@article{decker_exploring_2023,
	title = {Exploring {Redox} {Modulation} of {Plant} {UDP}-{Glucose} {Pyrophosphorylase}},
	volume = {24},
	copyright = {http://creativecommons.org/licenses/by/3.0/},
	issn = {1422-0067},
	url = {https://www.mdpi.com/1422-0067/24/10/8914},
	doi = {10.3390/ijms24108914},
	abstract = {UDP-glucose (UDPG) pyrophosphorylase (UGPase) catalyzes a reversible reaction, producing UDPG, which serves as an essential precursor for hundreds of glycosyltransferases in all organisms. In this study, activities of purified UGPases from sugarcane and barley were found to be reversibly redox modulated in vitro through oxidation by hydrogen peroxide or oxidized glutathione (GSSG) and through reduction by dithiothreitol or glutathione. Generally, while oxidative treatment decreased UGPase activity, a subsequent reduction restored the activity. The oxidized enzyme had increased Km values with substrates, especially pyrophosphate. The increased Km values were also observed, regardless of redox status, for UGPase cysteine mutants (Cys102Ser and Cys99Ser for sugarcane and barley UGPases, respectively). However, activities and substrate affinities (Kms) of sugarcane Cys102Ser mutant, but not barley Cys99Ser, were still prone to redox modulation. The data suggest that plant UGPase is subject to redox control primarily via changes in the redox status of a single cysteine. Other cysteines may also, to some extent, contribute to UGPase redox status, as seen for sugarcane enzymes. The results are discussed with respect to earlier reported details of redox modulation of eukaryotic UGPases and regarding the structure/function properties of these proteins.},
	language = {en},
	number = {10},
	urldate = {2023-06-01},
	journal = {International Journal of Molecular Sciences},
	author = {Decker, Daniel and Aubert, Juliette and Wilczynska, Malgorzata and Kleczkowski, Leszek A.},
	month = jan,
	year = {2023},
	note = {Number: 10
Publisher: Multidisciplinary Digital Publishing Institute},
	keywords = {UDP-glucose pyrophosphorylase, carbohydrate metabolism, glutathione, hydrogen peroxide, protein structure, redox regulation, substrate affinity},
	pages = {8914},
}

UDP-glucose (UDPG) pyrophosphorylase (UGPase) catalyzes a reversible reaction, producing UDPG, which serves as an essential precursor for hundreds of glycosyltransferases in all organisms. In this study, activities of purified UGPases from sugarcane and barley were found to be reversibly redox modulated in vitro through oxidation by hydrogen peroxide or oxidized glutathione (GSSG) and through reduction by dithiothreitol or glutathione. Generally, while oxidative treatment decreased UGPase activity, a subsequent reduction restored the activity. The oxidized enzyme had increased Km values with substrates, especially pyrophosphate. The increased Km values were also observed, regardless of redox status, for UGPase cysteine mutants (Cys102Ser and Cys99Ser for sugarcane and barley UGPases, respectively). However, activities and substrate affinities (Kms) of sugarcane Cys102Ser mutant, but not barley Cys99Ser, were still prone to redox modulation. The data suggest that plant UGPase is subject to redox control primarily via changes in the redox status of a single cysteine. Other cysteines may also, to some extent, contribute to UGPase redox status, as seen for sugarcane enzymes. The results are discussed with respect to earlier reported details of redox modulation of eukaryotic UGPases and regarding the structure/function properties of these proteins.

@article{he_evolutionary_2023,
	title = {Evolutionary origin and establishment of a dioecious diploid-tetraploid complex},
	volume = {32},
	issn = {1365-294X},
	url = {https://onlinelibrary.wiley.com/doi/abs/10.1111/mec.16902},
	doi = {10.1111/mec.16902},
	abstract = {Polyploids recurrently emerge in angiosperms, but most polyploids are likely to go extinct before establishment due to minority cytotype exclusion, which may be specifically a constraint for dioecious plants. Here we test the hypothesis that a stable sex-determination system and spatial/ecological isolation facilitate the establishment of dioecious polyploids. We determined the ploidy levels of 351 individuals from 28 populations of the dioecious species Salix polyclona, and resequenced 190 individuals of S. polyclona and related taxa for genomic diversity analyses. The ploidy survey revealed a frequency 52\% of tetraploids in S. polyclona, and genomic k-mer spectra analyses suggested an autopolyploid origin for them. Comparisons of diploid male and female genomes identified a female heterogametic sex-determining factor on chromosome 15, which probably also acts in the dioecious tetraploids. Phylogenetic analyses revealed two diploid clades and a separate clade/grade of tetraploids with a distinct geographic distribution confined to western and central China, where complex mountain systems create higher levels of environmental heterogeneity. Fossil-calibrated phylogenies showed that the polyploids emerged during 7.6–2.3 million years ago, and population demographic histories largely matched the geological and climatic history of the region. Our results suggest that inheritance of the sex-determining system from the diploid progenitor as intrinsic factor and spatial isolation as extrinsic factor may have facilitated the preservation and establishment of polyploid dioecious populations.},
	language = {en},
	number = {11},
	urldate = {2023-05-26},
	journal = {Molecular Ecology},
	author = {He, Li and Guo, Fei-Yi and Cai, Xin-Jie and Chen, Hong-Pu and Lian, Chun-Lan and Wang, Yuan and Shang, Ce and Zhang, Yue and Wagner, Natascha Dorothea and Zhang, Zhi-Xiang and Hörandl, Elvira and Wang, Xiao-Ru},
	month = jun,
	year = {2023},
	note = {\_eprint: https://onlinelibrary.wiley.com/doi/pdf/10.1111/mec.16902},
	keywords = {dioecious plants, mountain biodiversity, polyploidization, population history, sex determination system},
	pages = {2732--2749},
}

Polyploids recurrently emerge in angiosperms, but most polyploids are likely to go extinct before establishment due to minority cytotype exclusion, which may be specifically a constraint for dioecious plants. Here we test the hypothesis that a stable sex-determination system and spatial/ecological isolation facilitate the establishment of dioecious polyploids. We determined the ploidy levels of 351 individuals from 28 populations of the dioecious species Salix polyclona, and resequenced 190 individuals of S. polyclona and related taxa for genomic diversity analyses. The ploidy survey revealed a frequency 52% of tetraploids in S. polyclona, and genomic k-mer spectra analyses suggested an autopolyploid origin for them. Comparisons of diploid male and female genomes identified a female heterogametic sex-determining factor on chromosome 15, which probably also acts in the dioecious tetraploids. Phylogenetic analyses revealed two diploid clades and a separate clade/grade of tetraploids with a distinct geographic distribution confined to western and central China, where complex mountain systems create higher levels of environmental heterogeneity. Fossil-calibrated phylogenies showed that the polyploids emerged during 7.6–2.3 million years ago, and population demographic histories largely matched the geological and climatic history of the region. Our results suggest that inheritance of the sex-determining system from the diploid progenitor as intrinsic factor and spatial isolation as extrinsic factor may have facilitated the preservation and establishment of polyploid dioecious populations.

@article{bernacka-wojcik_flexible_2023,
	title = {Flexible {Organic} {Electronic} {Ion} {Pump} for {Flow}-{Free} {Phytohormone} {Delivery} into {Vasculature} of {Intact} {Plants}},
	volume = {10},
	issn = {2198-3844},
	url = {https://onlinelibrary.wiley.com/doi/abs/10.1002/advs.202206409},
	doi = {10.1002/advs.202206409},
	abstract = {Plant vasculature transports molecules that play a crucial role in plant signaling including systemic responses and acclimation to diverse environmental conditions. Targeted controlled delivery of molecules to the vascular tissue can be a biomimetic way to induce long distance responses, providing a new tool for the fundamental studies and engineering of stress-tolerant plants. Here, a flexible organic electronic ion pump, an electrophoretic delivery device, for controlled delivery of phytohormones directly in plant vascular tissue is developed. The c-OEIP is based on polyimide-coated glass capillaries that significantly enhance the mechanical robustness of these microscale devices while being minimally disruptive for the plant. The polyelectrolyte channel is based on low-cost and commercially available precursors that can be photocured with blue light, establishing much cheaper and safer system than the state-of-the-art. To trigger OEIP-induced plant response, the phytohormone abscisic acid (ABA) in the petiole of intact Arabidopsis plants is delivered. ABA is one of the main phytohormones involved in plant stress responses and induces stomata closure under drought conditions to reduce water loss and prevent wilting. The OEIP-mediated ABA delivery triggered fast and long-lasting stomata closure far away from the delivery point demonstrating systemic vascular transport of the delivered ABA, verified delivering deuterium-labeled ABA.},
	language = {en},
	number = {14},
	urldate = {2023-05-26},
	journal = {Advanced Science},
	author = {Bernacka-Wojcik, Iwona and Talide, Loïc and Abdel Aziz, Ilaria and Simura, Jan and Oikonomou, Vasileios K. and Rossi, Stefano and Mohammadi, Mohsen and Dar, Abdul Manan and Seitanidou, Maria and Berggren, Magnus and Simon, Daniel T. and Tybrandt, Klas and Jonsson, Magnus P. and Ljung, Karin and Niittylä, Totte and Stavrinidou, Eleni},
	month = may,
	year = {2023},
	note = {\_eprint: https://onlinelibrary.wiley.com/doi/pdf/10.1002/advs.202206409},
	keywords = {bioelectronic devices, drug delivery, photo-crosslinking, plants vasculature, polyelectrolytes},
	pages = {2206409},
}

Plant vasculature transports molecules that play a crucial role in plant signaling including systemic responses and acclimation to diverse environmental conditions. Targeted controlled delivery of molecules to the vascular tissue can be a biomimetic way to induce long distance responses, providing a new tool for the fundamental studies and engineering of stress-tolerant plants. Here, a flexible organic electronic ion pump, an electrophoretic delivery device, for controlled delivery of phytohormones directly in plant vascular tissue is developed. The c-OEIP is based on polyimide-coated glass capillaries that significantly enhance the mechanical robustness of these microscale devices while being minimally disruptive for the plant. The polyelectrolyte channel is based on low-cost and commercially available precursors that can be photocured with blue light, establishing much cheaper and safer system than the state-of-the-art. To trigger OEIP-induced plant response, the phytohormone abscisic acid (ABA) in the petiole of intact Arabidopsis plants is delivered. ABA is one of the main phytohormones involved in plant stress responses and induces stomata closure under drought conditions to reduce water loss and prevent wilting. The OEIP-mediated ABA delivery triggered fast and long-lasting stomata closure far away from the delivery point demonstrating systemic vascular transport of the delivered ABA, verified delivering deuterium-labeled ABA.

@article{brunoni_amino_2023,
	title = {Amino acid conjugation of {oxIAA} is a secondary metabolic regulation involved in auxin homeostasis},
	volume = {238},
	issn = {1469-8137},
	url = {https://onlinelibrary.wiley.com/doi/abs/10.1111/nph.18887},
	doi = {10.1111/nph.18887},
	language = {en},
	number = {6},
	urldate = {2023-05-26},
	journal = {New Phytologist},
	author = {Brunoni, Federica and Pěnčík, Aleš and Žukauskaitė, Asta and Ament, Anita and Kopečná, Martina and Collani, Silvio and Kopečný, David and Novák, Ondřej},
	month = jun,
	year = {2023},
	note = {\_eprint: https://onlinelibrary.wiley.com/doi/pdf/10.1111/nph.18887},
	keywords = {Arabidopsis, auxin inactivation, conjugation, moss, oxidation, spruce},
	pages = {2264--2270},
}

@article{yang_chromosome-level_2023,
	title = {The chromosome-level genome assembly and genes involved in biosynthesis of nervonic acid of {Malania} oleifera},
	volume = {10},
	copyright = {2023 The Author(s)},
	issn = {2052-4463},
	url = {https://www.nature.com/articles/s41597-023-02218-8},
	doi = {10.1038/s41597-023-02218-8},
	abstract = {Nervonic acid (C24:1 Δ15, NA) is a very long-chain monounsaturated fatty acid, a clinically indispensable resource in maintaining the brain and nerve cells development and regeneration. Till now, NA has been found in 38 plant species, among which the garlic-fruit tree (Malania oleifera) has been evaluated to be the best candidate for NA production. Here, we generated a high-quality chromosome-scale assembly of M. oleifera employing PacBio long-read, short-read Illumina as well as Hi-C sequencing data. The genome assembly consisted of 1.5 Gb with a contig N50 of {\textasciitilde}4.9 Mb and a scaffold N50 of {\textasciitilde}112.6 Mb. {\textasciitilde}98.2\% of the assembly was anchored into 13 pseudo-chromosomes. It contains {\textasciitilde}1123 Mb repeat sequences, and 27,638 protein-coding genes, 568 tRNAs, 230 rRNAs and 352 other non-coding RNAs. Additionally, we documented candidate genes involved in NA biosynthesis including 20 KCSs, 4 KCRs, 1 HCD and 1 ECR, and profiled the expression patterns of these genes in developing seeds. The high-quality assembly of the genome provides insights into the genome evolution of the M. oleifera genome and candidate genes involved in NA biosynthesis in the seeds of this important woody tree.},
	language = {en},
	number = {1},
	urldate = {2023-05-26},
	journal = {Scientific Data},
	author = {Yang, Tianquan and Zhang, Rengang and Tian, Xiaoling and Yao, Gang and Shen, Yuanting and Wang, Sihai and Mao, Jianfeng and Li, Guangyuan and Liu, Aizhong and Sun, Weibang and Ma, Yongpeng},
	month = may,
	year = {2023},
	note = {Number: 1
Publisher: Nature Publishing Group},
	keywords = {Genome, Genomics},
	pages = {298},
}

Nervonic acid (C24:1 Δ15, NA) is a very long-chain monounsaturated fatty acid, a clinically indispensable resource in maintaining the brain and nerve cells development and regeneration. Till now, NA has been found in 38 plant species, among which the garlic-fruit tree (Malania oleifera) has been evaluated to be the best candidate for NA production. Here, we generated a high-quality chromosome-scale assembly of M. oleifera employing PacBio long-read, short-read Illumina as well as Hi-C sequencing data. The genome assembly consisted of 1.5 Gb with a contig N50 of ~4.9 Mb and a scaffold N50 of ~112.6 Mb. ~98.2% of the assembly was anchored into 13 pseudo-chromosomes. It contains ~1123 Mb repeat sequences, and 27,638 protein-coding genes, 568 tRNAs, 230 rRNAs and 352 other non-coding RNAs. Additionally, we documented candidate genes involved in NA biosynthesis including 20 KCSs, 4 KCRs, 1 HCD and 1 ECR, and profiled the expression patterns of these genes in developing seeds. The high-quality assembly of the genome provides insights into the genome evolution of the M. oleifera genome and candidate genes involved in NA biosynthesis in the seeds of this important woody tree.

@article{wieloch_model_2023,
	title = {A model of photosynthetic {CO2} assimilation in {C3} leaves accounting for respiration and energy recycling by the plastidial oxidative pentose phosphate pathway},
	volume = {n/a},
	issn = {1469-8137},
	url = {https://onlinelibrary.wiley.com/doi/abs/10.1111/nph.18965},
	doi = {10.1111/nph.18965},
	abstract = {Recently, we reported estimates of anaplerotic carbon flux through the oxidative pentose phosphate pathway (OPPP) in chloroplasts into the Calvin–Benson cycle. These estimates were based on intramolecular hydrogen isotope analysis of sunflower leaf starch. However, the isotope method is believed to underestimate the actual flux at low atmospheric CO2 concentration (Ca). Since the OPPP releases CO2 and reduces NADP+, it can be expected to affect leaf gas exchange under both rubisco- and RuBP-regeneration-limited conditions. Therefore, we expanded Farquhar-von Caemmerer–Berry models to account for OPPP metabolism. Based on model parameterisation with values from the literature, we estimated OPPP-related effects on leaf carbon and energy metabolism in the sunflowers analysed previously. We found that flux through the plastidial OPPP increases both above and below Ca ≈ 450 ppm (the condition the plants were acclimated to). This is qualitatively consistent with our previous isotope-based estimates, yet gas-exchange-based estimates are larger at low Ca. We discuss our results in relation to regulatory properties of the plastidial and cytosolic OPPP, the proposed variability of CO2 mesophyll conductance, and the contribution of day respiration to the A/Ci curve drop at high Ca. Furthermore, we critically examine the models and parameterisation and derive recommendations for follow-up studies.},
	language = {en},
	number = {n/a},
	urldate = {2023-05-24},
	journal = {New Phytologist},
	author = {Wieloch, Thomas and Augusti, Angela and Schleucher, Jürgen},
	month = may,
	year = {2023},
	keywords = {ATP : NADPH ratio, CO2 mesophyll conductance, Calvin–Benson cycle, Farquhar-von Caemmerer–Berry photosynthesis model, day respiration, glucose-6-phosphate shunt, net CO2 assimilation, oxidative pentose phosphate pathway},
}

Recently, we reported estimates of anaplerotic carbon flux through the oxidative pentose phosphate pathway (OPPP) in chloroplasts into the Calvin–Benson cycle. These estimates were based on intramolecular hydrogen isotope analysis of sunflower leaf starch. However, the isotope method is believed to underestimate the actual flux at low atmospheric CO2 concentration (Ca). Since the OPPP releases CO2 and reduces NADP+, it can be expected to affect leaf gas exchange under both rubisco- and RuBP-regeneration-limited conditions. Therefore, we expanded Farquhar-von Caemmerer–Berry models to account for OPPP metabolism. Based on model parameterisation with values from the literature, we estimated OPPP-related effects on leaf carbon and energy metabolism in the sunflowers analysed previously. We found that flux through the plastidial OPPP increases both above and below Ca ≈ 450 ppm (the condition the plants were acclimated to). This is qualitatively consistent with our previous isotope-based estimates, yet gas-exchange-based estimates are larger at low Ca. We discuss our results in relation to regulatory properties of the plastidial and cytosolic OPPP, the proposed variability of CO2 mesophyll conductance, and the contribution of day respiration to the A/Ci curve drop at high Ca. Furthermore, we critically examine the models and parameterisation and derive recommendations for follow-up studies.

@article{qu_functional_2023,
	title = {Functional significance of asymmetrical retention of parental alleles in a hybrid pine species complex},
	issn = {1759-6831},
	url = {https://onlinelibrary.wiley.com/doi/abs/10.1111/jse.12953},
	doi = {10.1111/jse.12953},
	abstract = {Hybrid genomes usually harbor asymmetrical parental contributions. However, it is challenging to infer the functional significance of asymmetrical retention of parental alleles in hybrid populations of conifer trees. Here we investigated the diversity in the glutathione S-transferase (GST) gene family in a hybrid pine Pinus densata and its parents (Pinus tabuliformis and Pinus yunnanensis). Plant GSTs play major roles in protecting plants against biotic and abiotic stresses. In this study, 19 orthologous groups of GST genes were identified and cloned from these three species. We examined their expression in different tissues, and then purified the corresponding proteins to characterize their enzymatic activities and specificities toward different substrates. We found that among the 19 GST orthologous groups, divergence in gene expression and in enzymatic activities toward different substrates was prevalent. P. densata preferentially retained P. yunnanensis-like GSTs for 17 out of the 19 gene loci. We determined the first GST crystal structure from conifer species at a resolution of 2.19 Å. Based on this structure, we performed site-directed mutagenesis to replace amino acid residuals in different wild-types of GSTs to understand their functional impacts. Reciprocal replacement of amino acid residuals in native GSTs of P. densata and P. tabuliformis demonstrated significant changes in enzyme functions and identified key sites controlling GSTs activities. This study illustrates an approach to evaluating the functional significance of sequence variations in conifer genomes. Our study also sheds light on plausible mechanisms for controlling the selective retention of parental alleles in the P. densata genome.},
	language = {en},
	urldate = {2023-04-28},
	journal = {Journal of Systematics and Evolution},
	author = {Qu, Chang and Kao, Hong-Na and Xu, Hui and Wang, Bao-Sheng and Yang, Zhi-Ling and Yang, Qi and Liu, Gui-Feng and Wang, Xiao-Ru and Liu, Yan-Jing and Zeng, Qing-Yin},
	month = mar,
	year = {2023},
	note = {\_eprint: https://onlinelibrary.wiley.com/doi/pdf/10.1111/jse.12953},
	keywords = {enzymatic function, functional divergence, gene expression, glutathione S-transferases, homoploid hybrid species},
}

Hybrid genomes usually harbor asymmetrical parental contributions. However, it is challenging to infer the functional significance of asymmetrical retention of parental alleles in hybrid populations of conifer trees. Here we investigated the diversity in the glutathione S-transferase (GST) gene family in a hybrid pine Pinus densata and its parents (Pinus tabuliformis and Pinus yunnanensis). Plant GSTs play major roles in protecting plants against biotic and abiotic stresses. In this study, 19 orthologous groups of GST genes were identified and cloned from these three species. We examined their expression in different tissues, and then purified the corresponding proteins to characterize their enzymatic activities and specificities toward different substrates. We found that among the 19 GST orthologous groups, divergence in gene expression and in enzymatic activities toward different substrates was prevalent. P. densata preferentially retained P. yunnanensis-like GSTs for 17 out of the 19 gene loci. We determined the first GST crystal structure from conifer species at a resolution of 2.19 Å. Based on this structure, we performed site-directed mutagenesis to replace amino acid residuals in different wild-types of GSTs to understand their functional impacts. Reciprocal replacement of amino acid residuals in native GSTs of P. densata and P. tabuliformis demonstrated significant changes in enzyme functions and identified key sites controlling GSTs activities. This study illustrates an approach to evaluating the functional significance of sequence variations in conifer genomes. Our study also sheds light on plausible mechanisms for controlling the selective retention of parental alleles in the P. densata genome.

@article{aryal_lrr_2023,
	title = {An {LRR} receptor kinase controls {ABC} transporter substrate preferences during plant growth-defense decisions},
	volume = {33},
	issn = {0960-9822},
	url = {https://www.cell.com/current-biology/abstract/S0960-9822(23)00477-3},
	doi = {10.1016/j.cub.2023.04.029},
	abstract = {The exporter of the auxin precursor indole-3-butyric acid (IBA), ABCG36/PDR8/PEN3, from the model plant Arabidopsis has recently been proposed to also function in the transport of the phytoalexin camalexin. Based on these bonafide substrates, it has been suggested that ABCG36 functions at the interface between growth and defense.
Here, we provide evidence that ABCG36 catalyzes the direct, ATP-dependent export of camalexin across the plasma membrane. We identify the leucine-rich repeat receptor kinase, QIAN SHOU KINASE1 (QSK1), as a functional kinase that physically interacts with and phosphorylates ABCG36. Phosphorylation of ABCG36 by QSK1 unilaterally represses IBA export, allowing camalexin export by ABCG36 conferring pathogen resistance. As a consequence, phospho-dead mutants of ABCG36, as well as qsk1 and abcg36 alleles, are hypersensitive to infection with the root pathogen Fusarium oxysporum, caused by elevated fungal progression.
Our findings indicate a direct regulatory circuit between a receptor kinase and an ABC transporter that functions to control transporter substrate preference during plant growth and defense balance decisions.},
	language = {English},
	number = {10},
	urldate = {2023-05-24},
	journal = {Current Biology},
	author = {Aryal, Bibek and Xia, Jian and Hu, Zehan and Stumpe, Michael and Tsering, Tashi and Liu, Jie and Huynh, John and Fukao, Yoichiro and Glöckner, Nina and Huang, Hsin-Yao and Sáncho-Andrés, Gloria and Pakula, Konrad and Ziegler, Joerg and Gorzolka, Karin and Zwiewka, Marta and Nodzynski, Tomasz and Harter, Klaus and Sánchez-Rodríguez, Clara and Jasiński, Michał and Rosahl, Sabine and Geisler, Markus M.},
	month = may,
	year = {2023},
	keywords = {ABCG36, Arabidopsis thaliana, Botrytis cinerea, Fusarium oxysporum, IBA, PDR8, PEN3, Phytophtora infestans, QSK1, auxin, camalexin, defense, growth},
	pages = {2008--2023.e8},
}

The exporter of the auxin precursor indole-3-butyric acid (IBA), ABCG36/PDR8/PEN3, from the model plant Arabidopsis has recently been proposed to also function in the transport of the phytoalexin camalexin. Based on these bonafide substrates, it has been suggested that ABCG36 functions at the interface between growth and defense. Here, we provide evidence that ABCG36 catalyzes the direct, ATP-dependent export of camalexin across the plasma membrane. We identify the leucine-rich repeat receptor kinase, QIAN SHOU KINASE1 (QSK1), as a functional kinase that physically interacts with and phosphorylates ABCG36. Phosphorylation of ABCG36 by QSK1 unilaterally represses IBA export, allowing camalexin export by ABCG36 conferring pathogen resistance. As a consequence, phospho-dead mutants of ABCG36, as well as qsk1 and abcg36 alleles, are hypersensitive to infection with the root pathogen Fusarium oxysporum, caused by elevated fungal progression. Our findings indicate a direct regulatory circuit between a receptor kinase and an ABC transporter that functions to control transporter substrate preference during plant growth and defense balance decisions.

@article{jobert_auxin_2023,
	title = {Auxin as an architect of the pectin matrix},
	issn = {0022-0957},
	url = {https://doi.org/10.1093/jxb/erad174},
	doi = {10.1093/jxb/erad174},
	abstract = {Auxin is a versatile plant growth regulator that triggers multiple signalling pathways at different spatial and temporal resolutions. A plant cell is surrounded by the cell wall, a complex and dynamic network of polysaccharides. The cell wall needs to be rigid to provide mechanical support and protection and highly flexible to allow cell growth and shape acquisition. The modification of the pectin components, among other processes, is a mechanism by which auxin activity alters the mechanical properties of the cell wall. Auxin signalling precisely controls the transcriptional output of several pectin remodelling enzyme-encoded genes, their local activity and pectin deposition and modulation in different developmental contexts. This review examines the mechanism of auxin activity in regulating pectin chemistry at organ, cellular and subcellular levels across diverse plant species and asks questions that remain to be addressed to fully understand the interplay between auxin and pectin in plant growth and development.},
	urldate = {2023-05-19},
	journal = {Journal of Experimental Botany},
	author = {Jobert, François and Yadav, Sandeep and Robert, Stéphanie},
	month = may,
	year = {2023},
	pages = {erad174},
}

Auxin is a versatile plant growth regulator that triggers multiple signalling pathways at different spatial and temporal resolutions. A plant cell is surrounded by the cell wall, a complex and dynamic network of polysaccharides. The cell wall needs to be rigid to provide mechanical support and protection and highly flexible to allow cell growth and shape acquisition. The modification of the pectin components, among other processes, is a mechanism by which auxin activity alters the mechanical properties of the cell wall. Auxin signalling precisely controls the transcriptional output of several pectin remodelling enzyme-encoded genes, their local activity and pectin deposition and modulation in different developmental contexts. This review examines the mechanism of auxin activity in regulating pectin chemistry at organ, cellular and subcellular levels across diverse plant species and asks questions that remain to be addressed to fully understand the interplay between auxin and pectin in plant growth and development.

@article{wu_threatened_2023,
	title = {Threatened forests},
	volume = {24},
	issn = {1469-221X},
	url = {https://www.embopress.org/doi/full/10.15252/embr.202357106},
	doi = {10.15252/embr.202357106},
	abstract = {Climate change is having dramatic effects on forest health and growth ? tree genomics provides tools for understanding and mitigating these effects.},
	number = {5},
	urldate = {2023-05-12},
	journal = {EMBO reports},
	author = {Wu, Harry and Nilsson, Ove},
	month = may,
	year = {2023},
	note = {Publisher: John Wiley \& Sons, Ltd},
	pages = {e57106},
}

Climate change is having dramatic effects on forest health and growth ? tree genomics provides tools for understanding and mitigating these effects.

@article{dube_transcriptomics_2023,
	title = {Transcriptomics of ivermectin response in {Caenorhabditis} elegans: {Integrating} abamectin quantitative trait loci and comparison to the {Ivermectin}-exposed {DA1316} strain},
	volume = {18},
	issn = {1932-6203},
	shorttitle = {Transcriptomics of ivermectin response in {Caenorhabditis} elegans},
	url = {https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0285262},
	doi = {10.1371/journal.pone.0285262},
	abstract = {Parasitic nematodes pose a significant threat to human and animal health, as well as cause economic losses in the agricultural sector. The use of anthelmintic drugs, such as Ivermectin (IVM), to control these parasites has led to widespread drug resistance. Identifying genetic markers of resistance in parasitic nematodes can be challenging, but the free-living nematode Caenorhabditis elegans provides a suitable model. In this study, we aimed to analyze the transcriptomes of adult C. elegans worms of the N2 strain exposed to the anthelmintic drug Ivermectin (IVM), and compare them to those of the resistant strain DA1316 and the recently identified Abamectin Quantitative Trait Loci (QTL) on chromosome V. We exposed pools of 300 adult N2 worms to IVM (10−7 and 10−8 M) for 4 hours at 20°C, extracted total RNA and sequenced it on the Illumina NovaSeq6000 platform. Differentially expressed genes (DEGs) were determined using an in-house pipeline. The DEGs were compared to genes from a previous microarray study on IVM-resistant C. elegans and Abamectin-QTL. Our results revealed 615 DEGs (183 up-regulated and 432 down-regulated genes) from diverse gene families in the N2 C. elegans strain. Of these DEGs, 31 overlapped with genes from IVM-exposed adult worms of the DA1316 strain. We identified 19 genes, including the folate transporter (folt-2) and the transmembrane transporter (T22F3.11), which exhibited an opposite expression in N2 and the DA1316 strain and were deemed potential candidates. Additionally, we compiled a list of potential candidates for further research including T-type calcium channel (cca-1), potassium chloride cotransporter (kcc-2), as well as other genes such as glutamate-gated channel (glc-1) that mapped to the Abamectin-QTL.},
	language = {en},
	number = {5},
	urldate = {2023-05-12},
	journal = {PLOS ONE},
	author = {Dube, Faruk and Hinas, Andrea and Delhomme, Nicolas and Åbrink, Magnus and Svärd, Staffan and Tydén, Eva},
	year = {2023},
	note = {Publisher: Public Library of Science},
	keywords = {Apoptosis, Caenorhabditis elegans, Gene expression, Quantitative trait loci, Transcription factors, Transcriptional control, Transmembrane receptors, Transmembrane transport proteins},
	pages = {e0285262},
}

Parasitic nematodes pose a significant threat to human and animal health, as well as cause economic losses in the agricultural sector. The use of anthelmintic drugs, such as Ivermectin (IVM), to control these parasites has led to widespread drug resistance. Identifying genetic markers of resistance in parasitic nematodes can be challenging, but the free-living nematode Caenorhabditis elegans provides a suitable model. In this study, we aimed to analyze the transcriptomes of adult C. elegans worms of the N2 strain exposed to the anthelmintic drug Ivermectin (IVM), and compare them to those of the resistant strain DA1316 and the recently identified Abamectin Quantitative Trait Loci (QTL) on chromosome V. We exposed pools of 300 adult N2 worms to IVM (10−7 and 10−8 M) for 4 hours at 20°C, extracted total RNA and sequenced it on the Illumina NovaSeq6000 platform. Differentially expressed genes (DEGs) were determined using an in-house pipeline. The DEGs were compared to genes from a previous microarray study on IVM-resistant C. elegans and Abamectin-QTL. Our results revealed 615 DEGs (183 up-regulated and 432 down-regulated genes) from diverse gene families in the N2 C. elegans strain. Of these DEGs, 31 overlapped with genes from IVM-exposed adult worms of the DA1316 strain. We identified 19 genes, including the folate transporter (folt-2) and the transmembrane transporter (T22F3.11), which exhibited an opposite expression in N2 and the DA1316 strain and were deemed potential candidates. Additionally, we compiled a list of potential candidates for further research including T-type calcium channel (cca-1), potassium chloride cotransporter (kcc-2), as well as other genes such as glutamate-gated channel (glc-1) that mapped to the Abamectin-QTL.

@article{zhao_haplotype-resolved_2023,
	title = {Haplotype-resolved genome assembly of {Coriaria} nepalensis a non-legume nitrogen-fixing shrub},
	volume = {10},
	copyright = {2023 The Author(s)},
	issn = {2052-4463},
	url = {https://www.nature.com/articles/s41597-023-02171-6},
	doi = {10.1038/s41597-023-02171-6},
	abstract = {Coriaria nepalensis Wall. (Coriariaceae) is a nitrogen-fixing shrub which forms root nodules with the actinomycete Frankia. Oils and extracts of C. nepalensis have been reported to be bacteriostatic and insecticidal, and C. nepalensis bark provides a valuable tannin resource. Here, by combining PacBio HiFi sequencing and Hi-C scaffolding techniques, we generated a haplotype-resolved chromosome-scale genome assembly for C. nepalensis. This genome assembly is approximately 620 Mb in size with a contig N50 of 11 Mb, with 99.9\% of the total assembled sequences anchored to 40 pseudochromosomes. We predicted 60,862 protein-coding genes of which 99.5\% were annotated from databases. We further identified 939 tRNAs, 7,297 rRNAs, and 982 ncRNAs. The chromosome-scale genome of C. nepalensis is expected to be a significant resource for understanding the genetic basis of root nodulation with Frankia, toxicity, and tannin biosynthesis.},
	language = {en},
	number = {1},
	urldate = {2023-05-12},
	journal = {Scientific Data},
	author = {Zhao, Shi-Wei and Guo, Jing-Fang and Kong, Lei and Nie, Shuai and Yan, Xue-Mei and Shi, Tian-Le and Tian, Xue-Chan and Ma, Hai-Yao and Bao, Yu-Tao and Li, Zhi-Chao and Chen, Zhao-Yang and Zhang, Ren-Gang and Ma, Yong-Peng and El-Kassaby, Yousry A. and Porth, Ilga and Zhao, Wei and Mao, Jian-Feng},
	month = may,
	year = {2023},
	note = {Number: 1
Publisher: Nature Publishing Group},
	keywords = {Computational biology and bioinformatics, Plant sciences},
	pages = {259},
}

Coriaria nepalensis Wall. (Coriariaceae) is a nitrogen-fixing shrub which forms root nodules with the actinomycete Frankia. Oils and extracts of C. nepalensis have been reported to be bacteriostatic and insecticidal, and C. nepalensis bark provides a valuable tannin resource. Here, by combining PacBio HiFi sequencing and Hi-C scaffolding techniques, we generated a haplotype-resolved chromosome-scale genome assembly for C. nepalensis. This genome assembly is approximately 620 Mb in size with a contig N50 of 11 Mb, with 99.9% of the total assembled sequences anchored to 40 pseudochromosomes. We predicted 60,862 protein-coding genes of which 99.5% were annotated from databases. We further identified 939 tRNAs, 7,297 rRNAs, and 982 ncRNAs. The chromosome-scale genome of C. nepalensis is expected to be a significant resource for understanding the genetic basis of root nodulation with Frankia, toxicity, and tannin biosynthesis.

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

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

@article{wang_chromosome-scale_2023,
	title = {Chromosome-scale genome assembly and insights into the metabolome and gene regulation of leaf color transition in an important oak species, {Quercus} dentata},
	volume = {238},
	issn = {1469-8137},
	url = {https://onlinelibrary.wiley.com/doi/abs/10.1111/nph.18814},
	doi = {10.1111/nph.18814},
	abstract = {Quercus dentata Thunb., a dominant forest tree species in northern China, has significant ecological and ornamental value due to its adaptability and beautiful autumn coloration, with color changes from green to yellow into red resulting from the autumnal shifts in leaf pigmentation. However, the key genes and molecular regulatory mechanisms for leaf color transition remain to be investigated. First, we presented a high-quality chromosome-scale assembly for Q. dentata. This 893.54 Mb sized genome (contig N50 = 4.21 Mb, scaffold N50 = 75.55 Mb; 2n = 24) harbors 31 584 protein-coding genes. Second, our metabolome analyses uncovered pelargonidin-3-O-glucoside, cyanidin-3-O-arabinoside, and cyanidin-3-O-glucoside as the main pigments involved in leaf color transition. Third, gene co-expression further identified the MYB-bHLH-WD40 (MBW) transcription activation complex as central to anthocyanin biosynthesis regulation. Notably, transcription factor (TF) QdNAC (QD08G038820) was highly co-expressed with this MBW complex and may regulate anthocyanin accumulation and chlorophyll degradation during leaf senescence through direct interaction with another TF, QdMYB (QD01G020890), as revealed by our further protein–protein and DNA–protein interaction assays. Our high-quality genome assembly, metabolome, and transcriptome resources further enrich Quercus genomics and will facilitate upcoming exploration of ornamental values and environmental adaptability in this important genus.},
	language = {en},
	number = {5},
	urldate = {2023-05-05},
	journal = {New Phytologist},
	author = {Wang, Wen-Bo and He, Xiang-Feng and Yan, Xue-Mei and Ma, Bo and Lu, Cun-Fu and Wu, Jing and Zheng, Yi and Wang, Wen-He and Xue, Wen-Bo and Tian, Xue-Chan and Guo, Jing-Fang and El-Kassaby, Yousry A. and Porth, Ilga and Leng, Ping-Sheng and Hu, Zeng-Hui and Mao, Jian-Feng},
	year = {2023},
	note = {\_eprint: https://onlinelibrary.wiley.com/doi/pdf/10.1111/nph.18814},
	keywords = {Quercus, co-expression network, flavonoids, gene regulation, leaf color transition},
	pages = {2016--2032},
}

Quercus dentata Thunb., a dominant forest tree species in northern China, has significant ecological and ornamental value due to its adaptability and beautiful autumn coloration, with color changes from green to yellow into red resulting from the autumnal shifts in leaf pigmentation. However, the key genes and molecular regulatory mechanisms for leaf color transition remain to be investigated. First, we presented a high-quality chromosome-scale assembly for Q. dentata. This 893.54 Mb sized genome (contig N50 = 4.21 Mb, scaffold N50 = 75.55 Mb; 2n = 24) harbors 31 584 protein-coding genes. Second, our metabolome analyses uncovered pelargonidin-3-O-glucoside, cyanidin-3-O-arabinoside, and cyanidin-3-O-glucoside as the main pigments involved in leaf color transition. Third, gene co-expression further identified the MYB-bHLH-WD40 (MBW) transcription activation complex as central to anthocyanin biosynthesis regulation. Notably, transcription factor (TF) QdNAC (QD08G038820) was highly co-expressed with this MBW complex and may regulate anthocyanin accumulation and chlorophyll degradation during leaf senescence through direct interaction with another TF, QdMYB (QD01G020890), as revealed by our further protein–protein and DNA–protein interaction assays. Our high-quality genome assembly, metabolome, and transcriptome resources further enrich Quercus genomics and will facilitate upcoming exploration of ornamental values and environmental adaptability in this important genus.

@article{green_formate_2023,
	title = {Formate overflow drives toxic folate trapping in {MTHFD1} inhibited cancer cells},
	volume = {5},
	copyright = {2023 The Author(s)},
	issn = {2522-5812},
	url = {https://www.nature.com/articles/s42255-023-00771-5},
	doi = {10.1038/s42255-023-00771-5},
	abstract = {Cancer cells fuel their increased need for nucleotide supply by upregulating one-carbon (1C) metabolism, including the enzymes methylenetetrahydrofolate dehydrogenase–cyclohydrolase 1 and 2 (MTHFD1 and MTHFD2). TH9619 is a potent inhibitor of dehydrogenase and cyclohydrolase activities in both MTHFD1 and MTHFD2, and selectively kills cancer cells. Here, we reveal that, in cells, TH9619 targets nuclear MTHFD2 but does not inhibit mitochondrial MTHFD2. Hence, overflow of formate from mitochondria continues in the presence of TH9619. TH9619 inhibits the activity of MTHFD1 occurring downstream of mitochondrial formate release, leading to the accumulation of 10-formyl-tetrahydrofolate, which we term a ‘folate trap’. This results in thymidylate depletion and death of MTHFD2-expressing cancer cells. This previously uncharacterized folate trapping mechanism is exacerbated by physiological hypoxanthine levels that block the de novo purine synthesis pathway, and additionally prevent 10-formyl-tetrahydrofolate consumption for purine synthesis. The folate trapping mechanism described here for TH9619 differs from other MTHFD1/2 inhibitors and antifolates. Thus, our findings uncover an approach to attack cancer and reveal a regulatory mechanism in 1C metabolism.},
	language = {en},
	number = {4},
	urldate = {2023-05-05},
	journal = {Nature Metabolism},
	author = {Green, Alanna C. and Marttila, Petra and Kiweler, Nicole and Chalkiadaki, Christina and Wiita, Elisée and Cookson, Victoria and Lesur, Antoine and Eiden, Kim and Bernardin, François and Vallin, Karl S. A. and Borhade, Sanjay and Long, Maeve and Ghahe, Elahe Kamali and Jiménez-Alonso, Julio J. and Jemth, Ann-Sofie and Loseva, Olga and Mortusewicz, Oliver and Meyers, Marianne and Viry, Elodie and Johansson, Annika I. and Hodek, Ondřej and Homan, Evert and Bonagas, Nadilly and Ramos, Louise and Sandberg, Lars and Frödin, Morten and Moussay, Etienne and Slipicevic, Ana and Letellier, Elisabeth and Paggetti, Jérôme and Sørensen, Claus Storgaard and Helleday, Thomas and Henriksson, Martin and Meiser, Johannes},
	month = apr,
	year = {2023},
	note = {Number: 4
Publisher: Nature Publishing Group},
	keywords = {Cancer metabolism, Cell death, Metabolism},
	pages = {642--659},
}

Cancer cells fuel their increased need for nucleotide supply by upregulating one-carbon (1C) metabolism, including the enzymes methylenetetrahydrofolate dehydrogenase–cyclohydrolase 1 and 2 (MTHFD1 and MTHFD2). TH9619 is a potent inhibitor of dehydrogenase and cyclohydrolase activities in both MTHFD1 and MTHFD2, and selectively kills cancer cells. Here, we reveal that, in cells, TH9619 targets nuclear MTHFD2 but does not inhibit mitochondrial MTHFD2. Hence, overflow of formate from mitochondria continues in the presence of TH9619. TH9619 inhibits the activity of MTHFD1 occurring downstream of mitochondrial formate release, leading to the accumulation of 10-formyl-tetrahydrofolate, which we term a ‘folate trap’. This results in thymidylate depletion and death of MTHFD2-expressing cancer cells. This previously uncharacterized folate trapping mechanism is exacerbated by physiological hypoxanthine levels that block the de novo purine synthesis pathway, and additionally prevent 10-formyl-tetrahydrofolate consumption for purine synthesis. The folate trapping mechanism described here for TH9619 differs from other MTHFD1/2 inhibitors and antifolates. Thus, our findings uncover an approach to attack cancer and reveal a regulatory mechanism in 1C metabolism.

@article{giaume_two_2023,
	title = {Two florigens and a florigen-like protein form a triple regulatory module at the shoot apical meristem to promote reproductive transitions in rice},
	volume = {9},
	copyright = {2023 The Author(s), under exclusive licence to Springer Nature Limited},
	issn = {2055-0278},
	url = {https://www.nature.com/articles/s41477-023-01383-3},
	doi = {10.1038/s41477-023-01383-3},
	abstract = {Many plant species monitor and respond to changes in day length (photoperiod) for aligning reproduction with a favourable season. Day length is measured in leaves and, when appropriate, leads to the production of floral stimuli called florigens that are transmitted to the shoot apical meristem to initiate inflorescence development1. Rice possesses two florigens encoded by HEADING DATE 3a (Hd3a) and RICE FLOWERING LOCUS T 1 (RFT1)2. Here we show that the arrival of Hd3a and RFT1 at the shoot apical meristem activates FLOWERING LOCUS T-LIKE 1 (FT-L1), encoding a florigen-like protein that shows features partially differentiating it from typical florigens. FT-L1 potentiates the effects of Hd3a and RFT1 during the conversion of the vegetative meristem into an inflorescence meristem and organizes panicle branching by imposing increasing determinacy to distal meristems. A module comprising Hd3a, RFT1 and FT-L1 thus enables the initiation and balanced progression of panicle development towards determinacy.},
	language = {en},
	number = {4},
	urldate = {2023-04-28},
	journal = {Nature Plants},
	author = {Giaume, Francesca and Bono, Giulia Ave and Martignago, Damiano and Miao, Yiling and Vicentini, Giulio and Toriba, Taiyo and Wang, Rui and Kong, Dali and Cerise, Martina and Chirivì, Daniele and Biancucci, Marco and Khahani, Bahman and Morandini, Piero and Tameling, Wladimir and Martinotti, Michela and Goretti, Daniela and Coupland, George and Kater, Martin and Brambilla, Vittoria and Miki, Daisuke and Kyozuka, Junko and Fornara, Fabio},
	month = apr,
	year = {2023},
	note = {Number: 4
Publisher: Nature Publishing Group},
	keywords = {Flowering, Light responses, Plant signalling},
	pages = {525--534},
}

Many plant species monitor and respond to changes in day length (photoperiod) for aligning reproduction with a favourable season. Day length is measured in leaves and, when appropriate, leads to the production of floral stimuli called florigens that are transmitted to the shoot apical meristem to initiate inflorescence development1. Rice possesses two florigens encoded by HEADING DATE 3a (Hd3a) and RICE FLOWERING LOCUS T 1 (RFT1)2. Here we show that the arrival of Hd3a and RFT1 at the shoot apical meristem activates FLOWERING LOCUS T-LIKE 1 (FT-L1), encoding a florigen-like protein that shows features partially differentiating it from typical florigens. FT-L1 potentiates the effects of Hd3a and RFT1 during the conversion of the vegetative meristem into an inflorescence meristem and organizes panicle branching by imposing increasing determinacy to distal meristems. A module comprising Hd3a, RFT1 and FT-L1 thus enables the initiation and balanced progression of panicle development towards determinacy.

@article{guo_genomic_2023,
	title = {Genomic clines across the species boundary between a hybrid pine and its progenitor in the eastern {Tibetan} {Plateau}},
	issn = {2590-3462},
	url = {https://www.sciencedirect.com/science/article/pii/S259034622300072X},
	doi = {10.1016/j.xplc.2023.100574},
	abstract = {Most species have clearly defined distribution ranges and ecological niches. The genetic and ecological causes of species differentiation and the mechanisms that maintain species boundaries between newly evolved taxa and their progenitors are, however, less clearly defined. This study investigated the genetic structure and clines in Pinus densata, a pine of hybrid origin on the southeastern Tibetan Plateau, to gain an understanding of the contemporary dynamics of species barriers. We analyzed genetic diversity in a range-wide collection of P. densata and representative populations of its progenitors, Pinus tabuliformis and Pinus yunnanensis, using exome capture sequencing. We detected four distinct genetic groups within P. densata that reflect its migration history and major gene-flow barriers across the landscape. The demographies of these genetic groups in the Pleistocene were associated with regional glaciation histories. Interestingly, population sizes rebounded rapidly during interglacial periods, suggesting persistence and resilience of the species during the Quaternary ice age. In the contact zone between P. densata and P. yunnanensis, 3.36\% of the analyzed loci (57 849) showed exceptional patterns of introgression, suggesting their potential roles in either adaptive introgression or reproductive isolation. These outliers showed strong clines along critical climate gradients and enrichment in a number of biological processes relevant to high-altitude adaptation. This indicates that ecological selection played an important role in generating genomic heterogeneity and a genetic barrier across a zone of species transition. Our study highlights the forces that operate to maintain species boundaries and promote speciation in the Qinghai-Tibetan Plateau and other mountain systems.},
	language = {en},
	urldate = {2023-04-27},
	journal = {Plant Communications},
	author = {Guo, Jing-Fang and Zhao, Wei and Andersson, Bea and Mao, Jian-Feng and Wang, Xiao-Ru},
	month = mar,
	year = {2023},
	keywords = {demographic history, ecological selection, genomic cline, introgression outliers, reproductive isolation, species boundary},
	pages = {100574},
}

Most species have clearly defined distribution ranges and ecological niches. The genetic and ecological causes of species differentiation and the mechanisms that maintain species boundaries between newly evolved taxa and their progenitors are, however, less clearly defined. This study investigated the genetic structure and clines in Pinus densata, a pine of hybrid origin on the southeastern Tibetan Plateau, to gain an understanding of the contemporary dynamics of species barriers. We analyzed genetic diversity in a range-wide collection of P. densata and representative populations of its progenitors, Pinus tabuliformis and Pinus yunnanensis, using exome capture sequencing. We detected four distinct genetic groups within P. densata that reflect its migration history and major gene-flow barriers across the landscape. The demographies of these genetic groups in the Pleistocene were associated with regional glaciation histories. Interestingly, population sizes rebounded rapidly during interglacial periods, suggesting persistence and resilience of the species during the Quaternary ice age. In the contact zone between P. densata and P. yunnanensis, 3.36% of the analyzed loci (57 849) showed exceptional patterns of introgression, suggesting their potential roles in either adaptive introgression or reproductive isolation. These outliers showed strong clines along critical climate gradients and enrichment in a number of biological processes relevant to high-altitude adaptation. This indicates that ecological selection played an important role in generating genomic heterogeneity and a genetic barrier across a zone of species transition. Our study highlights the forces that operate to maintain species boundaries and promote speciation in the Qinghai-Tibetan Plateau and other mountain systems.

@article{li_methylation_2023,
	title = {The methylation landscape of giga-genome and the epigenetic timer of age in {Chinese} pine},
	volume = {14},
	copyright = {2023 The Author(s)},
	issn = {2041-1723},
	url = {https://www.nature.com/articles/s41467-023-37684-6},
	doi = {10.1038/s41467-023-37684-6},
	abstract = {DNA methylation level declines during aging of mammals. Here, the authors report single-base resolution landscape of cytosine DNA methylation at different ages of Chinese pine and show that the global cytosine DNA methylation gradually increases as age progresses.},
	language = {en},
	number = {1},
	urldate = {2023-04-21},
	journal = {Nature Communications},
	author = {Li, Jiang and Han, Fangxu and Yuan, Tongqi and Li, Wei and Li, Yue and Wu, Harry X. and Wei, Hairong and Niu, Shihui},
	month = apr,
	year = {2023},
	note = {Number: 1
Publisher: Nature Publishing Group},
	keywords = {Agricultural genetics, DNA methylation, Plant development, Plant genetics},
	pages = {1--11},
}

DNA methylation level declines during aging of mammals. Here, the authors report single-base resolution landscape of cytosine DNA methylation at different ages of Chinese pine and show that the global cytosine DNA methylation gradually increases as age progresses.

@article{donev_field_2023,
	title = ,
	volume = {21},
	issn = {1467-7652},
	url = {https://onlinelibrary.wiley.com/doi/abs/10.1111/pbi.14012},
	doi = {10.1111/pbi.14012},
	abstract = {Trees constitute promising renewable feedstocks for biorefinery using biochemical conversion, but their recalcitrance restricts their attractiveness for the industry. To obtain trees with reduced recalcitrance, large-scale genetic engineering experiments were performed in hybrid aspen blindly targeting genes expressed during wood formation and 32 lines representing seven constructs were selected for characterization in the field. Here we report phenotypes of five-year old trees considering 49 traits related to growth and wood properties. The best performing construct considering growth and glucose yield in saccharification with acid pretreatment had suppressed expression of the gene encoding an uncharacterized 2-oxoglutarate-dependent dioxygenase (2OGD). It showed minor changes in wood chemistry but increased nanoporosity and glucose conversion. Suppressed levels of SUCROSE SYNTHASE, (SuSy), CINNAMATE 4-HYDROXYLASE (C4H) and increased levels of GTPase activating protein for ADP-ribosylation factor ZAC led to significant growth reductions and anatomical abnormalities. However, C4H and SuSy constructs greatly improved glucose yields in saccharification without and with pretreatment, respectively. Traits associated with high glucose yields were different for saccharification with and without pretreatment. While carbohydrates, phenolics and tension wood contents positively impacted the yields without pretreatment and growth, lignin content and S/G ratio were negative factors, the yields with pretreatment positively correlated with S lignin and negatively with carbohydrate contents. The genotypes with high glucose yields had increased nanoporosity and mGlcA/Xyl ratio, and some had shorter polymers extractable with subcritical water compared to wild-type. The pilot-scale industrial-like pretreatment of best-performing 2OGD construct confirmed its superior sugar yields, supporting our strategy.},
	language = {en},
	number = {5},
	urldate = {2023-04-21},
	journal = {Plant Biotechnology Journal},
	author = {Donev, Evgeniy N. and Derba-Maceluch, Marta and Yassin, Zakiya and Gandla, Madhavi Latha and Pramod, Sivan and Heinonen, Emilia and Kumar, Vikash and Scheepers, Gerhard and Vilaplana, Francisco and Johansson, Ulf and Hertzberg, Magnus and Sundberg, Björn and Winestrand, Sandra and Hörnberg, Andreas and Alriksson, Björn and Jönsson, Leif J. and Mellerowicz, Ewa J.},
	year = {2023},
	note = {\_eprint: https://onlinelibrary.wiley.com/doi/pdf/10.1111/pbi.14012},
	keywords = {BET analysis, Populus, SilviScan, enzymatic saccharification, field trial, secondary cell wall, subcritical water extraction, transgenic Populus, transgenic trees, wood quality},
	pages = {1005--1021},
}

Trees constitute promising renewable feedstocks for biorefinery using biochemical conversion, but their recalcitrance restricts their attractiveness for the industry. To obtain trees with reduced recalcitrance, large-scale genetic engineering experiments were performed in hybrid aspen blindly targeting genes expressed during wood formation and 32 lines representing seven constructs were selected for characterization in the field. Here we report phenotypes of five-year old trees considering 49 traits related to growth and wood properties. The best performing construct considering growth and glucose yield in saccharification with acid pretreatment had suppressed expression of the gene encoding an uncharacterized 2-oxoglutarate-dependent dioxygenase (2OGD). It showed minor changes in wood chemistry but increased nanoporosity and glucose conversion. Suppressed levels of SUCROSE SYNTHASE, (SuSy), CINNAMATE 4-HYDROXYLASE (C4H) and increased levels of GTPase activating protein for ADP-ribosylation factor ZAC led to significant growth reductions and anatomical abnormalities. However, C4H and SuSy constructs greatly improved glucose yields in saccharification without and with pretreatment, respectively. Traits associated with high glucose yields were different for saccharification with and without pretreatment. While carbohydrates, phenolics and tension wood contents positively impacted the yields without pretreatment and growth, lignin content and S/G ratio were negative factors, the yields with pretreatment positively correlated with S lignin and negatively with carbohydrate contents. The genotypes with high glucose yields had increased nanoporosity and mGlcA/Xyl ratio, and some had shorter polymers extractable with subcritical water compared to wild-type. The pilot-scale industrial-like pretreatment of best-performing 2OGD construct confirmed its superior sugar yields, supporting our strategy.

@article{hodek_structural_2023,
	title = {Structural elucidation of 3-nitrophenylhydrazine derivatives of tricarboxylic acid cycle acids and optimization of their fragmentation to boost sensitivity in liquid chromatography-mass spectrometry},
	volume = {1222},
	issn = {1570-0232},
	url = {https://www.sciencedirect.com/science/article/pii/S1570023223001290},
	doi = {10.1016/j.jchromb.2023.123719},
	abstract = {Carboxylic acids participate in many metabolic pathways including tricarboxylic acid (TCA) cycle. Therefore, there have been ongoing attempts to develop sensitive liquid chromatography-mass spectrometry methods over the last decades. Derivatization of the carboxylic acids with 3-nitrophenylhydrazine presents a well-established methodology, and yet the derivatized species of polycarboxylic acids and their fragmentation in collision-induced dissociation have not been fully studied before. In our study, we elucidated how annotation of most abundant 3-nitrophenylhydrazine derivatives and optimization of their fragmentation in multiple reaction monitoring can boost the sensitivity, especially for polycarboxylic acids. Finally, the optimized liquid chromatography-tandem mass spectrometry method allowed for low detection limits ranging from 10 pM for 2-oxoglutaric acid to 800 pM for pyruvic acid. All TCA carboxylates were quantified in 20 µL of human plasma and the targeted method was validated in the same matrix. The same methodology with a modified gradient elution was also applied to untargeted screening of fatty acids by using high-resolution mass spectrometry enabling identification of 29 medium- to long-chain fatty acids in human plasma. The TCA carboxylates were also quantified in 105 of C2C12 mouse myuotube cells grown under different treatments to proof applicability of the methodology to biological studies in a wider sense. However, unfortunately all the TCA carboxylates were also found in the derivatized blanks in substantial amounts, which prevents from using the methodology for quantification of the carboxylates in less than 105 cells.},
	language = {en},
	urldate = {2023-04-21},
	journal = {Journal of Chromatography B},
	author = {Hodek, Ondřej and Henderson, John and Argemi-Muntadas, Lidia and Khan, Adnan and Moritz, Thomas},
	month = apr,
	year = {2023},
	keywords = {3-nitrophenylhydrazine, Carboxylic acid, Derivatization, Liquid chromatography-mass spectrometry},
	pages = {123719},
}

Carboxylic acids participate in many metabolic pathways including tricarboxylic acid (TCA) cycle. Therefore, there have been ongoing attempts to develop sensitive liquid chromatography-mass spectrometry methods over the last decades. Derivatization of the carboxylic acids with 3-nitrophenylhydrazine presents a well-established methodology, and yet the derivatized species of polycarboxylic acids and their fragmentation in collision-induced dissociation have not been fully studied before. In our study, we elucidated how annotation of most abundant 3-nitrophenylhydrazine derivatives and optimization of their fragmentation in multiple reaction monitoring can boost the sensitivity, especially for polycarboxylic acids. Finally, the optimized liquid chromatography-tandem mass spectrometry method allowed for low detection limits ranging from 10 pM for 2-oxoglutaric acid to 800 pM for pyruvic acid. All TCA carboxylates were quantified in 20 µL of human plasma and the targeted method was validated in the same matrix. The same methodology with a modified gradient elution was also applied to untargeted screening of fatty acids by using high-resolution mass spectrometry enabling identification of 29 medium- to long-chain fatty acids in human plasma. The TCA carboxylates were also quantified in 105 of C2C12 mouse myuotube cells grown under different treatments to proof applicability of the methodology to biological studies in a wider sense. However, unfortunately all the TCA carboxylates were also found in the derivatized blanks in substantial amounts, which prevents from using the methodology for quantification of the carboxylates in less than 105 cells.

@article{bizjak_presence_2023,
	title = {Presence and activity of nitrogen-fixing bacteria in {Scots} pine needles in a boreal forest: a nitrogen-addition experiment},
	issn = {1758-4469},
	shorttitle = {Presence and activity of nitrogen-fixing bacteria in {Scots} pine needles in a boreal forest},
	url = {https://doi.org/10.1093/treephys/tpad048},
	doi = {10.1093/treephys/tpad048},
	abstract = {Endophytic nitrogen-fixing bacteria have been detected and isolated from the needles of conifer trees growing in North American boreal forests. Because boreal forests are nutrient-limited, these bacteria could provide an important source of nitrogen for tree species. The aim of this study was to determine their presence and activity in a Scandinavian boreal forest, using immunodetection of nitrogenase enzyme subunits and acetylene-reduction assays of native Scots pine (Pinus sylvestris) needles. The presence and rate of nitrogen fixation by endophytic bacteria was compared between control plots and fertilized plots in a nitrogen-addition experiment. Contrary to the expectation that nitrogen-fixation rates would decline in fertilized plots, as seen, for instance, with nitrogen-fixing bacteria associated with bryophytes, there was no difference in the presence or activity of nitrogen-fixing bacteria between the two treatments. The extrapolated calculated rate of nitrogen fixation relevant for the forest stand was 20 g N ha−1 year−1, which is rather low compared to Scots pine annual nitrogen use but could be important for nitrogen poor forest in the long term. In addition, of 13 colonies of potential nitrogen-fixing bacteria isolated from the needles on nitrogen-free media, 10 showed in vitro nitrogen fixation. 16S rRNA sequencing identified the species as belonging to the genera Bacillus, Variovorax, Novosphingobium, Sphingomonas, Microbacterium and Priestia, which was confirmed by Illumina whole genome sequencing. Our results confirm the presence of endophytic nitrogen-fixing bacteria in Scots pine needles, and suggest that they could be important for the long-term nitrogen budget of the Scandinavian boreal forest.},
	urldate = {2023-04-21},
	journal = {Tree Physiology},
	author = {Bizjak, Tinkara and Sellstedt, Anita and Gratz, Regina and Nordin, Annika},
	month = apr,
	year = {2023},
	pages = {tpad048},
}

Endophytic nitrogen-fixing bacteria have been detected and isolated from the needles of conifer trees growing in North American boreal forests. Because boreal forests are nutrient-limited, these bacteria could provide an important source of nitrogen for tree species. The aim of this study was to determine their presence and activity in a Scandinavian boreal forest, using immunodetection of nitrogenase enzyme subunits and acetylene-reduction assays of native Scots pine (Pinus sylvestris) needles. The presence and rate of nitrogen fixation by endophytic bacteria was compared between control plots and fertilized plots in a nitrogen-addition experiment. Contrary to the expectation that nitrogen-fixation rates would decline in fertilized plots, as seen, for instance, with nitrogen-fixing bacteria associated with bryophytes, there was no difference in the presence or activity of nitrogen-fixing bacteria between the two treatments. The extrapolated calculated rate of nitrogen fixation relevant for the forest stand was 20 g N ha−1 year−1, which is rather low compared to Scots pine annual nitrogen use but could be important for nitrogen poor forest in the long term. In addition, of 13 colonies of potential nitrogen-fixing bacteria isolated from the needles on nitrogen-free media, 10 showed in vitro nitrogen fixation. 16S rRNA sequencing identified the species as belonging to the genera Bacillus, Variovorax, Novosphingobium, Sphingomonas, Microbacterium and Priestia, which was confirmed by Illumina whole genome sequencing. Our results confirm the presence of endophytic nitrogen-fixing bacteria in Scots pine needles, and suggest that they could be important for the long-term nitrogen budget of the Scandinavian boreal forest.

@article{priebe_spectrum_2023,
	title = {The spectrum of knowledge: integrating knowledge dimensions in the context of forests and climate change},
	issn = {1862-4057},
	shorttitle = {The spectrum of knowledge},
	url = {https://doi.org/10.1007/s11625-023-01309-0},
	doi = {10.1007/s11625-023-01309-0},
	abstract = {Integrated approaches to knowledge that recognize meaning, behavior, culture, and systems as domains of knowledge are increasingly employed in holistic views on sustainability transformation but often remain conceptually driven. In this study, we analyze empirical data from a collaborative process with local forest stakeholders in Sweden through the lens of individual, collective, interior, and exterior knowledge dimensions. We show that the participants’ understanding of knowledge about forests and climate change presents a nuanced picture of how knowledge and acting are connected. Meaning-making, cultural frames, and techno-scientific knowledge conceptions converge, interact, and, at times, replace or diminish each other. The connection and interplay of these dimensions, we suggest, can be understood as a knowledge spectrum. These insights into integrated knowledge, based on an empirical case, must be addressed in the production of knowledge, both to grasp the climate and sustainability issues that face us and to support action in response to them.},
	language = {en},
	urldate = {2023-04-21},
	journal = {Sustainability Science},
	author = {Priebe, Janina and Hallberg-Sramek, Isabella and Reimerson, Elsa and Mårald, Erland},
	month = mar,
	year = {2023},
	keywords = {Climate change, Forests, Knowledge, Sustainability, Sweden, Transformation},
}

Integrated approaches to knowledge that recognize meaning, behavior, culture, and systems as domains of knowledge are increasingly employed in holistic views on sustainability transformation but often remain conceptually driven. In this study, we analyze empirical data from a collaborative process with local forest stakeholders in Sweden through the lens of individual, collective, interior, and exterior knowledge dimensions. We show that the participants’ understanding of knowledge about forests and climate change presents a nuanced picture of how knowledge and acting are connected. Meaning-making, cultural frames, and techno-scientific knowledge conceptions converge, interact, and, at times, replace or diminish each other. The connection and interplay of these dimensions, we suggest, can be understood as a knowledge spectrum. These insights into integrated knowledge, based on an empirical case, must be addressed in the production of knowledge, both to grasp the climate and sustainability issues that face us and to support action in response to them.

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

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

@article{israeli_modulating_2023,
	title = {Modulating auxin response stabilizes tomato fruit set},
	issn = {0032-0889},
	url = {https://doi.org/10.1093/plphys/kiad205},
	doi = {10.1093/plphys/kiad205},
	abstract = {Fruit formation depends on successful fertilization and is highly sensitive to weather fluctuations that affect pollination. Auxin promotes fruit initiation and growth following fertilization. Class A auxin response factors (Class A ARFs) repress transcription in the absence of auxin and activate transcription in its presence. Here we explore how multiple members of the ARF family regulate fruit set and fruit growth in tomato (Solanum lycopersicum) and Arabidopsis thaliana, and test whether reduction of SlARF activity improves yield stability in fluctuating temperatures. We found that several tomato Slarf mutant combinations produced seedless parthenocarpic fruits, most notably mutants deficient in SlARF8A and SlARF8B genes. Arabidopsis Atarf8 mutants deficient in the orthologous gene had less complete parthenocarpy than did tomato Slarf8a Slarf8b mutants. Conversely, Atarf6 Atarf8 double mutants had reduced fruit growth after fertilization. AtARF6 and AtARF8 likely switch from repression to activation of fruit growth in response to a fertilization-induced auxin increase in gynoecia. Tomato plants with reduced SlARF8A and SlARF8B gene dosage had substantially higher yield than the wild type under controlled or ambient hot and cold growth conditions. In field trials, partial reduction in the SlARF8 dose increased yield under extreme temperature with minimal pleiotropic effects. The stable yield of the mutant plants resulted from a combination of early onset of fruit set, more fruit-bearing branches and more flowers setting fruits. Thus, ARF8 proteins mediate the control of fruit set, and relieving this control with Slarf8 mutations may be utilized in breeding to increase yield stability in tomato and other crops.},
	urldate = {2023-04-14},
	journal = {Plant Physiology},
	author = {Israeli, Alon and Schubert, Ramona and Man, Nave and Teboul, Naama and Serrani Yarce, Juan Carlos and Rosowski, Emily E and Wu, Miin-Feng and Levy, Matan and Efroni, Idan and Ljung, Karin and Hause, Bettina and Reed, Jason W and Ori, Naomi},
	month = apr,
	year = {2023},
	pages = {kiad205},
}

Fruit formation depends on successful fertilization and is highly sensitive to weather fluctuations that affect pollination. Auxin promotes fruit initiation and growth following fertilization. Class A auxin response factors (Class A ARFs) repress transcription in the absence of auxin and activate transcription in its presence. Here we explore how multiple members of the ARF family regulate fruit set and fruit growth in tomato (Solanum lycopersicum) and Arabidopsis thaliana, and test whether reduction of SlARF activity improves yield stability in fluctuating temperatures. We found that several tomato Slarf mutant combinations produced seedless parthenocarpic fruits, most notably mutants deficient in SlARF8A and SlARF8B genes. Arabidopsis Atarf8 mutants deficient in the orthologous gene had less complete parthenocarpy than did tomato Slarf8a Slarf8b mutants. Conversely, Atarf6 Atarf8 double mutants had reduced fruit growth after fertilization. AtARF6 and AtARF8 likely switch from repression to activation of fruit growth in response to a fertilization-induced auxin increase in gynoecia. Tomato plants with reduced SlARF8A and SlARF8B gene dosage had substantially higher yield than the wild type under controlled or ambient hot and cold growth conditions. In field trials, partial reduction in the SlARF8 dose increased yield under extreme temperature with minimal pleiotropic effects. The stable yield of the mutant plants resulted from a combination of early onset of fruit set, more fruit-bearing branches and more flowers setting fruits. Thus, ARF8 proteins mediate the control of fruit set, and relieving this control with Slarf8 mutations may be utilized in breeding to increase yield stability in tomato and other crops.

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

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

@article{hoffmann_cauliflower_2023,
	title = {Cauliflower mosaic virus protein {P6} is a multivalent node for {RNA} granule proteins and interferes with stress granule responses during plant infection},
	issn = {1040-4651},
	url = {https://doi.org/10.1093/plcell/koad101},
	doi = {10.1093/plcell/koad101},
	abstract = {Biomolecular condensation is a multipurpose cellular process that viruses use ubiquitously during their multiplication. Cauliflower mosaic virus (CaMV) replication complexes are condensates that differ from those of most viruses, as they are non-membranous assemblies that consist of RNA and protein, mainly the viral protein P6. Although these viral factories (VFs) were described half a century ago, with many observations that followed since, functional details of the condensation process and the properties and relevance of VFs have remained enigmatic. Here we studied these issues in Arabidopsis thaliana and Nicotiana benthamiana. We observed a large dynamic mobility range of host proteins within VFs, while the viral matrix protein P6 is immobile, as it represents the central node of these condensates. We identified the stress granule (SG) nucleating factors G3BP7 and UBP1 family members as components of VFs. Similarly, as SG components localize to VFs during infection, ectopic P6 localizes to SGs and reduces their assembly after stress. Intriguingly, it appears that soluble rather than condensed P6 suppresses SG formation and mediates other essential P6 functions, suggesting that the increased condensation over the infection time-course may accompany a progressive shift in selected P6 functions. Together, this study highlights VFs as dynamic condensates and P6 as a complex modulator of SG responses.},
	urldate = {2023-04-14},
	journal = {The Plant Cell},
	author = {Hoffmann, Gesa and López-González, Silvia and Mahboubi, Amir and Hanson, Johannes and Hafrén, Anders},
	month = apr,
	year = {2023},
	pages = {koad101},
}

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

@article{boussardon_comparing_2023,
	title = {Comparing plastid proteomes points towards a higher plastidial redox turnover in vascular tissues than in mesophyll cells},
	issn = {0022-0957},
	url = {https://doi.org/10.1093/jxb/erad133},
	doi = {10.1093/jxb/erad133},
	abstract = {Plastids are complex organelles that vary in size and function depending on the cell type. Accordingly, they can be referred to as amyloplasts, chloroplasts, chromoplasts, etioplasts, proplasts to only cite a few denominations. Over the past decades, methods based on density gradients and differential centrifugations have been extensively used for the purification of plastids. However, these methods need large amounts of starting material, and hardly provide a tissue-specific resolution. Here, we applied our IPTACT (Isolation of Plastids TAgged in specific Cell Types) method, which involves the biotinylation of plastids in vivo using one-shot transgenic lines expressing the TOC64 gene coupled with a biotin ligase receptor particle and the BirA biotin ligase, to isolate plastids from mesophyll and companion cells of Arabidopsis thaliana using tissue specific pCAB3 and pSUC2 promoters, respectively. Subsequently, a proteome profiling was performed, and allowed the identification of 1672 proteins, among which 1342 were predicted plastidial, and 705 were fully confirmed according to SUBA5. Interestingly, although 92\% of plastidial proteins were equally distributed between the two tissues, we observed an accumulation of proteins associated with jasmonic acid biosynthesis, plastoglobuli (e.g. NDC1, VTE1, PGL34, ABC1K1) and cyclic electron flow in plastids originating from vascular tissues. Besides demonstrating the technical feasibility of isolating plastids in a tissue-specific manner, our work provides strong evidence that plastids from vascular tissue have a higher redox turnover to ensure optimal functioning, notably under high solute strength as encountered in vascular cells.},
	urldate = {2023-04-11},
	journal = {Journal of Experimental Botany},
	author = {Boussardon, Clément and Carrie, Chris and Keech, Olivier},
	month = apr,
	year = {2023},
	pages = {erad133},
}

Plastids are complex organelles that vary in size and function depending on the cell type. Accordingly, they can be referred to as amyloplasts, chloroplasts, chromoplasts, etioplasts, proplasts to only cite a few denominations. Over the past decades, methods based on density gradients and differential centrifugations have been extensively used for the purification of plastids. However, these methods need large amounts of starting material, and hardly provide a tissue-specific resolution. Here, we applied our IPTACT (Isolation of Plastids TAgged in specific Cell Types) method, which involves the biotinylation of plastids in vivo using one-shot transgenic lines expressing the TOC64 gene coupled with a biotin ligase receptor particle and the BirA biotin ligase, to isolate plastids from mesophyll and companion cells of Arabidopsis thaliana using tissue specific pCAB3 and pSUC2 promoters, respectively. Subsequently, a proteome profiling was performed, and allowed the identification of 1672 proteins, among which 1342 were predicted plastidial, and 705 were fully confirmed according to SUBA5. Interestingly, although 92% of plastidial proteins were equally distributed between the two tissues, we observed an accumulation of proteins associated with jasmonic acid biosynthesis, plastoglobuli (e.g. NDC1, VTE1, PGL34, ABC1K1) and cyclic electron flow in plastids originating from vascular tissues. Besides demonstrating the technical feasibility of isolating plastids in a tissue-specific manner, our work provides strong evidence that plastids from vascular tissue have a higher redox turnover to ensure optimal functioning, notably under high solute strength as encountered in vascular cells.

@article{chen_preselection_2023,
	title = {Preselection of {QTL} markers enhances accuracy of genomic selection in {Norway} spruce},
	volume = {24},
	issn = {1471-2164},
	url = {https://doi.org/10.1186/s12864-023-09250-3},
	doi = {10.1186/s12864-023-09250-3},
	abstract = {Genomic prediction (GP) or genomic selection is a method to predict the accumulative effect of all quantitative trait loci (QTLs) in a population by estimating the realized genomic relationships between the individuals and by capturing the linkage disequilibrium between markers and QTLs. Thus, marker preselection is considered a promising method to capture Mendelian segregation effects. Using QTLs detected in a genome-wide association study (GWAS) may improve GP. Here, we performed GWAS and GP in a population with 904 clones from 32 full-sib families using a newly developed 50 k SNP Norway spruce array. Through GWAS we identified 41 SNPs associated with budburst stage (BB) and the largest effect association explained 5.1\% of the phenotypic variation (PVE). For the other five traits such as growth and wood quality traits, only 2 – 13 associations were observed and the PVE of the strongest effects ranged from 1.2\% to 2.0\%. GP using approximately 100 preselected SNPs, based on the smallest p-values from GWAS showed the greatest predictive ability (PA) for the trait BB. For the other traits, a preselection of 2000–4000 SNPs, was found to offer the best model fit according to the Akaike information criterion being minimized. But PA-magnitudes from GP using such selections were still similar to that of GP using all markers. Analyses on both real-life and simulated data also showed that the inclusion of a large QTL SNP in the model as a fixed effect could improve PA and accuracy of GP provided that the PVE of the QTL was ≥ 2.5\%.},
	number = {1},
	urldate = {2023-04-11},
	journal = {BMC Genomics},
	author = {Chen, Zhi-Qiang and Klingberg, Adam and Hallingbäck, Henrik R. and Wu, Harry X.},
	month = mar,
	year = {2023},
	keywords = {GWAS, Genomic prediction, Marker preselection, Picea abies},
	pages = {147},
}

Genomic prediction (GP) or genomic selection is a method to predict the accumulative effect of all quantitative trait loci (QTLs) in a population by estimating the realized genomic relationships between the individuals and by capturing the linkage disequilibrium between markers and QTLs. Thus, marker preselection is considered a promising method to capture Mendelian segregation effects. Using QTLs detected in a genome-wide association study (GWAS) may improve GP. Here, we performed GWAS and GP in a population with 904 clones from 32 full-sib families using a newly developed 50 k SNP Norway spruce array. Through GWAS we identified 41 SNPs associated with budburst stage (BB) and the largest effect association explained 5.1% of the phenotypic variation (PVE). For the other five traits such as growth and wood quality traits, only 2 – 13 associations were observed and the PVE of the strongest effects ranged from 1.2% to 2.0%. GP using approximately 100 preselected SNPs, based on the smallest p-values from GWAS showed the greatest predictive ability (PA) for the trait BB. For the other traits, a preselection of 2000–4000 SNPs, was found to offer the best model fit according to the Akaike information criterion being minimized. But PA-magnitudes from GP using such selections were still similar to that of GP using all markers. Analyses on both real-life and simulated data also showed that the inclusion of a large QTL SNP in the model as a fixed effect could improve PA and accuracy of GP provided that the PVE of the QTL was ≥ 2.5%.

@article{rohricht_mitochondrial_2023,
	title = {Mitochondrial ferredoxin-like is essential for forming complex {I}-containing supercomplexes in {Arabidopsis}},
	volume = {191},
	issn = {0032-0889},
	url = {https://doi.org/10.1093/plphys/kiad040},
	doi = {10.1093/plphys/kiad040},
	abstract = {In eukaryotes, mitochondrial ATP is mainly produced by the oxidative phosphorylation (OXPHOS) system, which is composed of 5 multiprotein complexes (complexes I–V). Analyses of the OXPHOS system by native gel electrophoresis have revealed an organization of OXPHOS complexes into supercomplexes, but their roles and assembly pathways remain unclear. In this study, we characterized an atypical mitochondrial ferredoxin (mitochondrial ferredoxin-like, mFDX-like). This protein was previously found to be part of the bridge domain linking the matrix and membrane arms of the complex I. Phylogenetic analysis suggested that the Arabidopsis (Arabidopsis thaliana) mFDX-like evolved from classical mitochondrial ferredoxins (mFDXs) but lost one of the cysteines required for the coordination of the iron-sulfur (Fe-S) cluster, supposedly essential for the electron transfer function of FDXs. Accordingly, our biochemical study showed that AtmFDX-like does not bind an Fe-S cluster and is therefore unlikely to be involved in electron transfer reactions. To study the function of mFDX-like, we created deletion lines in Arabidopsis using a CRISPR/Cas9-based strategy. These lines did not show any abnormal phenotype under standard growth conditions. However, the characterization of the OXPHOS system demonstrated that mFDX-like is important for the assembly of complex I and essential for the formation of complex I-containing supercomplexes. We propose that mFDX-like and the bridge domain are required for the correct conformation of the membrane arm of complex I that is essential for the association of complex I with complex III2 to form supercomplexes.},
	number = {4},
	urldate = {2023-04-11},
	journal = {Plant Physiology},
	author = {Röhricht, Helene and Przybyla-Toscano, Jonathan and Forner, Joachim and Boussardon, Clément and Keech, Olivier and Rouhier, Nicolas and Meyer, Etienne H},
	month = apr,
	year = {2023},
	pages = {2170--2184},
}

In eukaryotes, mitochondrial ATP is mainly produced by the oxidative phosphorylation (OXPHOS) system, which is composed of 5 multiprotein complexes (complexes I–V). Analyses of the OXPHOS system by native gel electrophoresis have revealed an organization of OXPHOS complexes into supercomplexes, but their roles and assembly pathways remain unclear. In this study, we characterized an atypical mitochondrial ferredoxin (mitochondrial ferredoxin-like, mFDX-like). This protein was previously found to be part of the bridge domain linking the matrix and membrane arms of the complex I. Phylogenetic analysis suggested that the Arabidopsis (Arabidopsis thaliana) mFDX-like evolved from classical mitochondrial ferredoxins (mFDXs) but lost one of the cysteines required for the coordination of the iron-sulfur (Fe-S) cluster, supposedly essential for the electron transfer function of FDXs. Accordingly, our biochemical study showed that AtmFDX-like does not bind an Fe-S cluster and is therefore unlikely to be involved in electron transfer reactions. To study the function of mFDX-like, we created deletion lines in Arabidopsis using a CRISPR/Cas9-based strategy. These lines did not show any abnormal phenotype under standard growth conditions. However, the characterization of the OXPHOS system demonstrated that mFDX-like is important for the assembly of complex I and essential for the formation of complex I-containing supercomplexes. We propose that mFDX-like and the bridge domain are required for the correct conformation of the membrane arm of complex I that is essential for the association of complex I with complex III2 to form supercomplexes.

@article{jourquin_golven_2023,
	title = {{GOLVEN} peptides regulate lateral root spacing as part of a negative feedback loop on the establishment of auxin maxima},
	issn = {0022-0957},
	url = {https://doi.org/10.1093/jxb/erad123},
	doi = {10.1093/jxb/erad123},
	abstract = {Lateral root initiation requires the accumulation of auxin in lateral root founder cells, yielding a local auxin maximum. The positioning of auxin maxima along the primary root determines the density and spacing of lateral roots. The GOLVEN6 (GLV6) and GLV10 signaling peptides and their receptors have been established as regulators of lateral root spacing via their inhibitory effect on lateral root initiation in Arabidopsis. However, it remained unclear how these GLV peptides interfere with auxin signaling or homeostasis. Here, we show that GLV6/10 signaling regulates the expression of a subset of auxin response genes, downstream of the canonical auxin signaling pathway, while simultaneously inhibiting the establishment of auxin maxima within xylem-pole pericycle cells that neighbor lateral root initiation sites. We present genetic evidence that this inhibitory effect relies on the activity of the PIN3 and PIN7 auxin export proteins. Furthermore, GLV6/10 peptide signaling was found to enhance PIN7 abundance in the plasma membranes of xylem-pole pericycle cells, which likely stimulates auxin efflux from these cells. Based on these findings, we propose a model in which the GLV6/10 signaling pathway serves as a negative feedback mechanism that contributes to the robust patterning of auxin maxima along the primary root.},
	urldate = {2023-04-11},
	journal = {Journal of Experimental Botany},
	author = {Jourquin, Joris and Fernandez, Ana Ibis and Wang, Qing and Xu, Ke and Chen, Jian and Šimura, Jan and Ljung, Karin and Vanneste, Steffen and Beeckman, Tom},
	month = apr,
	year = {2023},
	pages = {erad123},
}

Lateral root initiation requires the accumulation of auxin in lateral root founder cells, yielding a local auxin maximum. The positioning of auxin maxima along the primary root determines the density and spacing of lateral roots. The GOLVEN6 (GLV6) and GLV10 signaling peptides and their receptors have been established as regulators of lateral root spacing via their inhibitory effect on lateral root initiation in Arabidopsis. However, it remained unclear how these GLV peptides interfere with auxin signaling or homeostasis. Here, we show that GLV6/10 signaling regulates the expression of a subset of auxin response genes, downstream of the canonical auxin signaling pathway, while simultaneously inhibiting the establishment of auxin maxima within xylem-pole pericycle cells that neighbor lateral root initiation sites. We present genetic evidence that this inhibitory effect relies on the activity of the PIN3 and PIN7 auxin export proteins. Furthermore, GLV6/10 peptide signaling was found to enhance PIN7 abundance in the plasma membranes of xylem-pole pericycle cells, which likely stimulates auxin efflux from these cells. Based on these findings, we propose a model in which the GLV6/10 signaling pathway serves as a negative feedback mechanism that contributes to the robust patterning of auxin maxima along the primary root.

@article{calderon_rubredoxin_2023,
	title = {Rubredoxin 1 promotes the proper folding of {D1} and is not required for heme b559 assembly in {Chlamydomonas} photosystem {II}},
	volume = {299},
	issn = {0021-9258, 1083-351X},
	url = {https://www.jbc.org/article/S0021-9258(23)00100-X/abstract},
	doi = {10.1016/j.jbc.2023.102968},
	abstract = {{\textless}p{\textgreater}Photosystem II (PSII), the water:plastoquinone oxidoreductase of oxygenic photosynthesis, contains a heme \textit{b}$_{\textrm{559}}$ iron whose axial ligands are provided by histidine residues from the α (PsbE) and β (PsbF) subunits. PSII assembly depends on accessory proteins that facilitate the step-wise association of its protein and pigment components into a functional complex, a process that is challenging to study due to the low accumulation of assembly intermediates. Here, we examined the putative role of the iron[1Fe-0S]-containing protein rubredoxin 1 (RBD1) as an assembly factor for cytochrome \textit{b}$_{\textrm{559}}$, using the RBD1-lacking \textit{2pac} mutant from \textit{Chlamydomonas reinhardtii}, in which the accumulation of PSII was rescued by the inactivation of the thylakoid membrane FtsH protease. To this end, we constructed the double mutant \textit{2pac ftsh1-1}, which harbored PSII dimers that sustained its photoautotrophic growth. We purified PSII from the \textit{2pac ftsh1-1} background and found that α and β cytochrome \textit{b}$_{\textrm{559}}$ subunits are still present and coordinate heme \textit{b}$_{\textrm{559}}$ as in the WT. Interestingly, immunoblot analysis of dark- and low light–grown \textit{2pac ftsh1-1} showed the accumulation of a 23-kDa fragment of the D1 protein, a marker typically associated with structural changes resulting from photodamage of PSII. Its cleavage occurs in the vicinity of a nonheme iron which binds to PSII on its electron acceptor side. Altogether, our findings demonstrate that RBD1 is not required for heme \textit{b}$_{\textrm{559}}$ assembly and point to a role for RBD1 in promoting the proper folding of D1, possibly \textit{via} delivery or reduction of the nonheme iron during PSII assembly.{\textless}/p{\textgreater}},
	language = {English},
	number = {3},
	urldate = {2023-03-31},
	journal = {Journal of Biological Chemistry},
	author = {Calderon, Robert H. and Vitry, Catherine de and Wollman, Francis-André and Niyogi, Krishna K.},
	month = mar,
	year = {2023},
	pmid = {36736898},
	note = {Publisher: Elsevier},
}

\textlessp\textgreaterPhotosystem II (PSII), the water:plastoquinone oxidoreductase of oxygenic photosynthesis, contains a heme b$_{\textrm{559}}$ iron whose axial ligands are provided by histidine residues from the α (PsbE) and β (PsbF) subunits. PSII assembly depends on accessory proteins that facilitate the step-wise association of its protein and pigment components into a functional complex, a process that is challenging to study due to the low accumulation of assembly intermediates. Here, we examined the putative role of the iron[1Fe-0S]-containing protein rubredoxin 1 (RBD1) as an assembly factor for cytochrome b$_{\textrm{559}}$, using the RBD1-lacking 2pac mutant from Chlamydomonas reinhardtii, in which the accumulation of PSII was rescued by the inactivation of the thylakoid membrane FtsH protease. To this end, we constructed the double mutant 2pac ftsh1-1, which harbored PSII dimers that sustained its photoautotrophic growth. We purified PSII from the 2pac ftsh1-1 background and found that α and β cytochrome b$_{\textrm{559}}$ subunits are still present and coordinate heme b$_{\textrm{559}}$ as in the WT. Interestingly, immunoblot analysis of dark- and low light–grown 2pac ftsh1-1 showed the accumulation of a 23-kDa fragment of the D1 protein, a marker typically associated with structural changes resulting from photodamage of PSII. Its cleavage occurs in the vicinity of a nonheme iron which binds to PSII on its electron acceptor side. Altogether, our findings demonstrate that RBD1 is not required for heme b$_{\textrm{559}}$ assembly and point to a role for RBD1 in promoting the proper folding of D1, possibly via delivery or reduction of the nonheme iron during PSII assembly.\textless/p\textgreater

@article{gao_phylogeography_2023,
	title = {Phylogeography and introgression between {Pinus} kesiya and {Pinus} yunnanensis in {Southeast} {Asia}},
	volume = {n/a},
	issn = {1759-6831},
	url = {https://onlinelibrary.wiley.com/doi/abs/10.1111/jse.12949},
	doi = {10.1111/jse.12949},
	abstract = {Southeast Asia (SEA) has seen strong climatic oscillations and fluctuations in sea levels during the Quaternary. The impact of past climate changes on the evolution and distribution of local flora in SEA is still poorly understood. Here we aim to infer how the Quaternary climate change affects the evolutionary process and range shifts in two pine species. We investigated the population genetic structure and diversity using cytoplasmic DNA markers, and performed ecological niche modeling to reconstruct the species past distribution and to project range shift under future climates. We found substantial gene flow across the continuous distribution of the subtropical Pinus yunnanensis. In contrast, the tropical Pinus kesiya showed a strong population structure in accordance with its disjunct distribution across montane islands in Indochina and the Philippines. A broad hybrid zone of the two species occurs in southern Yunnan. Asymmetric introgression from the two species was detected in this zone with dominant mitochondrial gene flow from P. yunnanensis and chloroplast gene flow from P. kesiya. The observed population structure suggests a typical postglaciation expansion in P. yunnanensis, and a glacial expansion and interglacial contraction in P. kesiya. Ecological niche modeling supports the inferred demographic history and predicts a decrease in range size for P. kesiya under future climates. Our results suggest that tropical pine species in SEA have undergone evolutionary trajectories different from high latitude species related to their Quaternary climate histories. We also illustrate the need for urgent conservation actions in this fragmented landscape.},
	language = {en},
	number = {n/a},
	urldate = {2023-03-31},
	journal = {Journal of Systematics and Evolution},
	author = {Gao, Jie and Tomlinson, Kyle W. and Zhao, Wei and Wang, Baosheng and Lapuz, Ralph Sedricke and Liu, Jing-Xin and Pasion, Bonifacio O. and Hai, Bach T. and Chanthayod, Souvick and Chen, Jin and Wang, Xiao-Ru},
	month = jan,
	year = {2023},
	note = {\_eprint: https://onlinelibrary.wiley.com/doi/pdf/10.1111/jse.12949},
	keywords = {Pinus kesiya, Pinus yunnanensis, cpDNA, introgression, mtDNA capture, phylogeography},
}

Southeast Asia (SEA) has seen strong climatic oscillations and fluctuations in sea levels during the Quaternary. The impact of past climate changes on the evolution and distribution of local flora in SEA is still poorly understood. Here we aim to infer how the Quaternary climate change affects the evolutionary process and range shifts in two pine species. We investigated the population genetic structure and diversity using cytoplasmic DNA markers, and performed ecological niche modeling to reconstruct the species past distribution and to project range shift under future climates. We found substantial gene flow across the continuous distribution of the subtropical Pinus yunnanensis. In contrast, the tropical Pinus kesiya showed a strong population structure in accordance with its disjunct distribution across montane islands in Indochina and the Philippines. A broad hybrid zone of the two species occurs in southern Yunnan. Asymmetric introgression from the two species was detected in this zone with dominant mitochondrial gene flow from P. yunnanensis and chloroplast gene flow from P. kesiya. The observed population structure suggests a typical postglaciation expansion in P. yunnanensis, and a glacial expansion and interglacial contraction in P. kesiya. Ecological niche modeling supports the inferred demographic history and predicts a decrease in range size for P. kesiya under future climates. Our results suggest that tropical pine species in SEA have undergone evolutionary trajectories different from high latitude species related to their Quaternary climate histories. We also illustrate the need for urgent conservation actions in this fragmented landscape.

@article{tian_unique_2023,
	title = {Unique gene duplications and conserved microsynteny potentially associated with resistance to wood decay in the {Lauraceae}},
	volume = {14},
	issn = {1664-462X},
	url = {https://www.frontiersin.org/articles/10.3389/fpls.2023.1122549},
	abstract = {Wood decay resistance (WDR) is marking the value of wood utilization. Many trees of the Lauraceae have exceptional WDR, as evidenced by their use in ancient royal palace buildings in China. However, the genetics of WDR remain elusive. Here, through comparative genomics, we revealed the unique characteristics related to the high WDR in Lauraceae trees. We present a 1.27-Gb chromosome-level assembly for Lindera megaphylla (Lauraceae). Comparative genomics integrating major groups of angiosperm revealed Lauraceae species have extensively shared gene microsynteny associated with the biosynthesis of specialized metabolites such as isoquinoline alkaloids, flavonoid, lignins and terpenoid, which play significant roles in WDR. In Lauraceae genomes, tandem and proximal duplications (TD/PD) significantly expanded the coding space of key enzymes of biosynthesis pathways related to WDR, which may enhance the decay resistance of wood by increasing the accumulation of these compounds. Among Lauraceae species, genes of WDR-related biosynthesis pathways showed remarkable expansion by TD/PD and conveyed unique and conserved motifs in their promoter and protein sequences, suggesting conserved gene collinearity, gene expansion and gene regulation supporting the high WDR. Our study thus reveals genomic profiles related to biochemical transitions among major plant groups and the genomic basis of WDR in the Lauraceae.},
	urldate = {2023-03-31},
	journal = {Frontiers in Plant Science},
	author = {Tian, Xue-Chan and Guo, Jing-Fang and Yan, Xue-Mei and Shi, Tian-Le and Nie, Shuai and Zhao, Shi-Wei and Bao, Yu-Tao and Li, Zhi-Chao and Kong, Lei and Su, Guang-Ju and Mao, Jian-Feng and Lin, Jinxing},
	month = mar,
	year = {2023},
}

Wood decay resistance (WDR) is marking the value of wood utilization. Many trees of the Lauraceae have exceptional WDR, as evidenced by their use in ancient royal palace buildings in China. However, the genetics of WDR remain elusive. Here, through comparative genomics, we revealed the unique characteristics related to the high WDR in Lauraceae trees. We present a 1.27-Gb chromosome-level assembly for Lindera megaphylla (Lauraceae). Comparative genomics integrating major groups of angiosperm revealed Lauraceae species have extensively shared gene microsynteny associated with the biosynthesis of specialized metabolites such as isoquinoline alkaloids, flavonoid, lignins and terpenoid, which play significant roles in WDR. In Lauraceae genomes, tandem and proximal duplications (TD/PD) significantly expanded the coding space of key enzymes of biosynthesis pathways related to WDR, which may enhance the decay resistance of wood by increasing the accumulation of these compounds. Among Lauraceae species, genes of WDR-related biosynthesis pathways showed remarkable expansion by TD/PD and conveyed unique and conserved motifs in their promoter and protein sequences, suggesting conserved gene collinearity, gene expansion and gene regulation supporting the high WDR. Our study thus reveals genomic profiles related to biochemical transitions among major plant groups and the genomic basis of WDR in the Lauraceae.

@article{grenzi_long-distance_2023,
	title = {Long-distance turgor pressure changes induce local activation of plant glutamate receptor-like channels},
	issn = {0960-9822},
	url = {https://www.sciencedirect.com/science/article/pii/S0960982223000763},
	doi = {10.1016/j.cub.2023.01.042},
	abstract = {In Arabidopsis thaliana, local wounding and herbivore feeding provoke leaf-to-leaf propagating Ca2+ waves that are dependent on the activity of members of the glutamate receptor-like channels (GLRs). In systemic tissues, GLRs are needed to sustain the synthesis of jasmonic acid (JA) with the subsequent activation of JA-dependent signaling response required for the plant acclimation to the perceived stress. Even though the role of GLRs is well established, the mechanism through which they are activated remains unclear. Here, we report that in vivo, the amino-acid-dependent activation of the AtGLR3.3 channel and systemic responses require a functional ligand-binding domain. By combining imaging and genetics, we show that leaf mechanical injury, such as wounds and burns, as well as hypo-osmotic stress in root cells, induces the systemic apoplastic increase of L-glutamate (L-Glu), which is largely independent of AtGLR3.3 that is instead required for systemic cytosolic Ca2+ elevation. Moreover, by using a bioelectronic approach, we show that the local release of minute concentrations of L-Glu in the leaf lamina fails to induce any long-distance Ca2+ waves.},
	language = {en},
	urldate = {2023-03-23},
	journal = {Current Biology},
	author = {Grenzi, Matteo and Buratti, Stefano and Parmagnani, Ambra Selene and Abdel Aziz, Ilaria and Bernacka-Wojcik, Iwona and Resentini, Francesca and Šimura, Jan and Doccula, Fabrizio Gandolfo and Alfieri, Andrea and Luoni, Laura and Ljung, Karin and Bonza, Maria Cristina and Stavrinidou, Eleni and Costa, Alex},
	month = feb,
	year = {2023},
	keywords = {glutamate receptor-like channels, implantable bioelectronic device, ligand-binding domain, long-distance Ca signaling},
}

In Arabidopsis thaliana, local wounding and herbivore feeding provoke leaf-to-leaf propagating Ca2+ waves that are dependent on the activity of members of the glutamate receptor-like channels (GLRs). In systemic tissues, GLRs are needed to sustain the synthesis of jasmonic acid (JA) with the subsequent activation of JA-dependent signaling response required for the plant acclimation to the perceived stress. Even though the role of GLRs is well established, the mechanism through which they are activated remains unclear. Here, we report that in vivo, the amino-acid-dependent activation of the AtGLR3.3 channel and systemic responses require a functional ligand-binding domain. By combining imaging and genetics, we show that leaf mechanical injury, such as wounds and burns, as well as hypo-osmotic stress in root cells, induces the systemic apoplastic increase of L-glutamate (L-Glu), which is largely independent of AtGLR3.3 that is instead required for systemic cytosolic Ca2+ elevation. Moreover, by using a bioelectronic approach, we show that the local release of minute concentrations of L-Glu in the leaf lamina fails to induce any long-distance Ca2+ waves.

@article{routier_chitosan-modified_2023,
	title = {Chitosan-{Modified} {Polyethyleneimine} {Nanoparticles} for {Enhancing} the {Carboxylation} {Reaction} and {Plants}’ {CO2} {Uptake}},
	volume = {17},
	issn = {1936-0851},
	url = {https://doi.org/10.1021/acsnano.2c09255},
	doi = {10.1021/acsnano.2c09255},
	abstract = {Increasing plants’ photosynthetic efficiency is a major challenge that must be addressed in order to cover the food demands of the growing population in the changing climate. Photosynthesis is greatly limited at the initial carboxylation reaction, where CO2 is converted to the organic acid 3-PGA, catalyzed by the RuBisCO enzyme. RuBisCO has poor affinity for CO2, but also the CO2 concentration at the RuBisCO site is limited by the diffusion of atmospheric CO2 through the various leaf compartments to the reaction site. Beyond genetic engineering, nanotechnology can offer a materials-based approach for enhancing photosynthesis, and yet, it has mostly been explored for the light-dependent reactions. In this work, we developed polyethyleneimine-based nanoparticles for enhancing the carboxylation reaction. We demonstrate that the nanoparticles can capture CO2 in the form of bicarbonate and increase the CO2 that reacts with the RuBisCO enzyme, enhancing the 3-PGA production in in vitro assays by 20\%. The nanoparticles can be introduced to the plant via leaf infiltration and, because of the functionalization with chitosan oligomers, they do not induce any toxic effect to the plant. In the leaves, the nanoparticles localize in the apoplastic space but also spontaneously reach the chloroplasts where photosynthetic activity takes place. Their CO2 loading-dependent fluorescence verifies that, in vivo, they maintain their ability to capture CO2 and can be therefore reloaded with atmospheric CO2 while in planta. Our results contribute to the development of a nanomaterials-based CO2-concentrating mechanism in plants that can potentially increase photosynthetic efficiency and overall plants’ CO2 storage.},
	number = {4},
	urldate = {2023-03-10},
	journal = {ACS Nano},
	author = {Routier, Cyril and Vallan, Lorenzo and Daguerre, Yohann and Juvany, Marta and Istif, Emin and Mantione, Daniele and Brochon, Cyril and Hadziioannou, Georges and Strand, Åsa and Näsholm, Torgny and Cloutet, Eric and Pavlopoulou, Eleni and Stavrinidou, Eleni},
	month = feb,
	year = {2023},
	note = {Publisher: American Chemical Society},
	pages = {3430--3441},
}

Increasing plants’ photosynthetic efficiency is a major challenge that must be addressed in order to cover the food demands of the growing population in the changing climate. Photosynthesis is greatly limited at the initial carboxylation reaction, where CO2 is converted to the organic acid 3-PGA, catalyzed by the RuBisCO enzyme. RuBisCO has poor affinity for CO2, but also the CO2 concentration at the RuBisCO site is limited by the diffusion of atmospheric CO2 through the various leaf compartments to the reaction site. Beyond genetic engineering, nanotechnology can offer a materials-based approach for enhancing photosynthesis, and yet, it has mostly been explored for the light-dependent reactions. In this work, we developed polyethyleneimine-based nanoparticles for enhancing the carboxylation reaction. We demonstrate that the nanoparticles can capture CO2 in the form of bicarbonate and increase the CO2 that reacts with the RuBisCO enzyme, enhancing the 3-PGA production in in vitro assays by 20%. The nanoparticles can be introduced to the plant via leaf infiltration and, because of the functionalization with chitosan oligomers, they do not induce any toxic effect to the plant. In the leaves, the nanoparticles localize in the apoplastic space but also spontaneously reach the chloroplasts where photosynthetic activity takes place. Their CO2 loading-dependent fluorescence verifies that, in vivo, they maintain their ability to capture CO2 and can be therefore reloaded with atmospheric CO2 while in planta. Our results contribute to the development of a nanomaterials-based CO2-concentrating mechanism in plants that can potentially increase photosynthetic efficiency and overall plants’ CO2 storage.

@article{pateras_short_2023,
	title = {Short term starvation potentiates the efficacy of chemotherapy in triple negative breast cancer via metabolic reprogramming},
	volume = {21},
	issn = {1479-5876},
	url = {https://doi.org/10.1186/s12967-023-03935-9},
	doi = {10.1186/s12967-023-03935-9},
	abstract = {Chemotherapy (CT) is central to the treatment of triple negative breast cancer (TNBC), but drug toxicity and resistance place strong restrictions on treatment regimes. Fasting sensitizes cancer cells to a range of chemotherapeutic agents and also ameliorates CT-associated adverse effects. However, the molecular mechanism(s) by which fasting, or short-term starvation (STS), improves the efficacy of CT is poorly characterized.},
	number = {1},
	urldate = {2023-03-10},
	journal = {Journal of Translational Medicine},
	author = {Pateras, Ioannis S. and Williams, Chloe and Gianniou, Despoina D. and Margetis, Aggelos T. and Avgeris, Margaritis and Rousakis, Pantelis and Legaki, Aigli-Ioanna and Mirtschink, Peter and Zhang, Wei and Panoutsopoulou, Konstantina and Delis, Anastasios D. and Pagakis, Stamatis N. and Tang, Wei and Ambs, Stefan and Warpman Berglund, Ulrika and Helleday, Thomas and Varvarigou, Anastasia and Chatzigeorgiou, Antonios and Nordström, Anders and Tsitsilonis, Ourania E. and Trougakos, Ioannis P. and Gilthorpe, Jonathan D. and Frisan, Teresa},
	month = mar,
	year = {2023},
	keywords = {Breast cancer, Caloric restriction, Fasting, Metabolic reprogramming, Mitochondria, Oncological treatment, Oxidative stress, Reactive oxygen species, Starvation, Triple negative breast cancer},
	pages = {169},
}

Chemotherapy (CT) is central to the treatment of triple negative breast cancer (TNBC), but drug toxicity and resistance place strong restrictions on treatment regimes. Fasting sensitizes cancer cells to a range of chemotherapeutic agents and also ameliorates CT-associated adverse effects. However, the molecular mechanism(s) by which fasting, or short-term starvation (STS), improves the efficacy of CT is poorly characterized.

@article{hallberg-sramek_combining_2023,
	title = {Combining scientific and local knowledge improves evaluating future scenarios of forest ecosystem services},
	volume = {60},
	issn = {2212-0416},
	url = {https://www.sciencedirect.com/science/article/pii/S2212041623000049},
	doi = {10.1016/j.ecoser.2023.101512},
	abstract = {Forest scenario analysis can help tackle sustainability issues by generating insight into the potential long-term effects of present-day management. In northern Sweden, forests provide important benefits including climate change mitigation, biodiversity conservation, reindeer husbandry, local livelihoods, and recreation. Informed by local stakeholders’ views on how forests can be enabled to deliver these benefits, we created four forest management scenarios: the close-to-nature scenario (CTN) which emphasises biodiversity conservation, the classic management scenario (CLA) optimising the forests’ net present value, the intensified scenario (INT) maximising harvested wood from the forest, and the combined scenario (COM) applying a combination of measures from the CTN and INT. The scenarios were applied to the local forest landscape and modelled over a 100-year simulation period, and the results of the modelling were then evaluated by a diverse group of stakeholders. For most ecosystem services, there was a time lag of 10–50 years before noticeable effects and differences between the scenarios became evident, highlighting the need to consider both the short- and long-term effects of forest management. Evaluation by the stakeholders put the modelled results into a local context. They raised considerations relating to wildlife and hunting, climate change risks, social acceptability, and conflict, highlighting the value of evaluating the scenarios qualitatively as well as quantitatively. Overall, stakeholders thought that the CTN and CLA scenarios promoted more ecosystem services and posed fewer climate risks, while also creating less conflict among stakeholders. Our results emphasise the value of combining scientific and local knowledge when developing and evaluating future forest scenarios.},
	language = {en},
	urldate = {2023-03-10},
	journal = {Ecosystem Services},
	author = {Hallberg-Sramek, Isabella and Nordström, Eva-Maria and Priebe, Janina and Reimerson, Elsa and Mårald, Erland and Nordin, Annika},
	month = apr,
	year = {2023},
	keywords = {Forest management, Indigenous and local knowledge, Inter- and transdisciplinary research, Knowledge co-production, Scenario modelling, Stakeholder participation},
	pages = {101512},
}

Forest scenario analysis can help tackle sustainability issues by generating insight into the potential long-term effects of present-day management. In northern Sweden, forests provide important benefits including climate change mitigation, biodiversity conservation, reindeer husbandry, local livelihoods, and recreation. Informed by local stakeholders’ views on how forests can be enabled to deliver these benefits, we created four forest management scenarios: the close-to-nature scenario (CTN) which emphasises biodiversity conservation, the classic management scenario (CLA) optimising the forests’ net present value, the intensified scenario (INT) maximising harvested wood from the forest, and the combined scenario (COM) applying a combination of measures from the CTN and INT. The scenarios were applied to the local forest landscape and modelled over a 100-year simulation period, and the results of the modelling were then evaluated by a diverse group of stakeholders. For most ecosystem services, there was a time lag of 10–50 years before noticeable effects and differences between the scenarios became evident, highlighting the need to consider both the short- and long-term effects of forest management. Evaluation by the stakeholders put the modelled results into a local context. They raised considerations relating to wildlife and hunting, climate change risks, social acceptability, and conflict, highlighting the value of evaluating the scenarios qualitatively as well as quantitatively. Overall, stakeholders thought that the CTN and CLA scenarios promoted more ecosystem services and posed fewer climate risks, while also creating less conflict among stakeholders. Our results emphasise the value of combining scientific and local knowledge when developing and evaluating future forest scenarios.

@article{derba-maceluch_xylan_2023,
	title = {Xylan glucuronic acid side chains fix suberin-like aliphatic compounds to wood cell walls},
	volume = {238},
	issn = {1469-8137},
	url = {https://onlinelibrary.wiley.com/doi/abs/10.1111/nph.18712},
	doi = {10.1111/nph.18712},
	abstract = {Wood is the most important repository of assimilated carbon in the biosphere, in the form of large polymers (cellulose, hemicelluloses including glucuronoxylan, and lignin) that interactively form a composite, together with soluble extractives including phenolic and aliphatic compounds. Molecular interactions among these compounds are not fully understood. We have targeted the expression of a fungal α-glucuronidase to the wood cell wall of aspen (Populus tremula L. × tremuloides Michx.) and Arabidopsis (Arabidopsis thaliana (L.) Heynh), to decrease contents of the 4-O-methyl glucuronopyranose acid (mGlcA) substituent of xylan, to elucidate mGlcA's functions. The enzyme affected the content of aliphatic insoluble cell wall components having composition similar to suberin, which required mGlcA for binding to cell walls. Such suberin-like compounds have been previously identified in decayed wood, but here, we show their presence in healthy wood of both hardwood and softwood species. By contrast, γ-ester bonds between mGlcA and lignin were insensitive to cell wall-localized α-glucuronidase, supporting the intracellular formation of these bonds. These findings challenge the current view of the wood cell wall composition and reveal a novel function of mGlcA substituent of xylan in fastening of suberin-like compounds to cell wall. They also suggest an intracellular initiation of lignin–carbohydrate complex assembly.},
	language = {en},
	number = {1},
	urldate = {2023-03-10},
	journal = {New Phytologist},
	author = {Derba-Maceluch, Marta and Mitra, Madhusree and Hedenström, Mattias and Liu, Xiaokun and Gandla, Madhavi L. and Barbut, Félix R. and Abreu, Ilka N. and Donev, Evgeniy N. and Urbancsok, János and Moritz, Thomas and Jönsson, Leif J. and Tsang, Adrian and Powlowski, Justin and Master, Emma R. and Mellerowicz, Ewa J.},
	month = jan,
	year = {2023},
	note = {\_eprint: https://onlinelibrary.wiley.com/doi/pdf/10.1111/nph.18712},
	keywords = {Populus, lignin-carbohydrate complexes (LCCs), lignin–carbohydrate complexes, saccharification, suberin, wood cell wall, xylan},
	pages = {297--312},
}

Wood is the most important repository of assimilated carbon in the biosphere, in the form of large polymers (cellulose, hemicelluloses including glucuronoxylan, and lignin) that interactively form a composite, together with soluble extractives including phenolic and aliphatic compounds. Molecular interactions among these compounds are not fully understood. We have targeted the expression of a fungal α-glucuronidase to the wood cell wall of aspen (Populus tremula L. × tremuloides Michx.) and Arabidopsis (Arabidopsis thaliana (L.) Heynh), to decrease contents of the 4-O-methyl glucuronopyranose acid (mGlcA) substituent of xylan, to elucidate mGlcA's functions. The enzyme affected the content of aliphatic insoluble cell wall components having composition similar to suberin, which required mGlcA for binding to cell walls. Such suberin-like compounds have been previously identified in decayed wood, but here, we show their presence in healthy wood of both hardwood and softwood species. By contrast, γ-ester bonds between mGlcA and lignin were insensitive to cell wall-localized α-glucuronidase, supporting the intracellular formation of these bonds. These findings challenge the current view of the wood cell wall composition and reveal a novel function of mGlcA substituent of xylan in fastening of suberin-like compounds to cell wall. They also suggest an intracellular initiation of lignin–carbohydrate complex assembly.

@article{chowdhury_fluorogenic_2023,
	title = {Fluorogenic properties of 4-dimethylaminocinnamaldehyde ({DMACA}) enable high resolution imaging of cell-wall-bound proanthocyanidins in plant root tissues},
	volume = {13},
	issn = {1664-462X},
	url = {https://www.frontiersin.org/articles/10.3389/fpls.2022.1060804},
	doi = {10.3389/fpls.2022.1060804},
	abstract = {Proanthocyanidins (PAs) are polymeric phenolic compounds found in plants and used in many industrial applications. Despite strong evidence of herbivore and pathogen resistance-related properties of PAs, their in planta function is not fully understood. Determining the location and dynamics of PAs in plant tissues and cellular compartments is crucial to understand their mode of action. Such an approach requires microscopic localization with fluorescent dyes that specifically bind to PAs. Such dyes have hitherto been lacking. Here, we show that 4-dimethylaminocinnamaldehyde (DMACA) can be used as a PA-specific fluorescent dye that allows localization of PAs at high resolution in cell walls and inside cells using confocal microscopy, revealing features of previously unreported wall-bound PAs. We demonstrate several novel usages of DMACA as a fluorophore by taking advantage of its double staining compatibility with other fluorescent dyes. We illustrate the use of the dye alone and its co-localization with cell wall polymers in different Populus root tissues. The easy-to-use fluorescent staining method, together with its high photostability and compatibility with other fluorogenic dyes, makes DMACA a valuable tool for uncovering the biological function of PAs at a cellular level in plant tissues. DMACA can also be used in other plant tissues than roots, however care needs to be taken when tissues contain compounds that autofluoresce in the red spectral region which can be confounded with the PA-specific DMACA signal.},
	urldate = {2023-02-10},
	journal = {Frontiers in Plant Science},
	author = {Chowdhury, Jamil and Ferdous, Jannatul and Lihavainen, Jenna and Albrectsen, Benedicte Riber and Lundberg-Felten, Judith},
	month = feb,
	year = {2023},
	keywords = {⛔ No DOI found},
}

Proanthocyanidins (PAs) are polymeric phenolic compounds found in plants and used in many industrial applications. Despite strong evidence of herbivore and pathogen resistance-related properties of PAs, their in planta function is not fully understood. Determining the location and dynamics of PAs in plant tissues and cellular compartments is crucial to understand their mode of action. Such an approach requires microscopic localization with fluorescent dyes that specifically bind to PAs. Such dyes have hitherto been lacking. Here, we show that 4-dimethylaminocinnamaldehyde (DMACA) can be used as a PA-specific fluorescent dye that allows localization of PAs at high resolution in cell walls and inside cells using confocal microscopy, revealing features of previously unreported wall-bound PAs. We demonstrate several novel usages of DMACA as a fluorophore by taking advantage of its double staining compatibility with other fluorescent dyes. We illustrate the use of the dye alone and its co-localization with cell wall polymers in different Populus root tissues. The easy-to-use fluorescent staining method, together with its high photostability and compatibility with other fluorogenic dyes, makes DMACA a valuable tool for uncovering the biological function of PAs at a cellular level in plant tissues. DMACA can also be used in other plant tissues than roots, however care needs to be taken when tissues contain compounds that autofluoresce in the red spectral region which can be confounded with the PA-specific DMACA signal.

@article{siddique_molecular_2023,
	title = {Molecular studies of rust on {European} aspen suggest an autochthonous relationship shaped by genotype},
	volume = {14},
	issn = {1664-462X},
	url = {https://www.frontiersin.org/articles/10.3389/fpls.2023.1111001},
	doi = {10.3389/fpls.2023.1111001},
	abstract = {Forests are at increasing risk from pathogen outbreak. Climate change for example enhance the risk of local disease outbreaks, and naturalization of exotic pathogens may follow human activities, warranting robust pest surveillance routines to support forest management. Melampsora pinitorqua (pine twisting rust) is of concern in Swedish forestry, and here we evaluate the use of visible rust scores (VRS) on its obligate summer host, European aspen (Populus tremula) as a tool for quantification of the pathogen. With use of species-specific primers, we could detect the native rust, but we failed to detect two exotic rusts (M. medusae and M. larici-populina). We found that aspen genotype determined the presence of fungal genetic markers (amplifying the ITS2 region of the fungal rDNA sequence) as well as DNA sequences specific to M. pinitorqua. We correlated VRS with the amount of fungal DNA in the same leaf, and we related the findings to aspen genotype-specific parameters such as the ability to synthesize and store leaf condensed tannins (CT).  At the genotype level both positive and negative relationships were observed between CTs, fungal markers, and rust infestations. However, at the population level, foliar CT concentrations correlated negatively with general fungal- and rust-specific marker abundances.  Our results, therefore, do not support the use of VRS to assess Melampsora infestation in Aspen. They do, however, suggest that the relationship between European aspen and rust infestation may be characterized as autochthonous in northern Sweden.},
	urldate = {2023-02-24},
	journal = {Frontiers in Plant Science},
	author = {Siddique, Abu Bakar and Menke, Laura and Dinedurga, Melis and Albrectsen, Benedicte Riber},
	month = feb,
	year = {2023},
}

Forests are at increasing risk from pathogen outbreak. Climate change for example enhance the risk of local disease outbreaks, and naturalization of exotic pathogens may follow human activities, warranting robust pest surveillance routines to support forest management. Melampsora pinitorqua (pine twisting rust) is of concern in Swedish forestry, and here we evaluate the use of visible rust scores (VRS) on its obligate summer host, European aspen (Populus tremula) as a tool for quantification of the pathogen. With use of species-specific primers, we could detect the native rust, but we failed to detect two exotic rusts (M. medusae and M. larici-populina). We found that aspen genotype determined the presence of fungal genetic markers (amplifying the ITS2 region of the fungal rDNA sequence) as well as DNA sequences specific to M. pinitorqua. We correlated VRS with the amount of fungal DNA in the same leaf, and we related the findings to aspen genotype-specific parameters such as the ability to synthesize and store leaf condensed tannins (CT). At the genotype level both positive and negative relationships were observed between CTs, fungal markers, and rust infestations. However, at the population level, foliar CT concentrations correlated negatively with general fungal- and rust-specific marker abundances. Our results, therefore, do not support the use of VRS to assess Melampsora infestation in Aspen. They do, however, suggest that the relationship between European aspen and rust infestation may be characterized as autochthonous in northern Sweden.

@article{ntefidou_physcomitrium_2023,
	title = {Physcomitrium patens {PpRIC}, an ancestral {CRIB}-domain {ROP} effector, inhibits auxin-induced differentiation of apical initial cells},
	volume = {42},
	issn = {2211-1247},
	url = {https://www.cell.com/cell-reports/abstract/S2211-1247(23)00141-9},
	doi = {10.1016/j.celrep.2023.112130},
	abstract = {RHO guanosine triphosphatases are important eukaryotic regulators of cell differentiation and behavior. Plant ROP (RHO of plant) family members activate specific, incompletely characterized downstream signaling. The structurally simple land plant Physcomitrium patens is missing homologs of key animal and flowering plant RHO effectors but contains a single CRIB (CDC42/RAC interactive binding)-domain-containing RIC (ROP-interacting CRIB-containing) protein (PpRIC). Protonemal P. patens filaments elongate based on regular division and PpROP-dependent tip growth of apical initial cells, which upon stimulation by the hormone auxin differentiate caulonemal characteristics. PpRIC interacts with active PpROP1, co-localizes with this protein at the plasma membrane at the tip of apical initial cells, and accumulates in the nucleus. Remarkably, PpRIC is not required for tip growth but is targeted to the nucleus to block caulonema differentiation downstream of auxin-controlled gene expression. These observations establish functions of PpRIC in mediating crosstalk between ROP and auxin signaling, which contributes to the maintenance of apical initial cell identity.},
	language = {English},
	number = {2},
	urldate = {2023-02-23},
	journal = {Cell Reports},
	author = {Ntefidou, Maria and Eklund, D. Magnus and Bail, Aude Le and Schulmeister, Sylwia and Scherbel, Franziska and Brandl, Lisa and Dörfler, Wolfgang and Eichstädt, Chantal and Bannmüller, Anna and Ljung, Karin and Kost, Benedikt},
	month = feb,
	year = {2023},
	pmid = {36790931},
	note = {Publisher: Elsevier},
	keywords = {CP: Developmental biology, CP: Plants, CRIB domain, Physcomitrium patens, RHO/ROP GTPases, RHO/ROP effectors, auxin, cell differentiation, initial cells, land plant evolution, nuclear targeting, tip growth},
}

RHO guanosine triphosphatases are important eukaryotic regulators of cell differentiation and behavior. Plant ROP (RHO of plant) family members activate specific, incompletely characterized downstream signaling. The structurally simple land plant Physcomitrium patens is missing homologs of key animal and flowering plant RHO effectors but contains a single CRIB (CDC42/RAC interactive binding)-domain-containing RIC (ROP-interacting CRIB-containing) protein (PpRIC). Protonemal P. patens filaments elongate based on regular division and PpROP-dependent tip growth of apical initial cells, which upon stimulation by the hormone auxin differentiate caulonemal characteristics. PpRIC interacts with active PpROP1, co-localizes with this protein at the plasma membrane at the tip of apical initial cells, and accumulates in the nucleus. Remarkably, PpRIC is not required for tip growth but is targeted to the nucleus to block caulonema differentiation downstream of auxin-controlled gene expression. These observations establish functions of PpRIC in mediating crosstalk between ROP and auxin signaling, which contributes to the maintenance of apical initial cell identity.

@article{le_provost_oak_2023,
	title = {Oak stands along an elevation gradient have different molecular strategies for regulating bud phenology},
	volume = {23},
	issn = {1471-2229},
	url = {https://doi.org/10.1186/s12870-023-04069-2},
	doi = {10.1186/s12870-023-04069-2},
	abstract = {Global warming raises serious concerns about the persistence of species and populations locally adapted to their environment, simply because of the shift it produces in their adaptive landscape. For instance, the phenological cycle of tree species may be strongly affected by higher winter temperatures and late frost in spring. Given the variety of ecosystem services they provide, the question of forest tree adaptation has received increasing attention in the scientific community and catalyzed research efforts in ecology, evolutionary biology and functional genomics to study their adaptive capacity to respond to such perturbations.},
	number = {1},
	urldate = {2023-03-03},
	journal = {BMC Plant Biology},
	author = {Le Provost, Gregoire and Lalanne, Céline and Lesur, Isabelle and Louvet, Jean-Marc and Delzon, Sylvain and Kremer, Antoine and Labadie, Karine and Aury, Jean-Marc and Da Silva, Corinne and Moritz, Thomas and Plomion, Christophe},
	month = feb,
	year = {2023},
	keywords = {Bud phenology, Elevation cline, Gene expression, Hormone quantification, Response to temperature, Sessile oak},
	pages = {108},
}

Global warming raises serious concerns about the persistence of species and populations locally adapted to their environment, simply because of the shift it produces in their adaptive landscape. For instance, the phenological cycle of tree species may be strongly affected by higher winter temperatures and late frost in spring. Given the variety of ecosystem services they provide, the question of forest tree adaptation has received increasing attention in the scientific community and catalyzed research efforts in ecology, evolutionary biology and functional genomics to study their adaptive capacity to respond to such perturbations.

@article{nie_gapless_2023,
	title = {Gapless genome assembly of azalea and multi-omics investigation into divergence between two species with distinct flower color},
	volume = {10},
	issn = {2052-7276},
	url = {https://doi.org/10.1093/hr/uhac241},
	doi = {10.1093/hr/uhac241},
	abstract = {The genus Rhododendron (Ericaceae), with more than 1000 species highly diverse in flower color, is providing distinct ornamental values and a model system for flower color studies. Here, we investigated the divergence between two parental species with different flower color widely used for azalea breeding. Gapless genome assembly was generated for the yellow-flowered azalea, Rhododendron molle. Comparative genomics found recent proliferation of  long terminal repeat retrotransposons (LTR-RTs), especially Gypsy, has resulted in a 125 Mb (19\%) genome size increase in species-specific regions, and a significant amount of dispersed gene duplicates (13 402) and pseudogenes (17 437). Metabolomic assessment revealed that yellow flower coloration is attributed to the dynamic changes of carotenoids/flavonols biosynthesis and chlorophyll degradation. Time-ordered gene co-expression networks (TO-GCNs) and the comparison confirmed the metabolome and uncovered the specific gene regulatory changes underpinning the distinct flower pigmentation. B3 and ERF TFs were found dominating the gene regulation of carotenoids/flavonols characterized pigmentation in R. molle, while WRKY, ERF, WD40, C2H2, and NAC TFs collectively regulated the anthocyanins characterized pigmentation in the red-flowered R simsii. This study employed a multi-omics strategy in disentangling the complex divergence between two important azaleas and provided references for further functional genetics and molecular breeding.},
	number = {1},
	urldate = {2023-03-03},
	journal = {Horticulture Research},
	author = {Nie, Shuai and Zhao, Shi-Wei and Shi, Tian-Le and Zhao, Wei and Zhang, Ren-Gang and Tian, Xue-Chan and Guo, Jing-Fang and Yan, Xue-Mei and Bao, Yu-Tao and Li, Zhi-Chao and Kong, Lei and Ma, Hai-Yao and Chen, Zhao-Yang and Liu, Hui and El-Kassaby, Yousry A and Porth, Ilga and Yang, Fu-Sheng and Mao, Jian-Feng},
	month = jan,
	year = {2023},
	pages = {uhac241},
}

The genus Rhododendron (Ericaceae), with more than 1000 species highly diverse in flower color, is providing distinct ornamental values and a model system for flower color studies. Here, we investigated the divergence between two parental species with different flower color widely used for azalea breeding. Gapless genome assembly was generated for the yellow-flowered azalea, Rhododendron molle. Comparative genomics found recent proliferation of long terminal repeat retrotransposons (LTR-RTs), especially Gypsy, has resulted in a 125 Mb (19%) genome size increase in species-specific regions, and a significant amount of dispersed gene duplicates (13 402) and pseudogenes (17 437). Metabolomic assessment revealed that yellow flower coloration is attributed to the dynamic changes of carotenoids/flavonols biosynthesis and chlorophyll degradation. Time-ordered gene co-expression networks (TO-GCNs) and the comparison confirmed the metabolome and uncovered the specific gene regulatory changes underpinning the distinct flower pigmentation. B3 and ERF TFs were found dominating the gene regulation of carotenoids/flavonols characterized pigmentation in R. molle, while WRKY, ERF, WD40, C2H2, and NAC TFs collectively regulated the anthocyanins characterized pigmentation in the red-flowered R simsii. This study employed a multi-omics strategy in disentangling the complex divergence between two important azaleas and provided references for further functional genetics and molecular breeding.

@article{boussardon_tissue-specific_2023,
	title = {Tissue-{Specific} {Isolation} of {Tagged} {Arabidopsis} {Plastids}},
	volume = {3},
	issn = {2691-1299},
	url = {https://onlinelibrary.wiley.com/doi/abs/10.1002/cpz1.673},
	doi = {10.1002/cpz1.673},
	abstract = {Plastids are found in all plant cell types. However, most extraction methods to study these organelles are performed at the organ level (e.g., leaf, root, fruit) and do not allow for tissue-specific resolution, which hinders our understanding of their physiology. Therefore, IPTACT (Isolation of Plastids TAgged in specific Cell Types) was developed to isolate plastids in a tissue-specific manner in Arabidopsis thaliana (Arabidopsis). Plastids are biotinylated using one-shot transgenic lines, and tissue specificity is achieved with a suitable promoter as long as such a promoter exists. Cell-specific biotinylated plastids are then isolated with 2.8-µm streptavidin beads. Plastids extracted by IPTACT are suitable for RNA or protein isolation and subsequent tissue-specific OMICs analyses. This method provides the user with a powerful tool to investigate plastidial functions at cell-type resolution. Furthermore, it can easily be combined with studies using diverse genetic backgrounds and/or different developmental or stress conditions. © 2022 The Authors. Current Protocols published by Wiley Periodicals LLC. Basic Protocol 1: Promoter cloning and plant selection Basic Protocol 2: Isolation of biotinylated plastids Basic Protocol 3: Quality control of isolated plastids},
	language = {en},
	number = {2},
	urldate = {2023-02-22},
	journal = {Current Protocols},
	author = {Boussardon, Clément and Keech, Olivier},
	year = {2023},
	note = {\_eprint: https://onlinelibrary.wiley.com/doi/pdf/10.1002/cpz1.673},
	keywords = {Arabidopsis, biotin-streptavidin interaction, editable Golden Gate plasmids, plastids, tissue-specific isolation},
	pages = {e673},
}

Plastids are found in all plant cell types. However, most extraction methods to study these organelles are performed at the organ level (e.g., leaf, root, fruit) and do not allow for tissue-specific resolution, which hinders our understanding of their physiology. Therefore, IPTACT (Isolation of Plastids TAgged in specific Cell Types) was developed to isolate plastids in a tissue-specific manner in Arabidopsis thaliana (Arabidopsis). Plastids are biotinylated using one-shot transgenic lines, and tissue specificity is achieved with a suitable promoter as long as such a promoter exists. Cell-specific biotinylated plastids are then isolated with 2.8-µm streptavidin beads. Plastids extracted by IPTACT are suitable for RNA or protein isolation and subsequent tissue-specific OMICs analyses. This method provides the user with a powerful tool to investigate plastidial functions at cell-type resolution. Furthermore, it can easily be combined with studies using diverse genetic backgrounds and/or different developmental or stress conditions. © 2022 The Authors. Current Protocols published by Wiley Periodicals LLC. Basic Protocol 1: Promoter cloning and plant selection Basic Protocol 2: Isolation of biotinylated plastids Basic Protocol 3: Quality control of isolated plastids

@article{jonsson_multiple_2023,
	title = {Multiple mechanisms behind plant bending},
	volume = {9},
	copyright = {2022 Springer Nature Limited},
	issn = {2055-0278},
	url = {https://www.nature.com/articles/s41477-022-01310-y},
	doi = {10.1038/s41477-022-01310-y},
	abstract = {To survive, plants constantly adapt their body shape to their environment. This often involves remarkably rapid bending of their organs such as stems, leaves and roots. Since plant cells are enclosed by stiff cell walls, they use various strategies for bending their organs, which differ from bending mechanisms of soft animal tissues and involve larger physical forces. Here we attempt to summarize and link different viewpoints on bending mechanisms: genes and signalling, mathematical modelling and biomechanics. We argue that quantifying cell growth and physical forces could open a new level in our understanding of bending and resolve some of its paradoxes.},
	language = {en},
	number = {1},
	urldate = {2023-02-03},
	journal = {Nature Plants},
	author = {Jonsson, Kristoffer and Ma, Yuan and Routier-Kierzkowska, Anne-Lise and Bhalerao, Rishikesh P.},
	month = jan,
	year = {2023},
	keywords = {Plant morphogenesis, Tropism},
	pages = {13--21},
}

To survive, plants constantly adapt their body shape to their environment. This often involves remarkably rapid bending of their organs such as stems, leaves and roots. Since plant cells are enclosed by stiff cell walls, they use various strategies for bending their organs, which differ from bending mechanisms of soft animal tissues and involve larger physical forces. Here we attempt to summarize and link different viewpoints on bending mechanisms: genes and signalling, mathematical modelling and biomechanics. We argue that quantifying cell growth and physical forces could open a new level in our understanding of bending and resolve some of its paradoxes.

@article{igamberdiev_toward_2023,
	title = {Toward understanding the emergence of life: {A} dual function of the system of nucleotides in the metabolically closed autopoietic organization},
	volume = {224},
	issn = {0303-2647},
	shorttitle = {Toward understanding the emergence of life},
	url = {https://www.sciencedirect.com/science/article/pii/S0303264723000126},
	doi = {10.1016/j.biosystems.2023.104837},
	abstract = {General structure of metabolism includes the reproduction of catalysts that govern metabolism. In this structure, the system becomes autopoietic in the sense of Maturana and Varela, and it is closed to efficient causation as defined by Robert Rosen. The autopoietic maintenance and operation of the catalysts takes place via the set of free nucleotides while the synthesis of catalysts occurs via the information encoded by the set of nucleotides arranged in polymers of RNA and DNA. Both energy charge and genetic information use the components of the same pool of nucleoside triphosphates, which is equilibrated by thermodynamic buffering enzymes such as nucleoside diphosphate kinase and adenylate kinase. This occurs in a way that the system becomes internally stable and metabolically closed, which initially could be realized at the level of ribozymes catalyzing basic metabolic reactions as well as own reproduction. The function of ATP, GTP, UTP, and CTP is dual, as these species participate both in the general metabolism as free nucleotides and in the transfer of genetic information via covalent polymerization to nucleic acids. The changes in their pools directly impact both bioenergetic pathways and nucleic acid turnover. Here we outline the concept of metabolic closure of biosystems grounded in the dual function of nucleotide coenzymes that serve both as energetic and informational molecules and through this duality generate the autopoietic performance and the ability for codepoietic evolutionary transformations of living systems starting from the emergence of prebiotic systems.},
	language = {en},
	urldate = {2023-01-20},
	journal = {Biosystems},
	author = {Igamberdiev, Abir U. and Kleczkowski, Leszek A.},
	month = feb,
	year = {2023},
	keywords = {Autopoiesis, Codepoiesis, Coenzyme, Metabolic closure, Nucleoside triphosphates, Ribozymes, Thermodynamic buffering},
	pages = {104837},
}

General structure of metabolism includes the reproduction of catalysts that govern metabolism. In this structure, the system becomes autopoietic in the sense of Maturana and Varela, and it is closed to efficient causation as defined by Robert Rosen. The autopoietic maintenance and operation of the catalysts takes place via the set of free nucleotides while the synthesis of catalysts occurs via the information encoded by the set of nucleotides arranged in polymers of RNA and DNA. Both energy charge and genetic information use the components of the same pool of nucleoside triphosphates, which is equilibrated by thermodynamic buffering enzymes such as nucleoside diphosphate kinase and adenylate kinase. This occurs in a way that the system becomes internally stable and metabolically closed, which initially could be realized at the level of ribozymes catalyzing basic metabolic reactions as well as own reproduction. The function of ATP, GTP, UTP, and CTP is dual, as these species participate both in the general metabolism as free nucleotides and in the transfer of genetic information via covalent polymerization to nucleic acids. The changes in their pools directly impact both bioenergetic pathways and nucleic acid turnover. Here we outline the concept of metabolic closure of biosystems grounded in the dual function of nucleotide coenzymes that serve both as energetic and informational molecules and through this duality generate the autopoietic performance and the ability for codepoietic evolutionary transformations of living systems starting from the emergence of prebiotic systems.

@article{kidwai_species-specific_2023,
	title = {Species-specific transcriptional reprogramming during adventitious root initiation},
	volume = {28},
	issn = {1360-1385},
	url = {https://www.sciencedirect.com/science/article/pii/S1360138522003028},
	doi = {10.1016/j.tplants.2022.11.003},
	abstract = {Adventitious roots or shoot-borne roots transdifferentiate from cells close to vascular tissues after cell reprogramming, which is associated with increased transcriptional activity. Recently, Garg et al. provided a genome-wide landscape of transcriptional signatures during the early stages of adventitious root initiation in rice and showed that conserved transcription factors acquire species-specific function.},
	language = {en},
	number = {2},
	urldate = {2023-01-26},
	journal = {Trends in Plant Science},
	author = {Kidwai, Maria and Mishra, Priyanka and Bellini, Catherine},
	month = feb,
	year = {2023},
	keywords = {adventitious root, dicotyledons, epigenetic regulation, monocotyledons, transcription factors},
	pages = {128--130},
}

Adventitious roots or shoot-borne roots transdifferentiate from cells close to vascular tissues after cell reprogramming, which is associated with increased transcriptional activity. Recently, Garg et al. provided a genome-wide landscape of transcriptional signatures during the early stages of adventitious root initiation in rice and showed that conserved transcription factors acquire species-specific function.

@article{chandra_transformer-based_2023,
	title = {Transformer-based deep learning for predicting protein properties in the life sciences},
	volume = {12},
	issn = {2050-084X},
	url = {https://doi.org/10.7554/eLife.82819},
	doi = {10.7554/eLife.82819},
	abstract = {Recent developments in deep learning, coupled with an increasing number of sequenced proteins, have led to a breakthrough in life science applications, in particular in protein property prediction. There is hope that deep learning can close the gap between the number of sequenced proteins and proteins with known properties based on lab experiments. Language models from the field of natural language processing have gained popularity for protein property predictions and have led to a new computational revolution in biology, where old prediction results are being improved regularly. Such models can learn useful multipurpose representations of proteins from large open repositories of protein sequences and can be used, for instance, to predict protein properties. The field of natural language processing is growing quickly because of developments in a class of models based on a particular model—the Transformer model. We review recent developments and the use of large-scale Transformer models in applications for predicting protein characteristics and how such models can be used to predict, for example, post-translational modifications. We review shortcomings of other deep learning models and explain how the Transformer models have quickly proven to be a very promising way to unravel information hidden in the sequences of amino acids.},
	urldate = {2023-01-20},
	journal = {eLife},
	author = {Chandra, Abel and Tünnermann, Laura and Löfstedt, Tommy and Gratz, Regina},
	editor = {Dötsch, Volker},
	month = jan,
	year = {2023},
	keywords = {deep learning, life sciences, machine learning, protein property prediction, transformers},
	pages = {e82819},
}

Recent developments in deep learning, coupled with an increasing number of sequenced proteins, have led to a breakthrough in life science applications, in particular in protein property prediction. There is hope that deep learning can close the gap between the number of sequenced proteins and proteins with known properties based on lab experiments. Language models from the field of natural language processing have gained popularity for protein property predictions and have led to a new computational revolution in biology, where old prediction results are being improved regularly. Such models can learn useful multipurpose representations of proteins from large open repositories of protein sequences and can be used, for instance, to predict protein properties. The field of natural language processing is growing quickly because of developments in a class of models based on a particular model—the Transformer model. We review recent developments and the use of large-scale Transformer models in applications for predicting protein characteristics and how such models can be used to predict, for example, post-translational modifications. We review shortcomings of other deep learning models and explain how the Transformer models have quickly proven to be a very promising way to unravel information hidden in the sequences of amino acids.

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

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

@article{zacharaki_non-coding_2023,
	title = {The non-coding {RNA} {SVALKA} locus produces a cis- natural antisense transcript that negatively regulates the expression of {CBF1} and biomass production at normal temperatures},
	issn = {2590-3462},
	url = {https://www.sciencedirect.com/science/article/pii/S2590346223000494},
	doi = {10.1016/j.xplc.2023.100551},
	abstract = {Non-coding transcription is present in all eukaryotic genomes, but we lack fundamental knowledge about its importance for an organism’s ability to develop properly. In plants, emerging evidence highlights the essential biological role of non-coding transcription in regulating coding transcription. However, the molecular insights into the regulation are largely unknown. Here, we show that a long isoform of the long non-coding RNA, SVALKA-L (SVK-L), forms a natural antisense transcript to the host gene CBF1 and negatively regulates CBF1 mRNA levels at normal temperatures in the model plant Arabidopsis thaliana. Furthermore, we show detailed evidence for the specific mode of action for SVK-L. This pathway includes the formation of double stranded RNA that is recognized by the DICER proteins and subsequent down-regulation of CBF1 mRNA levels. Thus, the CBF1-SVK regulatory circuit is not only important for the previously known role in cold temperature acclimation but also for biomass production at normal temperatures. Our study characterizes a developmental role of SVK-L and offers mechanistic insight into how biologically important overlapping natural antisense transcripts can act on and fine-tune the steady state levels of their host gene’s mRNA.},
	language = {en},
	urldate = {2023-01-24},
	journal = {Plant Communications},
	author = {Zacharaki, Vasiliki and Meena, Shiv Kumar and Kindgren, Peter},
	month = jan,
	year = {2023},
	keywords = {cis- natural antisense transcript, non-coding transcription},
	pages = {100551},
}

Non-coding transcription is present in all eukaryotic genomes, but we lack fundamental knowledge about its importance for an organism’s ability to develop properly. In plants, emerging evidence highlights the essential biological role of non-coding transcription in regulating coding transcription. However, the molecular insights into the regulation are largely unknown. Here, we show that a long isoform of the long non-coding RNA, SVALKA-L (SVK-L), forms a natural antisense transcript to the host gene CBF1 and negatively regulates CBF1 mRNA levels at normal temperatures in the model plant Arabidopsis thaliana. Furthermore, we show detailed evidence for the specific mode of action for SVK-L. This pathway includes the formation of double stranded RNA that is recognized by the DICER proteins and subsequent down-regulation of CBF1 mRNA levels. Thus, the CBF1-SVK regulatory circuit is not only important for the previously known role in cold temperature acclimation but also for biomass production at normal temperatures. Our study characterizes a developmental role of SVK-L and offers mechanistic insight into how biologically important overlapping natural antisense transcripts can act on and fine-tune the steady state levels of their host gene’s mRNA.

@article{liu_plant_2023,
	title = {The plant trans-{Golgi} network component {ECHIDNA} regulates defense, cell death, and endoplasmic reticulum stress},
	volume = {191},
	issn = {0032-0889},
	url = {https://doi.org/10.1093/plphys/kiac400},
	doi = {10.1093/plphys/kiac400},
	abstract = {The trans-Golgi network (TGN) acts as a central platform for sorting and secreting various cargoes to the cell surface, thus being essential for the full execution of plant immunity. However, the fine-tuned regulation of TGN components in plant defense and stress response has been not fully elucidated. Our study revealed that despite largely compromising penetration resistance, the loss-of-function mutation of the TGN component protein ECHIDNA (ECH) induced enhanced postinvasion resistance to powdery mildew in Arabidopsis thaliana. Genetic and transcriptome analyses and hormone profiling demonstrated that ECH loss resulted in salicylic acid (SA) hyperaccumulation via the ISOCHORISMATE SYNTHASE 1 biosynthesis pathway, thereby constitutively activating SA-dependent innate immunity that was largely responsible for the enhanced postinvasion resistance. Furthermore, the ech mutant displayed accelerated SA-independent spontaneous cell death and constitutive POWDERY MILDEW RESISTANCE 4-mediated callose depositions. In addition, ECH loss led to a chronically prolonged endoplasmic reticulum stress in the ech mutant. These results provide insights into understanding the role of TGN components in the regulation of plant immunity and stress responses.},
	number = {1},
	urldate = {2023-01-09},
	journal = {Plant Physiology},
	author = {Liu, Lijiang and Qin, Li and Safdar, Luqman Bin and Zhao, Chuanji and Cheng, Xiaohui and Xie, Meili and Zhang, Yi and Gao, Feng and Bai, Zetao and Huang, Junyan and Bhalerao, Rishikesh P and Liu, Shengyi and Wei, Yangdou},
	month = jan,
	year = {2023},
	pages = {558--574},
}

The trans-Golgi network (TGN) acts as a central platform for sorting and secreting various cargoes to the cell surface, thus being essential for the full execution of plant immunity. However, the fine-tuned regulation of TGN components in plant defense and stress response has been not fully elucidated. Our study revealed that despite largely compromising penetration resistance, the loss-of-function mutation of the TGN component protein ECHIDNA (ECH) induced enhanced postinvasion resistance to powdery mildew in Arabidopsis thaliana. Genetic and transcriptome analyses and hormone profiling demonstrated that ECH loss resulted in salicylic acid (SA) hyperaccumulation via the ISOCHORISMATE SYNTHASE 1 biosynthesis pathway, thereby constitutively activating SA-dependent innate immunity that was largely responsible for the enhanced postinvasion resistance. Furthermore, the ech mutant displayed accelerated SA-independent spontaneous cell death and constitutive POWDERY MILDEW RESISTANCE 4-mediated callose depositions. In addition, ECH loss led to a chronically prolonged endoplasmic reticulum stress in the ech mutant. These results provide insights into understanding the role of TGN components in the regulation of plant immunity and stress responses.

@article{walker_cytokinin_2023,
	title = {Cytokinin signaling regulates two-stage inflorescence arrest in {Arabidopsis}},
	volume = {191},
	issn = {0032-0889},
	url = {https://doi.org/10.1093/plphys/kiac514},
	doi = {10.1093/plphys/kiac514},
	abstract = {To maximize reproductive success, flowering plants must correctly time entry and exit from the reproductive phase. While much is known about mechanisms that regulate initiation of flowering, end-of-flowering remains largely uncharacterized. End-of-flowering in Arabidopsis (Arabidopsis thaliana) consists of quasi-synchronous arrest of inflorescences, but it is unclear how arrest is correctly timed with respect to environmental stimuli and reproductive success. Here, we showed that Arabidopsis inflorescence arrest is a complex developmental phenomenon, which includes the arrest of the inflorescence meristem (IM), coupled with a separable “floral arrest” of all unopened floral primordia; these events occur well before visible inflorescence arrest. We showed that global inflorescence removal delays both IM and floral arrest, but that local fruit removal only delays floral arrest, emphasizing their separability. We tested whether cytokinin regulates inflorescence arrest, and found that cytokinin signaling dynamics mirror IM activity, while cytokinin treatment can delay both IM and floral arrest. We further showed that gain-of-function cytokinin receptor mutants can delay IM and floral arrest; conversely, loss-of-function mutants prevented the extension of flowering in response to inflorescence removal. Collectively, our data suggest that the dilution of cytokinin among an increasing number of sink organs leads to end-of-flowering in Arabidopsis by triggering IM and floral arrest.},
	number = {1},
	urldate = {2023-01-09},
	journal = {Plant Physiology},
	author = {Walker, Catriona H and Ware, Alexander and Šimura, Jan and Ljung, Karin and Wilson, Zoe and Bennett, Tom},
	month = jan,
	year = {2023},
	pages = {479--495},
}

To maximize reproductive success, flowering plants must correctly time entry and exit from the reproductive phase. While much is known about mechanisms that regulate initiation of flowering, end-of-flowering remains largely uncharacterized. End-of-flowering in Arabidopsis (Arabidopsis thaliana) consists of quasi-synchronous arrest of inflorescences, but it is unclear how arrest is correctly timed with respect to environmental stimuli and reproductive success. Here, we showed that Arabidopsis inflorescence arrest is a complex developmental phenomenon, which includes the arrest of the inflorescence meristem (IM), coupled with a separable “floral arrest” of all unopened floral primordia; these events occur well before visible inflorescence arrest. We showed that global inflorescence removal delays both IM and floral arrest, but that local fruit removal only delays floral arrest, emphasizing their separability. We tested whether cytokinin regulates inflorescence arrest, and found that cytokinin signaling dynamics mirror IM activity, while cytokinin treatment can delay both IM and floral arrest. We further showed that gain-of-function cytokinin receptor mutants can delay IM and floral arrest; conversely, loss-of-function mutants prevented the extension of flowering in response to inflorescence removal. Collectively, our data suggest that the dilution of cytokinin among an increasing number of sink organs leads to end-of-flowering in Arabidopsis by triggering IM and floral arrest.

@article{kleczkowski_magnesium_2023,
	title = {Magnesium and cell energetics: {At} the junction of metabolism of adenylate and non-adenylate nucleotides},
	volume = {280},
	issn = {0176-1617},
	shorttitle = {Magnesium and cell energetics},
	url = {https://www.sciencedirect.com/science/article/pii/S0176161722002875},
	doi = {10.1016/j.jplph.2022.153901},
	abstract = {Free magnesium (Mg2+) represents a powerful signal arising from interconversions of adenylates (ATP, ADP and AMP). This is a consequence of the involvement of adenylate kinase (AK) which equilibrates adenylates and uses defined species of Mg-complexed and Mg-free adenylates in both directions of its reaction. However, cells contain also other reversible Mg2+-dependent enzymes that equilibrate non-adenylate nucleotides (uridylates, cytidylates and guanylates), i.e. nucleoside monophosphate kinases (NMPKs) and nucleoside diphosphate kinase (NDPK). Here, we propose that AK activity is tightly coupled to activities of NMPK and NDPK, linking adenylate equilibrium to equilibria of other nucleotides, and with [Mg2+] controlling the ratios of Mg-chelated and Mg-free nucleotides. This coupling establishes main hubs for adenylate-driven equilibration of non-adenylate nucleotides, with [Mg2+] acting as signal arising from all nucleotides rather than adenylates only. Further consequences involve an overall adenylate control of UTP-, GTP- and CTP-dependent pathways and the availability of substrates for RNA and DNA synthesis.},
	language = {en},
	urldate = {2022-12-30},
	journal = {Journal of Plant Physiology},
	author = {Kleczkowski, Leszek A. and Igamberdiev, Abir U.},
	month = jan,
	year = {2023},
	keywords = {Adenylate kinase, Guanylate kinase, Magnesium signaling, Nucleoside diphosphate kinase, Nucleoside monophosphate kinase, Uridylate-cytidylate kinase},
	pages = {153901},
}

Free magnesium (Mg2+) represents a powerful signal arising from interconversions of adenylates (ATP, ADP and AMP). This is a consequence of the involvement of adenylate kinase (AK) which equilibrates adenylates and uses defined species of Mg-complexed and Mg-free adenylates in both directions of its reaction. However, cells contain also other reversible Mg2+-dependent enzymes that equilibrate non-adenylate nucleotides (uridylates, cytidylates and guanylates), i.e. nucleoside monophosphate kinases (NMPKs) and nucleoside diphosphate kinase (NDPK). Here, we propose that AK activity is tightly coupled to activities of NMPK and NDPK, linking adenylate equilibrium to equilibria of other nucleotides, and with [Mg2+] controlling the ratios of Mg-chelated and Mg-free nucleotides. This coupling establishes main hubs for adenylate-driven equilibration of non-adenylate nucleotides, with [Mg2+] acting as signal arising from all nucleotides rather than adenylates only. Further consequences involve an overall adenylate control of UTP-, GTP- and CTP-dependent pathways and the availability of substrates for RNA and DNA synthesis.

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

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