-regulator for integration and transmission of signals from transcriptional regulators to RNA polymerase II. Using four Arabidopsis Mediator mutants, med16, med18, med25 and cdk8, we studied how differences in regulation of their transcript and metabolite levels correlate to their responses to Pseudomonas syringae infection. We found that med16 and cdk8 were susceptible, while med25 showed increased resistance. Glucosinolate, phytoalexin and carbohydrate levels were reduced already before infection in med16 and cdk8, but increased in med25, which also displayed increased benzenoids levels. Early after infection, wild type plants showed reduced glucosinolate and nucleoside levels, but increases in amino acids, benzenoids, oxylipins and the phytoalexin camalexin. The Mediator mutants showed altered levels of these metabolites and in regulation of genes encoding key enzymes for their metabolism. At later stage, mutants displayed defective levels of specific amino acids, carbohydrates, lipids and jasmonates which correlated to their infection response phenotypes. Our results reveal that MED16, MED25 and CDK8 are required for a proper, coordinated transcriptional response of genes which encode enzymes involved in important metabolic pathways for Arabidopsis responses to Pseudomonas syringae infections.

@article{karady_profiling_2024,
	title = {Profiling of 1-aminocyclopropane-1-carboxylic acid and selected phytohormones in {Arabidopsis} using liquid chromatography-tandem mass spectrometry},
	volume = {20},
	issn = {1746-4811},
	url = {https://doi.org/10.1186/s13007-024-01165-8},
	doi = {10.1186/s13007-024-01165-8},
	abstract = {Gaseous phytohormone ethylene levels are directly influenced by the production of its immediate non-volatile precursor 1-aminocyclopropane-1-carboxylic acid (ACC). Owing to the strongly acidic character of the ACC molecule, its quantification has been difficult to perform. Here, we present a simple and straightforward validated method for accurate quantification of not only ACC levels, but also major members of other important phytohormonal classes – auxins, cytokinins, jasmonic acid, abscisic acid and salicylic acid from the same biological sample.},
	number = {1},
	urldate = {2024-03-22},
	journal = {Plant Methods},
	author = {Karady, Michal and Hladík, Pavel and Cermanová, Kateřina and Jiroutová, Petra and Antoniadi, Ioanna and Casanova-Sáez, Rubén and Ljung, Karin and Novák, Ondřej},
	month = mar,
	year = {2024},
	keywords = {1-aminocyclopropane-1-carboxylic acid, ACC, Abscisic acid, Arabidopsis, Auxin, Cytokinin, Ethylene, Jasmonic acid, Liquid chromatography, Mass spectrometry, Plant hormones, Salicylic acid},
	pages = {41},
}

Gaseous phytohormone ethylene levels are directly influenced by the production of its immediate non-volatile precursor 1-aminocyclopropane-1-carboxylic acid (ACC). Owing to the strongly acidic character of the ACC molecule, its quantification has been difficult to perform. Here, we present a simple and straightforward validated method for accurate quantification of not only ACC levels, but also major members of other important phytohormonal classes – auxins, cytokinins, jasmonic acid, abscisic acid and salicylic acid from the same biological sample.

@article{sharma_fungal-bacterial_2024,
	title = {Fungal-{Bacterial} {Combinations} in {Plant} {Health} under {Stress}: {Physiological} and {Biochemical} {Characteristics} of the {Filamentous} {Fungus} {Serendipita} indica and the {Actinobacterium} {Zhihengliuella} sp. {ISTPL4} under {In} {Vitro} {Arsenic} {Stress}},
	volume = {12},
	copyright = {http://creativecommons.org/licenses/by/3.0/},
	issn = {2076-2607},
	shorttitle = {Fungal-{Bacterial} {Combinations} in {Plant} {Health} under {Stress}},
	url = {https://www.mdpi.com/2076-2607/12/2/405},
	doi = {10.3390/microorganisms12020405},
	abstract = {Fungal-bacterial combinations have a significant role in increasing and improving plant health under various stress conditions. Metabolites secreted by fungi and bacteria play an important role in this process. Our study emphasizes the significance of secondary metabolites secreted by the fungus Serendipita indica alone and by an actinobacterium Zhihengliuella sp. ISTPL4 under normal growth conditions and arsenic (As) stress condition. Here, we evaluated the arsenic tolerance ability of S. indica alone and in combination with Z. sp. ISTPL4 under in vitro conditions. The growth of S. indica and Z. sp. ISTPL4 was measured in varying concentrations of arsenic and the effect of arsenic on spore size and morphology of S. indica was determined using confocal microscopy and scanning electron microscopy. The metabolomics study indicated that S. indica alone in normal growth conditions and under As stress released pentadecanoic acid, glycerol tricaprylate, L-proline and cyclo(L-prolyl-L-valine). Similarly, d-Ribose, 2-deoxy-bis(thioheptyl)-dithioacetal were secreted by a combination of S. indica and Z. sp. ISTPL4. Confocal studies revealed that spore size of S. indica decreased by 18\% at 1.9 mM and by 15\% when in combination with Z. sp. ISTPL4 at a 2.4 mM concentration of As. Arsenic above this concentration resulted in spore degeneration and hyphae fragmentation. Scanning electron microscopy (SEM) results indicated an increased spore size of S. indica in the presence of Z. sp. ISTPL4 (18 ± 0.75 µm) compared to S. indica alone (14 ± 0.24 µm) under normal growth conditions. Our study concluded that the suggested combination of microbial consortium can be used to increase sustainable agriculture by combating biotic as well as abiotic stress. This is because the metabolites released by the microbial combination display antifungal and antibacterial properties. The metabolites, besides evading stress, also confer other survival strategies. Therefore, the choice of consortia and combination partners is important and can help in developing strategies for coping with As stress.},
	language = {en},
	number = {2},
	urldate = {2024-03-18},
	journal = {Microorganisms},
	author = {Sharma, Neha and Koul, Monika and Joshi, Naveen Chandra and Dufossé, Laurent and Mishra, Arti},
	month = feb,
	year = {2024},
	note = {Number: 2
Publisher: Multidisciplinary Digital Publishing Institute},
	keywords = {\textit{Oryza sativa}, \textit{Serendipita indica}, arsenic, heavy metal stress, secondary metabolites},
	pages = {405},
}

Fungal-bacterial combinations have a significant role in increasing and improving plant health under various stress conditions. Metabolites secreted by fungi and bacteria play an important role in this process. Our study emphasizes the significance of secondary metabolites secreted by the fungus Serendipita indica alone and by an actinobacterium Zhihengliuella sp. ISTPL4 under normal growth conditions and arsenic (As) stress condition. Here, we evaluated the arsenic tolerance ability of S. indica alone and in combination with Z. sp. ISTPL4 under in vitro conditions. The growth of S. indica and Z. sp. ISTPL4 was measured in varying concentrations of arsenic and the effect of arsenic on spore size and morphology of S. indica was determined using confocal microscopy and scanning electron microscopy. The metabolomics study indicated that S. indica alone in normal growth conditions and under As stress released pentadecanoic acid, glycerol tricaprylate, L-proline and cyclo(L-prolyl-L-valine). Similarly, d-Ribose, 2-deoxy-bis(thioheptyl)-dithioacetal were secreted by a combination of S. indica and Z. sp. ISTPL4. Confocal studies revealed that spore size of S. indica decreased by 18% at 1.9 mM and by 15% when in combination with Z. sp. ISTPL4 at a 2.4 mM concentration of As. Arsenic above this concentration resulted in spore degeneration and hyphae fragmentation. Scanning electron microscopy (SEM) results indicated an increased spore size of S. indica in the presence of Z. sp. ISTPL4 (18 ± 0.75 µm) compared to S. indica alone (14 ± 0.24 µm) under normal growth conditions. Our study concluded that the suggested combination of microbial consortium can be used to increase sustainable agriculture by combating biotic as well as abiotic stress. This is because the metabolites released by the microbial combination display antifungal and antibacterial properties. The metabolites, besides evading stress, also confer other survival strategies. Therefore, the choice of consortia and combination partners is important and can help in developing strategies for coping with As stress.

@article{parker_biohybrid_2024,
	title = {Biohybrid {Energy} {Storage} {Circuits} {Based} on {Electronically} {Functionalized} {Plant} {Roots}},
	issn = {1944-8244},
	url = {https://doi.org/10.1021/acsami.3c16861},
	doi = {10.1021/acsami.3c16861},
	abstract = {Biohybrid systems based on plants integrate plant structures and processes into technological components targeting more sustainable solutions. Plants’ biocatalytic machinery, for example, has been leveraged for the organization of electronic materials directly in the vasculature and roots of living plants, resulting in biohybrid electrochemical devices. Among other applications, energy storage devices were demonstrated where the charge storage electrodes were seamlessly integrated into the plant tissue. However, the capacitance and the voltage output of a single biohybrid supercapacitor are limited. Here, we developed biohybrid circuits based on functionalized conducting roots, extending the performance of plant based biohybrid energy storage systems. We show that root-supercapacitors can be combined in series and in parallel configuration, achieving up to 1.5 V voltage output or up to 11 mF capacitance, respectively. We further demonstrate that the supercapacitors circuit can be charged with an organic photovoltaic cell, and that the stored charge can be used to power an electrochromic display or a bioelectronic device. Furthermore, the functionalized roots degrade in composting similarly to native roots. The proof-of-concept demonstrations illustrate the potential of this technology to achieve more sustainable solutions for powering low consumption devices such as bioelectronics for agriculture or IoT applications.},
	urldate = {2024-03-08},
	journal = {ACS Applied Materials \& Interfaces},
	author = {Parker, Daniela and Dar, Abdul Manan and Armada-Moreira, Adam and Bernacka Wojcik, Iwona and Rai, Rajat and Mantione, Daniele and Stavrinidou, Eleni},
	month = mar,
	year = {2024},
	note = {Publisher: American Chemical Society},
}

Biohybrid systems based on plants integrate plant structures and processes into technological components targeting more sustainable solutions. Plants’ biocatalytic machinery, for example, has been leveraged for the organization of electronic materials directly in the vasculature and roots of living plants, resulting in biohybrid electrochemical devices. Among other applications, energy storage devices were demonstrated where the charge storage electrodes were seamlessly integrated into the plant tissue. However, the capacitance and the voltage output of a single biohybrid supercapacitor are limited. Here, we developed biohybrid circuits based on functionalized conducting roots, extending the performance of plant based biohybrid energy storage systems. We show that root-supercapacitors can be combined in series and in parallel configuration, achieving up to 1.5 V voltage output or up to 11 mF capacitance, respectively. We further demonstrate that the supercapacitors circuit can be charged with an organic photovoltaic cell, and that the stored charge can be used to power an electrochromic display or a bioelectronic device. Furthermore, the functionalized roots degrade in composting similarly to native roots. The proof-of-concept demonstrations illustrate the potential of this technology to achieve more sustainable solutions for powering low consumption devices such as bioelectronics for agriculture or IoT applications.

@article{liu_proxitome-rna-capture_2024,
	title = {A proxitome-{RNA}-capture approach reveals that processing bodies repress coregulated hub genes},
	volume = {36},
	issn = {1040-4651},
	url = {https://doi.org/10.1093/plcell/koad288},
	doi = {10.1093/plcell/koad288},
	abstract = {Cellular condensates are usually ribonucleoprotein assemblies with liquid- or solid-like properties. Because these subcellular structures lack a delineating membrane, determining their compositions is difficult. Here we describe a proximity-biotinylation approach for capturing the RNAs of the condensates known as processing bodies (PBs) in Arabidopsis (Arabidopsis thaliana). By combining this approach with RNA detection, in silico, and high-resolution imaging approaches, we studied PBs under normal conditions and heat stress. PBs showed a much more dynamic RNA composition than the total transcriptome. RNAs involved in cell wall development and regeneration, plant hormonal signaling, secondary metabolism/defense, and RNA metabolism were enriched in PBs. RNA-binding proteins and the liquidity of PBs modulated RNA recruitment, while RNAs were frequently recruited together with their encoded proteins. In PBs, RNAs follow distinct fates: in small liquid-like PBs, RNAs get degraded while in more solid-like larger ones, they are stored. PB properties can be regulated by the actin-polymerizing SCAR (suppressor of the cyclic AMP)-WAVE (WASP family verprolin homologous) complex. SCAR/WAVE modulates the shuttling of RNAs between PBs and the translational machinery, thereby adjusting ethylene signaling. In summary, we provide an approach to identify RNAs in condensates that allowed us to reveal a mechanism for regulating RNA fate.},
	number = {3},
	urldate = {2024-03-01},
	journal = {The Plant Cell},
	author = {Liu, Chen and Mentzelopoulou, Andriani and Hatzianestis, Ioannis H and Tzagkarakis, Epameinondas and Skaltsogiannis, Vasileios and Ma, Xuemin and Michalopoulou, Vassiliki A and Romero-Campero, Francisco J and Romero-Losada, Ana B and Sarris, Panagiotis F and Marhavy, Peter and Bölter, Bettina and Kanterakis, Alexandros and Gutierrez-Beltran, Emilio and Moschou, Panagiotis N},
	month = mar,
	year = {2024},
	pages = {559--584},
}

Cellular condensates are usually ribonucleoprotein assemblies with liquid- or solid-like properties. Because these subcellular structures lack a delineating membrane, determining their compositions is difficult. Here we describe a proximity-biotinylation approach for capturing the RNAs of the condensates known as processing bodies (PBs) in Arabidopsis (Arabidopsis thaliana). By combining this approach with RNA detection, in silico, and high-resolution imaging approaches, we studied PBs under normal conditions and heat stress. PBs showed a much more dynamic RNA composition than the total transcriptome. RNAs involved in cell wall development and regeneration, plant hormonal signaling, secondary metabolism/defense, and RNA metabolism were enriched in PBs. RNA-binding proteins and the liquidity of PBs modulated RNA recruitment, while RNAs were frequently recruited together with their encoded proteins. In PBs, RNAs follow distinct fates: in small liquid-like PBs, RNAs get degraded while in more solid-like larger ones, they are stored. PB properties can be regulated by the actin-polymerizing SCAR (suppressor of the cyclic AMP)-WAVE (WASP family verprolin homologous) complex. SCAR/WAVE modulates the shuttling of RNAs between PBs and the translational machinery, thereby adjusting ethylene signaling. In summary, we provide an approach to identify RNAs in condensates that allowed us to reveal a mechanism for regulating RNA fate.

@article{dube_gene_2024,
	title = {Gene co-expression network analysis reveal core responsive genes in {Parascaris} univalens tissues following ivermectin exposure},
	volume = {19},
	issn = {1932-6203},
	url = {https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0298039},
	doi = {10.1371/journal.pone.0298039},
	abstract = {Anthelmintic resistance in equine parasite Parascaris univalens, compromises ivermectin (IVM) effectiveness and necessitates an in-depth understanding of its resistance mechanisms. Most research, primarily focused on holistic gene expression analyses, may overlook vital tissue-specific responses and often limit the scope of novel genes. This study leveraged gene co-expression network analysis to elucidate tissue-specific transcriptional responses and to identify core genes implicated in the IVM response in P. univalens. Adult worms (n = 28) were exposed to 10−11 M and 10−9 M IVM in vitro for 24 hours. RNA-sequencing examined transcriptional changes in the anterior end and intestine. Differential expression analysis revealed pronounced tissue differences, with the intestine exhibiting substantially more IVM-induced transcriptional activity. Gene co-expression network analysis identified seven modules significantly associated with the response to IVM. Within these, 219 core genes were detected, largely expressed in the intestinal tissue and spanning diverse biological processes with unspecific patterns. After 10−11 M IVM, intestinal tissue core genes showed transcriptional suppression, cell cycle inhibition, and ribosomal alterations. Interestingly, genes PgR028\_g047 (sorb-1), PgB01\_g200 (gmap-1) and PgR046\_g017 (col-37 \& col-102) switched from downregulation at 10−11 M to upregulation at 10−9 M IVM. The 10−9 M concentration induced expression of cuticle and membrane integrity core genes in the intestinal tissue. No clear core gene patterns were visible in the anterior end after 10−11 M IVM. However, after 10−9 M IVM, the anterior end mostly displayed downregulation, indicating disrupted transcriptional regulation. One interesting finding was the non-modular calcium-signaling gene, PgR047\_g066 (gegf-1), which uniquely connected 71 genes across four modules. These genes were enriched for transmembrane signaling activity, suggesting that PgR047\_g066 (gegf-1) could have a key signaling role. By unveiling tissue-specific expression patterns and highlighting biological processes through unbiased core gene detection, this study reveals intricate IVM responses in P. univalens. These findings suggest alternative drug uptake of IVM and can guide functional validations to further IVM resistance mechanism understanding.},
	language = {en},
	number = {2},
	urldate = {2024-02-23},
	journal = {PLOS ONE},
	author = {Dube, Faruk and Delhomme, Nicolas and Martin, Frida and Hinas, Andrea and Åbrink, Magnus and Svärd, Staffan and Tydén, Eva},
	month = feb,
	year = {2024},
	note = {Publisher: Public Library of Science},
	keywords = {Cellular structures and organelles, Gastrointestinal tract, Gene expression, Gene ontologies, Gene regulatory networks, Genetic networks, Nematode infections, Signal transduction},
	pages = {e0298039},
}

Anthelmintic resistance in equine parasite Parascaris univalens, compromises ivermectin (IVM) effectiveness and necessitates an in-depth understanding of its resistance mechanisms. Most research, primarily focused on holistic gene expression analyses, may overlook vital tissue-specific responses and often limit the scope of novel genes. This study leveraged gene co-expression network analysis to elucidate tissue-specific transcriptional responses and to identify core genes implicated in the IVM response in P. univalens. Adult worms (n = 28) were exposed to 10−11 M and 10−9 M IVM in vitro for 24 hours. RNA-sequencing examined transcriptional changes in the anterior end and intestine. Differential expression analysis revealed pronounced tissue differences, with the intestine exhibiting substantially more IVM-induced transcriptional activity. Gene co-expression network analysis identified seven modules significantly associated with the response to IVM. Within these, 219 core genes were detected, largely expressed in the intestinal tissue and spanning diverse biological processes with unspecific patterns. After 10−11 M IVM, intestinal tissue core genes showed transcriptional suppression, cell cycle inhibition, and ribosomal alterations. Interestingly, genes PgR028_g047 (sorb-1), PgB01_g200 (gmap-1) and PgR046_g017 (col-37 & col-102) switched from downregulation at 10−11 M to upregulation at 10−9 M IVM. The 10−9 M concentration induced expression of cuticle and membrane integrity core genes in the intestinal tissue. No clear core gene patterns were visible in the anterior end after 10−11 M IVM. However, after 10−9 M IVM, the anterior end mostly displayed downregulation, indicating disrupted transcriptional regulation. One interesting finding was the non-modular calcium-signaling gene, PgR047_g066 (gegf-1), which uniquely connected 71 genes across four modules. These genes were enriched for transmembrane signaling activity, suggesting that PgR047_g066 (gegf-1) could have a key signaling role. By unveiling tissue-specific expression patterns and highlighting biological processes through unbiased core gene detection, this study reveals intricate IVM responses in P. univalens. These findings suggest alternative drug uptake of IVM and can guide functional validations to further IVM resistance mechanism understanding.

@article{blume-werry_situ_2024,
	title = {In situ seasonal patterns of root auxin concentrations and meristem length in an arctic sedge},
	copyright = {© 2024 The Authors. New Phytologist © 2024 New Phytologist Foundation},
	issn = {1469-8137},
	url = {https://onlinelibrary.wiley.com/doi/abs/10.1111/nph.19616},
	doi = {10.1111/nph.19616},
	abstract = {Seasonal dynamics of root growth play an important role in large-scale ecosystem processes; they are largely governed by growth regulatory compounds and influenced by environmental conditions. Yet, our knowledge about physiological drivers of root growth is mostly limited to laboratory-based studies on model plant species. We sampled root tips of Eriophorum vaginatum and analyzed their auxin concentrations and meristem lengths biweekly over a growing season in situ in a subarctic peatland, both in surface soil and at the permafrost thawfront. Auxin concentrations were almost five times higher in surface than in thawfront soils and increased over the season, especially at the thawfront. Surprisingly, meristem length showed an opposite pattern and was almost double in thawfront compared with surface soils. Meristem length increased from peak to late season in the surface soils but decreased at the thawfront. Our study of in situ seasonal dynamics in root physiological parameters illustrates the potential for physiological methods to be applied in ecological studies and emphasizes the importance of in situ measurements. The strong effect of root location and the unexpected opposite patterns of meristem length and auxin concentrations likely show that auxin actively governs root growth to ensure a high potential for nutrient uptake at the thawfront.},
	language = {en},
	urldate = {2024-02-23},
	journal = {New Phytologist},
	author = {Blume-Werry, Gesche and Semenchuk, Philipp and Ljung, Karin and Milbau, Ann and Novak, Ondrej and Olofsson, Johan and Brunoni, Federica},
	month = feb,
	year = {2024},
	note = {\_eprint: https://onlinelibrary.wiley.com/doi/pdf/10.1111/nph.19616},
	keywords = {Eriophorum vaginatum, auxin, meristem length, permafrost, root growth, root phenology},
}

Seasonal dynamics of root growth play an important role in large-scale ecosystem processes; they are largely governed by growth regulatory compounds and influenced by environmental conditions. Yet, our knowledge about physiological drivers of root growth is mostly limited to laboratory-based studies on model plant species. We sampled root tips of Eriophorum vaginatum and analyzed their auxin concentrations and meristem lengths biweekly over a growing season in situ in a subarctic peatland, both in surface soil and at the permafrost thawfront. Auxin concentrations were almost five times higher in surface than in thawfront soils and increased over the season, especially at the thawfront. Surprisingly, meristem length showed an opposite pattern and was almost double in thawfront compared with surface soils. Meristem length increased from peak to late season in the surface soils but decreased at the thawfront. Our study of in situ seasonal dynamics in root physiological parameters illustrates the potential for physiological methods to be applied in ecological studies and emphasizes the importance of in situ measurements. The strong effect of root location and the unexpected opposite patterns of meristem length and auxin concentrations likely show that auxin actively governs root growth to ensure a high potential for nutrient uptake at the thawfront.

@article{renstrom_effect_2024,
	title = {The effect of nitrogen source and levels on hybrid aspen tree physiology and wood formation},
	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.14219},
	doi = {10.1111/ppl.14219},
	abstract = {Nitrogen can be taken up by trees in the form of nitrate, ammonium and amino acids, but the influence of the different forms on tree growth and development is poorly understood in angiosperm species like Populus. We studied the effects of both organic and inorganic forms of nitrogen on growth and wood formation of hybrid aspen trees in experimental conditions that allowed growth under four distinct steady-state nitrogen levels. Increased nitrogen availability had a positive influence on biomass accumulation and the radial dimensions of both xylem vessels and fibers, and a negative influence on wood density. An optimal level of nitrogen availability was identified where increases in biomass accumulation outweighed decreases in wood density. None of these responses depended on the source of nitrogen except for shoot biomass accumulation, which was stimulated more by treatments complemented with nitrate than by ammonium alone or the organic source arginine. The most striking difference between the nitrogen sources was the effect on lignin composition, whereby the abundance of H-type lignin increased only in the presence of nitrate. The differential effect of nitrate is possibly related to the well-known role of nitrate as a signaling compound. RNA-sequencing revealed that while the lignin-biosynthetic genes did not significantly (FDR {\textless}0.01) respond to added NO3−, the expression of several laccases, catalysing lignin polymerization, was dependent on N-availability. These results reveal a unique role of nitrate in wood formation and contribute to the knowledge basis for decision-making in utilizing hybrid aspen as a bioresource.},
	language = {en},
	number = {1},
	urldate = {2024-02-23},
	journal = {Physiologia Plantarum},
	author = {Renström, Anna and Choudhary, Shruti and Gandla, Madhavi Latha and Jönsson, Leif J. and Hedenström, Mattias and Jämtgård, Sandra and Tuominen, Hannele},
	month = feb,
	year = {2024},
	note = {\_eprint: https://onlinelibrary.wiley.com/doi/pdf/10.1111/ppl.14219},
	keywords = {H-type lignin, N-nutrition, Populus tremula x P. tremuloides, Pyrolysis-GC/MS, lignin composition, organic vs. inorganic N, xylogenesis},
	pages = {e14219},
}

Nitrogen can be taken up by trees in the form of nitrate, ammonium and amino acids, but the influence of the different forms on tree growth and development is poorly understood in angiosperm species like Populus. We studied the effects of both organic and inorganic forms of nitrogen on growth and wood formation of hybrid aspen trees in experimental conditions that allowed growth under four distinct steady-state nitrogen levels. Increased nitrogen availability had a positive influence on biomass accumulation and the radial dimensions of both xylem vessels and fibers, and a negative influence on wood density. An optimal level of nitrogen availability was identified where increases in biomass accumulation outweighed decreases in wood density. None of these responses depended on the source of nitrogen except for shoot biomass accumulation, which was stimulated more by treatments complemented with nitrate than by ammonium alone or the organic source arginine. The most striking difference between the nitrogen sources was the effect on lignin composition, whereby the abundance of H-type lignin increased only in the presence of nitrate. The differential effect of nitrate is possibly related to the well-known role of nitrate as a signaling compound. RNA-sequencing revealed that while the lignin-biosynthetic genes did not significantly (FDR \textless0.01) respond to added NO3−, the expression of several laccases, catalysing lignin polymerization, was dependent on N-availability. These results reveal a unique role of nitrate in wood formation and contribute to the knowledge basis for decision-making in utilizing hybrid aspen as a bioresource.

@article{nie_progress_2024,
	title = {Progress in phylogenetics, multi-omics and flower coloration studies in \textit{{Rhododendron}}},
	volume = {4},
	copyright = {2024 The Author(s)},
	issn = {2769-2094},
	url = {https://www.maxapress.com/rticle/doi/10.48130/opr-0024-0001},
	doi = {10.48130/opr-0024-0001},
	abstract = {{\textless}p{\textgreater}The genus {\textless}italic{\textgreater}Rhododendron{\textless}/italic{\textgreater} exhibits an immense diversity of flower colors and represents one of the largest groups of woody plants, which is of great importance for ornamental plant research. This review summarizes recent progress in deciphering the genetic basis for flower coloration in {\textless}italic{\textgreater}Rhododendron{\textless}/italic{\textgreater}. We describe advances in phylogenetic reconstruction and genome sequencing of {\textless}italic{\textgreater}Rhododendron{\textless}/italic{\textgreater} species. The metabolic pathways of flower color are outlined, focusing on key structural and regulatory genes involved in pigment synthesis. Gene duplications and losses associated with color diversification are discussed. In addition, the application of multi-omics approaches and analysis of gene co-expression networks to elucidate complex gene regulatory mechanisms is emphasized. This synthesis of current knowledge provides a foundation for future research on the evolution of flower color diversity within the {\textless}italic{\textgreater}Rhododendron{\textless}/italic{\textgreater} lineage. Ultimately, these discoveries will support breeding endeavors aimed at harnessing the genetics of flower coloration and developing novel cultivars that exhibit desired floral traits.{\textless}/p{\textgreater}},
	language = {en},
	number = {1},
	urldate = {2024-02-23},
	journal = {Ornamental Plant Research},
	author = {Nie, Shuai and Ma, Hai-Yao and Shi, Tian-Le and Tian, Xue-Chan and El-Kassaby, Yousry A. and Porth, Ilga and Yang, Fu-Sheng and Mao, Jian-Feng and Nie, Shuai and Ma, Hai-Yao and Shi, Tian-Le and Tian, Xue-Chan and El-Kassaby, Yousry A. and Porth, Ilga and Yang, Fu-Sheng and Mao, Jian-Feng},
	month = jan,
	year = {2024},
	note = {Bandiera\_abtest: a
Cc\_license\_type: cc\_by
Cg\_type: Maximum Academic Press
Number: opr-0024-0001
Primary\_atype: Ornamental Plant Research
Publisher: Maximum Academic Press
Subject\_term: REVIEW
Subject\_term\_id: REVIEW},
}

\textlessp\textgreaterThe genus \textlessitalic\textgreaterRhododendron\textless/italic\textgreater exhibits an immense diversity of flower colors and represents one of the largest groups of woody plants, which is of great importance for ornamental plant research. This review summarizes recent progress in deciphering the genetic basis for flower coloration in \textlessitalic\textgreaterRhododendron\textless/italic\textgreater. We describe advances in phylogenetic reconstruction and genome sequencing of \textlessitalic\textgreaterRhododendron\textless/italic\textgreater species. The metabolic pathways of flower color are outlined, focusing on key structural and regulatory genes involved in pigment synthesis. Gene duplications and losses associated with color diversification are discussed. In addition, the application of multi-omics approaches and analysis of gene co-expression networks to elucidate complex gene regulatory mechanisms is emphasized. This synthesis of current knowledge provides a foundation for future research on the evolution of flower color diversity within the \textlessitalic\textgreaterRhododendron\textless/italic\textgreater lineage. Ultimately, these discoveries will support breeding endeavors aimed at harnessing the genetics of flower coloration and developing novel cultivars that exhibit desired floral traits.\textless/p\textgreater

@article{forsmark_shifts_2024,
	title = {Shifts in microbial community composition and metabolism correspond with rapid soil carbon accumulation in response to 20 years of simulated nitrogen deposition},
	volume = {918},
	issn = {0048-9697},
	doi = {10.1016/j.scitotenv.2024.170741},
	abstract = {Anthropogenic nitrogen (N) deposition and fertilization in boreal forests frequently reduces decomposition and soil respiration and enhances C storage in the topsoil. This enhancement of the C sink can be as strong as the aboveground biomass response to N additions and has implications for the global C cycle, but the mechanisms remain elusive. We hypothesized that this effect would be associated with a shift in the microbial community and its activity, and particularly by fungal taxa reported to be capable of lignin degradation and organic N acquisition. We sampled the organic layer below the intact litter of a Norway spruce (Picea abies (L.) Karst) forest in northern Sweden after 20 years of annual N additions at low (12.5 kg N ha−1 yr−1) and high (50 kg N ha−1 yr−1) rates. We measured microbial biomass using phospholipid fatty-acid analysis (PLFA) and ergosterol measurements and used ITS metagenomics to profile the fungal community of soil and fine-roots. We probed the metabolic activity of the soil community by measuring the activity of extracellular enzymes and evaluated its relationships with the most N responsive soil fungal species. Nitrogen addition decreased the abundance of fungal PLFA markers and changed the fungal community in humus and fine-roots. Specifically, the humus community changed in part due to a shift from Oidiodendron pilicola, Cenococcum geophilum, and Cortinarius caperatus to Tylospora fibrillosa and Russula griseascens. These microbial community changes were associated with decreased activity of Mn-peroxidase and peptidase, and an increase in the activity of C acquiring enzymes. Our results show that the rapid accumulation of C in the humus layer frequently observed in areas with high N deposition is consistent with a shift in microbial metabolism, where decomposition associated with organic N acquisition is downregulated when inorganic N forms are readily available. © 2024 The Authors},
	language = {English},
	number = {170741},
	journal = {Science of the Total Environment},
	author = {Forsmark, B. and Bizjak, T. and Nordin, A. and Rosenstock, N.P. and Wallander, H. and Gundale, M.J.},
	month = feb,
	year = {2024},
	keywords = {Boreal forest, Carbon sequestration, Ectomycorrhizal fungi, Extracellular enzymes, Microbial community, Nitrogen deposition},
}

Anthropogenic nitrogen (N) deposition and fertilization in boreal forests frequently reduces decomposition and soil respiration and enhances C storage in the topsoil. This enhancement of the C sink can be as strong as the aboveground biomass response to N additions and has implications for the global C cycle, but the mechanisms remain elusive. We hypothesized that this effect would be associated with a shift in the microbial community and its activity, and particularly by fungal taxa reported to be capable of lignin degradation and organic N acquisition. We sampled the organic layer below the intact litter of a Norway spruce (Picea abies (L.) Karst) forest in northern Sweden after 20 years of annual N additions at low (12.5 kg N ha−1 yr−1) and high (50 kg N ha−1 yr−1) rates. We measured microbial biomass using phospholipid fatty-acid analysis (PLFA) and ergosterol measurements and used ITS metagenomics to profile the fungal community of soil and fine-roots. We probed the metabolic activity of the soil community by measuring the activity of extracellular enzymes and evaluated its relationships with the most N responsive soil fungal species. Nitrogen addition decreased the abundance of fungal PLFA markers and changed the fungal community in humus and fine-roots. Specifically, the humus community changed in part due to a shift from Oidiodendron pilicola, Cenococcum geophilum, and Cortinarius caperatus to Tylospora fibrillosa and Russula griseascens. These microbial community changes were associated with decreased activity of Mn-peroxidase and peptidase, and an increase in the activity of C acquiring enzymes. Our results show that the rapid accumulation of C in the humus layer frequently observed in areas with high N deposition is consistent with a shift in microbial metabolism, where decomposition associated with organic N acquisition is downregulated when inorganic N forms are readily available. © 2024 The Authors

@article{shi_differential_2024,
	title = {Differential gene expression and potential regulatory network of fatty acid biosynthesis during fruit and leaf development in yellowhorn ({Xanthoceras} sorbifolium), an oil-producing tree with significant deployment values},
	volume = {14},
	issn = {1664-462X},
	url = {https://www.frontiersin.org/journals/plant-science/articles/10.3389/fpls.2023.1297817},
	abstract = {Xanthoceras sorbifolium (yellowhorn) is a woody oil plant with super stress resistance and excellent oil characteristics. The yellowhorn oil can be used as biofuel and edible oil with high nutritional and medicinal value. However, genetic studies on yellowhorn are just in the beginning, and fundamental biological questions regarding its very long-chain fatty acid (VLCFA) biosynthesis pathway remain largely unknown. In this study, we reconstructed the VLCFA biosynthesis pathway and annotated 137 genes encoding relevant enzymes. We identified four oleosin genes that package triacylglycerols (TAGs) and are specifically expressed in fruits, likely playing key roles in yellowhorn oil production. Especially, by examining time-ordered gene co-expression network (TO-GCN) constructed from fruit and leaf developments, we identified key enzymatic genes and potential regulatory transcription factors involved in VLCFA synthesis. In fruits, we further inferred a hierarchical regulatory network with MYB-related (XS03G0296800) and B3 (XS02G0057600) transcription factors as top-tier regulators, providing clues into factors controlling carbon flux into fatty acids. Our results offer new insights into key genes and transcriptional regulators governing fatty acid production in yellowhorn, laying the foundation for efforts to optimize oil content and fatty acid composition. Moreover, the gene expression patterns and putative regulatory relationships identified here will inform metabolic engineering and molecular breeding approaches tailored to meet biofuel and bioproduct demands.},
	urldate = {2024-02-16},
	journal = {Frontiers in Plant Science},
	author = {Shi, Tian-Le and Ma, Hai-Yao and Wang, Xinrui and Liu, Hui and Yan, Xue-Mei and Tian, Xue-Chan and Li, Zhi-Chao and Bao, Yu-Tao and Chen, Zhao-Yang and Zhao, Shi-Wei and Xiang, Qiuhong and Jia, Kai-Hua and Nie, Shuai and Guan, Wenbin and Mao, Jian-Feng},
	month = jan,
	year = {2024},
	keywords = {⛔ No DOI found},
}

Xanthoceras sorbifolium (yellowhorn) is a woody oil plant with super stress resistance and excellent oil characteristics. The yellowhorn oil can be used as biofuel and edible oil with high nutritional and medicinal value. However, genetic studies on yellowhorn are just in the beginning, and fundamental biological questions regarding its very long-chain fatty acid (VLCFA) biosynthesis pathway remain largely unknown. In this study, we reconstructed the VLCFA biosynthesis pathway and annotated 137 genes encoding relevant enzymes. We identified four oleosin genes that package triacylglycerols (TAGs) and are specifically expressed in fruits, likely playing key roles in yellowhorn oil production. Especially, by examining time-ordered gene co-expression network (TO-GCN) constructed from fruit and leaf developments, we identified key enzymatic genes and potential regulatory transcription factors involved in VLCFA synthesis. In fruits, we further inferred a hierarchical regulatory network with MYB-related (XS03G0296800) and B3 (XS02G0057600) transcription factors as top-tier regulators, providing clues into factors controlling carbon flux into fatty acids. Our results offer new insights into key genes and transcriptional regulators governing fatty acid production in yellowhorn, laying the foundation for efforts to optimize oil content and fatty acid composition. Moreover, the gene expression patterns and putative regulatory relationships identified here will inform metabolic engineering and molecular breeding approaches tailored to meet biofuel and bioproduct demands.

@article{tognacca_unveiling_2024,
	title = {Unveiling {Molecular} {Signatures} in {Light}-{Induced} {Seed} {Germination}: {Insights} from {PIN3}, {PIN7}, and {AUX1} in {Arabidopsis} thaliana},
	volume = {13},
	copyright = {http://creativecommons.org/licenses/by/3.0/},
	issn = {2223-7747},
	shorttitle = {Unveiling {Molecular} {Signatures} in {Light}-{Induced} {Seed} {Germination}},
	url = {https://www.mdpi.com/2223-7747/13/3/408},
	doi = {10.3390/plants13030408},
	abstract = {Light provides seeds with information that is essential for the adjustment of their germination to the conditions that are most favorable for the successful establishment of the future seedling. The promotion of germination depends mainly on environmental factors, like temperature and light, as well as internal factors associated with the hormonal balance between gibberellins (GA) and abscisic acid (ABA), although other hormones such as auxins may act secondarily. While transcriptomic studies of light-germinating Arabidopsis thaliana seeds suggest that auxins and auxin transporters are necessary, there are still no functional studies connecting the activity of the auxin transporters in light-induced seed germination. In this study, we investigated the roles of two auxin efflux carrier (PIN3 and PIN7) proteins and one auxin influx (AUX1) carrier protein during Arabidopsis thaliana seed germination. By using next-generation sequencing (RNAseq), gene expression analyses, hormonal sensitivity assays, and the quantification of indole-3-acetic acid (IAA) levels, we assessed the functional roles of PIN3, PIN7, and AUX1 during light-induced seed germination. We showed that auxin levels are increased 24 h after a red-pulse (Rp). Additionally, we evaluated the germination responses of pin3, pin7, and aux1 mutant seeds and showed that PIN3, PIN7, and AUX1 auxin carriers are important players in the regulation of seed germination. By using gene expression analysis in water, fluridone (F), and ABA+F treated seeds, we confirmed that Rp-induced seed germination is associated with auxin transport, and ABA controls the function of PIN3, PIN7, and AUX1 during this process. Overall, our results highlight the relevant and positive role of auxin transporters in germinating the seeds of Arabidopsis thaliana.},
	language = {en},
	number = {3},
	urldate = {2024-02-16},
	journal = {Plants},
	author = {Tognacca, Rocío Soledad and Ljung, Karin and Botto, Javier Francisco},
	month = jan,
	year = {2024},
	note = {Number: 3
Publisher: Multidisciplinary Digital Publishing Institute},
	keywords = {\textit{Arabidopsis thaliana}, ABA, AUX1, PIN3, PIN7, auxin, hormonal crosstalk, molecular regulation, seed germination},
	pages = {408},
}

Light provides seeds with information that is essential for the adjustment of their germination to the conditions that are most favorable for the successful establishment of the future seedling. The promotion of germination depends mainly on environmental factors, like temperature and light, as well as internal factors associated with the hormonal balance between gibberellins (GA) and abscisic acid (ABA), although other hormones such as auxins may act secondarily. While transcriptomic studies of light-germinating Arabidopsis thaliana seeds suggest that auxins and auxin transporters are necessary, there are still no functional studies connecting the activity of the auxin transporters in light-induced seed germination. In this study, we investigated the roles of two auxin efflux carrier (PIN3 and PIN7) proteins and one auxin influx (AUX1) carrier protein during Arabidopsis thaliana seed germination. By using next-generation sequencing (RNAseq), gene expression analyses, hormonal sensitivity assays, and the quantification of indole-3-acetic acid (IAA) levels, we assessed the functional roles of PIN3, PIN7, and AUX1 during light-induced seed germination. We showed that auxin levels are increased 24 h after a red-pulse (Rp). Additionally, we evaluated the germination responses of pin3, pin7, and aux1 mutant seeds and showed that PIN3, PIN7, and AUX1 auxin carriers are important players in the regulation of seed germination. By using gene expression analysis in water, fluridone (F), and ABA+F treated seeds, we confirmed that Rp-induced seed germination is associated with auxin transport, and ABA controls the function of PIN3, PIN7, and AUX1 during this process. Overall, our results highlight the relevant and positive role of auxin transporters in germinating the seeds of Arabidopsis thaliana.

@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},
	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},
	note = {Publisher: Proceedings of the National Academy of Sciences},
	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{fuchs_plant_2024,
	title = {{PLANT} {UNCOUPLING} {MITOCHONDRIAL} {PROTEIN} 2 localizes to the {Golgi}},
	volume = {194},
	issn = {0032-0889},
	url = {https://doi.org/10.1093/plphys/kiad540},
	doi = {10.1093/plphys/kiad540},
	abstract = {Mitochondria act as cellular hubs of energy transformation and metabolite conversion in most eukaryotes. Plant mitochondrial electron transport chains are particularly flexible, featuring components that can bypass proton translocation steps, such as ALTERNATIVE NAD(P)H DEHYDROGENASES and ALTERNATIVE OXIDASES (AOXs). PLANT UNCOUPLING MITOCHONDRIAL PROTEINS (PUMPs or plant UNCOUPLING PROTEINS [UCPs]) have been identified in plants as homologs of mammalian UCPs, and their physiological roles have been investigated in the context of mitochondrial energy metabolism. To dissect UCP function in Arabidopsis (Arabidopsis thaliana), the 2 most conserved family members, UCP1 and UCP2, have been genetically ablated assuming that they both reside in the inner mitochondrial membrane. Yet, contradicting results have been reported on plant UCP2 localization. After UCP1 (Maia et al. 1998) and UCP2 (Watanabe et al. 1999) were identified as plant homologs of mammalian UCP1, 6 Arabidopsis isogenes were named PUMP1 to PUMP6 (Borecký et al. 2006). However, PUMP4 to PUMP6 exhibit properties typical of the phylogenetically related mitochondrial dicarboxylate carrier (DIC) proteins (Palmieri et al. 2008). Accordingly, PUMPs were regrouped into plant UCP1 to UCP3 and plant DIC1 to DIC3 (Supplemental Fig. S1) (Palmieri et al. 2008). UCP1 and UCP2 are highly similar in sequence and share 72\% amino acid identity (Supplemental Fig. S2A) (Monné et al. 2018). We provide evidence that UCP2 localizes to the Golgi unlike UCP1, which localizes to the mitochondria, and we provide perspectives on UCP protein function, Golgi membrane transport, and subcellular targeting principles of membrane proteins.},
	number = {2},
	urldate = {2024-02-02},
	journal = {Plant Physiology},
	author = {Fuchs, Philippe and Feixes-Prats, Elisenda and Arruda, Paulo and Feitosa-Araújo, Elias and Fernie, Alisdair R and Grefen, Christopher and Lichtenauer, Sophie and Linka, Nicole and de Godoy Maia, Ivan and Meyer, Andreas J and Schilasky, Sören and Sweetlove, Lee J and Wege, Stefanie and Weber, Andreas P M and Millar, A Harvey and Keech, Olivier and Florez-Sarasa, Igor and Barreto, Pedro and Schwarzländer, Markus},
	month = feb,
	year = {2024},
	pages = {623--628},
}

Mitochondria act as cellular hubs of energy transformation and metabolite conversion in most eukaryotes. Plant mitochondrial electron transport chains are particularly flexible, featuring components that can bypass proton translocation steps, such as ALTERNATIVE NAD(P)H DEHYDROGENASES and ALTERNATIVE OXIDASES (AOXs). PLANT UNCOUPLING MITOCHONDRIAL PROTEINS (PUMPs or plant UNCOUPLING PROTEINS [UCPs]) have been identified in plants as homologs of mammalian UCPs, and their physiological roles have been investigated in the context of mitochondrial energy metabolism. To dissect UCP function in Arabidopsis (Arabidopsis thaliana), the 2 most conserved family members, UCP1 and UCP2, have been genetically ablated assuming that they both reside in the inner mitochondrial membrane. Yet, contradicting results have been reported on plant UCP2 localization. After UCP1 (Maia et al. 1998) and UCP2 (Watanabe et al. 1999) were identified as plant homologs of mammalian UCP1, 6 Arabidopsis isogenes were named PUMP1 to PUMP6 (Borecký et al. 2006). However, PUMP4 to PUMP6 exhibit properties typical of the phylogenetically related mitochondrial dicarboxylate carrier (DIC) proteins (Palmieri et al. 2008). Accordingly, PUMPs were regrouped into plant UCP1 to UCP3 and plant DIC1 to DIC3 (Supplemental Fig. S1) (Palmieri et al. 2008). UCP1 and UCP2 are highly similar in sequence and share 72% amino acid identity (Supplemental Fig. S2A) (Monné et al. 2018). We provide evidence that UCP2 localizes to the Golgi unlike UCP1, which localizes to the mitochondria, and we provide perspectives on UCP protein function, Golgi membrane transport, and subcellular targeting principles of membrane proteins.

@article{estravis_barcala_whole-genome_2024,
	title = {Whole-genome resequencing facilitates the development of a {50K} single nucleotide polymorphism genotyping array for {Scots} pine ({Pinus} sylvestris {L}.) and its transferability to other pine species},
	volume = {117},
	copyright = {© 2023 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.16535},
	doi = {10.1111/tpj.16535},
	abstract = {Scots pine (Pinus sylvestris L.) is one of the most widespread and economically important conifer species in the world. Applications like genomic selection and association studies, which could help accelerate breeding cycles, are challenging in Scots pine because of its large and repetitive genome. For this reason, genotyping tools for conifer species, and in particular for Scots pine, are commonly based on transcribed regions of the genome. In this article, we present the Axiom Psyl50K array, the first single nucleotide polymorphism (SNP) genotyping array for Scots pine based on whole-genome resequencing, that represents both genic and intergenic regions. This array was designed following a two-step procedure: first, 192 trees were sequenced, and a 430K SNP screening array was constructed. Then, 480 samples, including haploid megagametophytes, full-sib family trios, breeding population, and range-wide individuals from across Eurasia were genotyped with the screening array. The best 50K SNPs were selected based on quality, replicability, distribution across the draft genome assembly, balance between genic and intergenic regions, and genotype–environment and genotype–phenotype associations. Of the final 49 877 probes tiled in the array, 20 372 (40.84\%) occur inside gene models, while the rest lie in intergenic regions. We also show that the Psyl50K array can yield enough high-confidence SNPs for genetic studies in pine species from North America and Eurasia. This new genotyping tool will be a valuable resource for high-throughput fundamental and applied research of Scots pine and other pine species.},
	language = {en},
	number = {3},
	urldate = {2024-02-02},
	journal = {The Plant Journal},
	author = {Estravis Barcala, Maximiliano and van der Valk, Tom and Chen, Zhiqiang and Funda, Tomas and Chaudhary, Rajiv and Klingberg, Adam and Fundova, Irena and Suontama, Mari and Hallingbäck, Henrik and Bernhardsson, Carolina and Nystedt, Björn and Ingvarsson, Pär K. and Sherwood, Ellen and Street, Nathaniel and Gyllensten, Ulf and Nilsson, Ove and Wu, Harry X.},
	year = {2024},
	note = {\_eprint: https://onlinelibrary.wiley.com/doi/pdf/10.1111/tpj.16535},
	keywords = {Pinus sylvestris, SNP array, genome resequencing, genome-wide association studies, genomic selection, pines},
	pages = {944--955},
}

Scots pine (Pinus sylvestris L.) is one of the most widespread and economically important conifer species in the world. Applications like genomic selection and association studies, which could help accelerate breeding cycles, are challenging in Scots pine because of its large and repetitive genome. For this reason, genotyping tools for conifer species, and in particular for Scots pine, are commonly based on transcribed regions of the genome. In this article, we present the Axiom Psyl50K array, the first single nucleotide polymorphism (SNP) genotyping array for Scots pine based on whole-genome resequencing, that represents both genic and intergenic regions. This array was designed following a two-step procedure: first, 192 trees were sequenced, and a 430K SNP screening array was constructed. Then, 480 samples, including haploid megagametophytes, full-sib family trios, breeding population, and range-wide individuals from across Eurasia were genotyped with the screening array. The best 50K SNPs were selected based on quality, replicability, distribution across the draft genome assembly, balance between genic and intergenic regions, and genotype–environment and genotype–phenotype associations. Of the final 49 877 probes tiled in the array, 20 372 (40.84%) occur inside gene models, while the rest lie in intergenic regions. We also show that the Psyl50K array can yield enough high-confidence SNPs for genetic studies in pine species from North America and Eurasia. This new genotyping tool will be a valuable resource for high-throughput fundamental and applied research of Scots pine and other pine species.

@article{oikonomou_esoil_2024,
	title = {{eSoil}: {A} low-power bioelectronic growth scaffold that enhances crop seedling growth},
	volume = {121},
	shorttitle = {{eSoil}},
	url = {https://www.pnas.org/doi/10.1073/pnas.2304135120},
	doi = {10.1073/pnas.2304135120},
	abstract = {Active hydroponic substrates that stimulate on demand the plant growth have not been demonstrated so far. Here, we developed the eSoil, a low-power bioelectronic growth scaffold that can provide electrical stimulation to the plants’ root system and growth environment in hydroponics settings. eSoil’s active material is an organic mixed ionic electronic conductor while its main structural component is cellulose, the most abundant biopolymer. We demonstrate that barley seedlings that are widely used for fodder grow within the eSoil with the root system integrated within its porous matrix. Simply by polarizing the eSoil, seedling growth is accelerated resulting in increase of dry weight on average by 50\% after 15 d of growth. The effect is evident both on root and shoot development and occurs during the growth period after the stimulation. The stimulated plants reduce and assimilate NO3− more efficiently than controls, a finding that may have implications on minimizing fertilizer use. However, more studies are required to provide a mechanistic understanding of the physical and biological processes involved. eSoil opens the pathway for the development of active hydroponic scaffolds that may increase crop yield in a sustainable manner.},
	number = {2},
	urldate = {2023-12-29},
	journal = {Proceedings of the National Academy of Sciences},
	author = {Oikonomou, Vasileios K. and Huerta, Miriam and Sandéhn, Alexandra and Dreier, Till and Daguerre, Yohann and Lim, Hyungwoo and Berggren, Magnus and Pavlopoulou, Eleni and Näsholm, Torgny and Bech, Martin and Stavrinidou, Eleni},
	month = jan,
	year = {2024},
	note = {Publisher: Proceedings of the National Academy of Sciences},
	pages = {e2304135120},
}

Active hydroponic substrates that stimulate on demand the plant growth have not been demonstrated so far. Here, we developed the eSoil, a low-power bioelectronic growth scaffold that can provide electrical stimulation to the plants’ root system and growth environment in hydroponics settings. eSoil’s active material is an organic mixed ionic electronic conductor while its main structural component is cellulose, the most abundant biopolymer. We demonstrate that barley seedlings that are widely used for fodder grow within the eSoil with the root system integrated within its porous matrix. Simply by polarizing the eSoil, seedling growth is accelerated resulting in increase of dry weight on average by 50% after 15 d of growth. The effect is evident both on root and shoot development and occurs during the growth period after the stimulation. The stimulated plants reduce and assimilate NO3− more efficiently than controls, a finding that may have implications on minimizing fertilizer use. However, more studies are required to provide a mechanistic understanding of the physical and biological processes involved. eSoil opens the pathway for the development of active hydroponic scaffolds that may increase crop yield in a sustainable manner.

@article{niemi_quantitative_2024,
	title = {Quantitative and qualitative saccharide analysis of {North} {Atlantic} brown seaweed by gas chromatography/mass spectrometry and infrared spectroscopy},
	volume = {254},
	issn = {0141-8130},
	url = {https://www.sciencedirect.com/science/article/pii/S0141813023047694},
	doi = {10.1016/j.ijbiomac.2023.127870},
	abstract = {Brown seaweeds contain a variety of saccharides which have potential industrial uses. The most abundant polysaccharide in brown seaweed is typically alginate, consisting of mannuronic (M) and guluronic acid (G). The ratio of these residues fundamentally determines the physicochemical properties of alginate. In the present study, gas chromatography/mass spectrometry (GC/MS) was used to give a detailed breakdown of the monosaccharide species in North Atlantic brown seaweeds. The anthrone method was used for determination of crystalline cellulose. The experimental data was used to calibrate multivariate prediction models for estimation of total carbohydrates, crystalline cellulose, total alginate and alginate M/G ratio directly in dried, brown seaweed using three types of infrared spectroscopy, using relative error (RE) as a measure of predictive accuracy. Diffuse reflectance infrared Fourier transform spectroscopy (DRIFTS) performed well for the estimation of total alginate (RE = 0.12, R2 = 0.82), and attenuated total reflectance (ATR) showed good prediction of M/G ratio (RE = 0.14, R2 = 0.86). Both DRIFTS, ATR and near infrared (NIR) were unable to predict crystalline cellulose and only DRIFTS performed better in determining total carbohydrates. Multivariate spectral analysis is a promising method for easy and rapid characterization of alginate and M/G ratio in seaweed.},
	urldate = {2023-11-17},
	journal = {International Journal of Biological Macromolecules},
	author = {Niemi, Calle and Takahashi, Junko and Gorzsás, András and Gentili, Francesco G.},
	month = jan,
	year = {2024},
	keywords = {Alginate, FTIR, GC/MS, MG ratio, North Atlantic brown seaweed},
	pages = {127870},
}

Brown seaweeds contain a variety of saccharides which have potential industrial uses. The most abundant polysaccharide in brown seaweed is typically alginate, consisting of mannuronic (M) and guluronic acid (G). The ratio of these residues fundamentally determines the physicochemical properties of alginate. In the present study, gas chromatography/mass spectrometry (GC/MS) was used to give a detailed breakdown of the monosaccharide species in North Atlantic brown seaweeds. The anthrone method was used for determination of crystalline cellulose. The experimental data was used to calibrate multivariate prediction models for estimation of total carbohydrates, crystalline cellulose, total alginate and alginate M/G ratio directly in dried, brown seaweed using three types of infrared spectroscopy, using relative error (RE) as a measure of predictive accuracy. Diffuse reflectance infrared Fourier transform spectroscopy (DRIFTS) performed well for the estimation of total alginate (RE = 0.12, R2 = 0.82), and attenuated total reflectance (ATR) showed good prediction of M/G ratio (RE = 0.14, R2 = 0.86). Both DRIFTS, ATR and near infrared (NIR) were unable to predict crystalline cellulose and only DRIFTS performed better in determining total carbohydrates. Multivariate spectral analysis is a promising method for easy and rapid characterization of alginate and M/G ratio in seaweed.