@article{guo_near-gapless_2025,
	title = {Near-gapless telomere-to-telomere reference nuclear genome and variable mitochondrial genome of \textit{{Amborella} trichopoda}},
	volume = {52},
	issn = {1673-8527},
	url = {https://www.sciencedirect.com/science/article/pii/S1673852725001250},
	doi = {10.1016/j.jgg.2025.04.016},
	number = {9},
	urldate = {2025-09-26},
	journal = {Journal of Genetics and Genomics},
	author = {Guo, Zhonglong and Guo, Jing-Fang and Wei, Zhi-Yan and Zhang, Ren-Gang and McMahan, Scott and Nie, Shuai and Yan, Xue-Mei and Zhou, Shan-Shan and Yun, Quan-Zheng and Wu, Jia-Yi and Ge, Jing and Yang, Yong and Xue, Jia-Yu and Mao, Jian-Feng},
	month = sep,
	year = {2025},
	pages = {1151--1154},
}

@article{donev_glucuronoyl_2025,
	title = {Glucuronoyl {Esterase} of {Pathogenic} {Phanerochaete} carnosa {Induces} {Immune} {Responses} in {Aspen} {Independently} of {Its} {Enzymatic} {Activity}},
	volume = {n/a},
	copyright = {© 2025 The Author(s). Plant Biotechnology Journal published by Society for Experimental Biology and The Association of Applied Biologists and John Wiley \& Sons Ltd.},
	issn = {1467-7652},
	url = {https://onlinelibrary.wiley.com/doi/abs/10.1111/pbi.70357},
	doi = {10.1111/pbi.70357},
	abstract = {Microbial enzymes expressed in plants add new functionalities but occasionally trigger undesirable immune responses. Phanerochaete carnosa glucuronoyl esterase (PcGCE) hydrolyses the bond between lignin and 4-O-methyl-α-D-glucuronic acid substituent of glucuronoxylan. PcGCE constitutively expressed in Arabidopsis or hybrid aspen (Populus tremula × tremuloides) improved saccharification but also induced premature leaf senescence. To understand what triggered this senescence, we characterised PcGCE-expressing hybrid aspen by microscopy and omics approaches, supplemented by grafting and recombinant protein application experiments. PcGCE induced massive immune responses followed by senescence in the leaves. Expressing an inactive (PcGCES217A) enzyme has led to similar phenotypes, excluding a possibility that damage-associated molecular patterns (DAMPs) released by glucuronoyl esterase triggered immune responses. Grafting experiments showed that PcGCE transcripts are not mobile but they induce systemic responses. Recombinant PcGCE protein applied to leaves did not induce such responses; thus, PcGCE is probably not perceived as a pathogen-associated molecular pattern (PAMP). We suggest that the observed high expression of PcGCE from the 35S promoter triggers the unfolded protein response. Indeed, restricting PcGCE expression to short-lived xylem cells by using the wood-specific promoter avoided all detrimental effects. Thus, wood-specific expression is a viable strategy for PcGCE deployment in planta, which might be applicable for other stress-inducing proteins.},
	language = {en},
	number = {n/a},
	urldate = {2025-09-19},
	journal = {Plant Biotechnology Journal},
	author = {Donev, Evgeniy N. and Derba-Maceluch, Marta and Liu, Xiao-Kun and Bwanika, Henri Colyn and Dobrowolska, Izabela and Thapa, Mohit and Leśniewska, Joanna and Šimura, Jan and Yi-Lin Tsai, Alex and Krajewski, Konrad S. and Boström, Dan and Kleczkowski, Leszek A. and Eriksson, Maria E. and Ljung, Karin and Master, Emma R. and Mellerowicz, Ewa J.},
	year = {2025},
	note = {\_eprint: https://onlinelibrary.wiley.com/doi/pdf/10.1111/pbi.70357},
	keywords = {PTI, Populus, biotic stress, glucuronoyl esterase, lignocellulose improvement, transgenic crops, unfolded protein response},
}

Microbial enzymes expressed in plants add new functionalities but occasionally trigger undesirable immune responses. Phanerochaete carnosa glucuronoyl esterase (PcGCE) hydrolyses the bond between lignin and 4-O-methyl-α-D-glucuronic acid substituent of glucuronoxylan. PcGCE constitutively expressed in Arabidopsis or hybrid aspen (Populus tremula × tremuloides) improved saccharification but also induced premature leaf senescence. To understand what triggered this senescence, we characterised PcGCE-expressing hybrid aspen by microscopy and omics approaches, supplemented by grafting and recombinant protein application experiments. PcGCE induced massive immune responses followed by senescence in the leaves. Expressing an inactive (PcGCES217A) enzyme has led to similar phenotypes, excluding a possibility that damage-associated molecular patterns (DAMPs) released by glucuronoyl esterase triggered immune responses. Grafting experiments showed that PcGCE transcripts are not mobile but they induce systemic responses. Recombinant PcGCE protein applied to leaves did not induce such responses; thus, PcGCE is probably not perceived as a pathogen-associated molecular pattern (PAMP). We suggest that the observed high expression of PcGCE from the 35S promoter triggers the unfolded protein response. Indeed, restricting PcGCE expression to short-lived xylem cells by using the wood-specific promoter avoided all detrimental effects. Thus, wood-specific expression is a viable strategy for PcGCE deployment in planta, which might be applicable for other stress-inducing proteins.

@article{lei_comprehensive_2025,
	title = {Comprehensive analysis of 1,771 transcriptomes from 7 tissues enhance genetic and biological interpretations of maize complex traits},
	volume = {15},
	issn = {2160-1836},
	url = {https://doi.org/10.1093/g3journal/jkaf140},
	doi = {10.1093/g3journal/jkaf140},
	abstract = {By reanalyzing 1,771 RNA-seq datasets from 7 tissues in a maize diversity panel, we explored the landscape of multi-tissue transcriptome variation, evolution patterns of tissue-specific genes, and built a comprehensive multi-tissue gene regulation atlas to understand the genetic regulation of maize complex traits. Through an integrative analysis of tissue-specific gene regulatory variation with genome-wide association studies, we detected relevant tissue types and several candidate genes for a number of agronomic traits, including leaf during the day for the anthesis-silking interval, leaf during the day for kernel Zeinoxanthin level, and root for ear height, highlighting the potential contribution of tissue-specific gene expression to variation in agronomic traits. Using transcriptome-wide association and colocalization analysis, we associated tissue-specific expression variation of 74 genes to agronomic traits variation. Our findings provide novel insights into the genetic and biological mechanisms underlying maize complex traits, and the multi-tissue regulatory atlas serves as a primary source for biological interpretation, functional validation, and genomic improvement of maize.},
	number = {9},
	urldate = {2025-09-19},
	journal = {G3 Genes{\textbar}Genomes{\textbar}Genetics},
	author = {Lei, Mengyu and Si, Huan and Zhu, Mingjia and Han, Yu and Liu, Wei and Dai, Yifei and Ji, Yan and Liu, Zhengwen and Hao, Fan and Hao, Ran and Zhao, Jiarui and Ye, Guoyou and Zan, Yanjun},
	month = sep,
	year = {2025},
	pages = {jkaf140},
}

By reanalyzing 1,771 RNA-seq datasets from 7 tissues in a maize diversity panel, we explored the landscape of multi-tissue transcriptome variation, evolution patterns of tissue-specific genes, and built a comprehensive multi-tissue gene regulation atlas to understand the genetic regulation of maize complex traits. Through an integrative analysis of tissue-specific gene regulatory variation with genome-wide association studies, we detected relevant tissue types and several candidate genes for a number of agronomic traits, including leaf during the day for the anthesis-silking interval, leaf during the day for kernel Zeinoxanthin level, and root for ear height, highlighting the potential contribution of tissue-specific gene expression to variation in agronomic traits. Using transcriptome-wide association and colocalization analysis, we associated tissue-specific expression variation of 74 genes to agronomic traits variation. Our findings provide novel insights into the genetic and biological mechanisms underlying maize complex traits, and the multi-tissue regulatory atlas serves as a primary source for biological interpretation, functional validation, and genomic improvement of maize.

@article{marcon_transcriptional_2025,
	title = {A transcriptional roadmap of the yearly growth cycle in {Populus} trees},
	volume = {37},
	issn = {1040-4651},
	url = {https://doi.org/10.1093/plcell/koaf208},
	doi = {10.1093/plcell/koaf208},
	abstract = {Populus species have adapted to many different boreal environments, characterized by fluctuating seasons. The environmental shifts throughout the year trigger molecular responses in trees, regulating crucial developmental processes. To study these molecular responses, we performed RNA sequencing on 207 samples from European aspen (Populus tremula) trees grown outdoors during different stages of their annual growth cycle, together with samples from hybrid aspen (Populus tremula × tremuloides hybrid T89) trees grown in controlled conditions mimicking seasonal changes in day length and temperature. This created a complete transcriptional roadmap of the yearly growth cycle of Populus trees. Co-expression network analyses produced 46 modules, 36 of which show a seasonal expression profile where many aspects were mimicked by indoor samples. However, several modules differed between outdoor and indoor conditions, indicating that important aspects of growth regulation are missed in experiments conducted under controlled conditions. The module networks identify gene hubs involved in season-specific molecular processes of Populus trees during the year. To make the dataset easily accessible, we developed POPUL-R (https://lauragarciaromanach.shinyapps.io/popul\_r\_mini/), a Shiny app enabling users to visualize gene expression data and create interactive networks. POPUL-R will be a valuable tool for the scientific community to explore the role of specific genes in the annual growth cycle of trees.},
	number = {9},
	urldate = {2025-09-12},
	journal = {The Plant Cell},
	author = {Marcon, Alice and Romañach, Laura García and André, Domenique and Ding, Jihua and Zhang, Bo and Hvidsten, Torgeir R and Nilsson, Ove},
	month = sep,
	year = {2025},
	pages = {koaf208},
}

Populus species have adapted to many different boreal environments, characterized by fluctuating seasons. The environmental shifts throughout the year trigger molecular responses in trees, regulating crucial developmental processes. To study these molecular responses, we performed RNA sequencing on 207 samples from European aspen (Populus tremula) trees grown outdoors during different stages of their annual growth cycle, together with samples from hybrid aspen (Populus tremula × tremuloides hybrid T89) trees grown in controlled conditions mimicking seasonal changes in day length and temperature. This created a complete transcriptional roadmap of the yearly growth cycle of Populus trees. Co-expression network analyses produced 46 modules, 36 of which show a seasonal expression profile where many aspects were mimicked by indoor samples. However, several modules differed between outdoor and indoor conditions, indicating that important aspects of growth regulation are missed in experiments conducted under controlled conditions. The module networks identify gene hubs involved in season-specific molecular processes of Populus trees during the year. To make the dataset easily accessible, we developed POPUL-R (https://lauragarciaromanach.shinyapps.io/popul_r_mini/), a Shiny app enabling users to visualize gene expression data and create interactive networks. POPUL-R will be a valuable tool for the scientific community to explore the role of specific genes in the annual growth cycle of trees.

@article{boussardon_comparative_2025,
	title = {Comparative {Study} of the {Mitochondrial} {Proteome} {From} {Mesophyll}, {Vascular}, and {Guard} {Cells} in {Response} to {Carbon} {Starvation}},
	volume = {177},
	copyright = {© 2025 The Author(s). Physiologia Plantarum published by John Wiley \& Sons Ltd on behalf of Scandinavian Plant Physiology Society.},
	issn = {1399-3054},
	url = {https://onlinelibrary.wiley.com/doi/abs/10.1111/ppl.70465},
	doi = {10.1111/ppl.70465},
	abstract = {A leaf is an organ composed of different tissues that fulfill specific functions. We hypothesized that since cells in vascular or mesophyll tissues as well as in stoma are developmentally tuned to operate their functions, mitochondria from these cells could exhibit significant metabolic differences. Using the IMTACT method, mitochondria were isolated from these three specific cell types, and the subsequent proteomes were analyzed. At steady state, mitochondria from vascular and guard cells had a significantly higher abundance of proteins associated with the mtETC, the TCA cycle, and the metabolic use of amino acids (glutamate, proline, isoleucine, leucine, and valine) as alternative substrates. Intriguingly, the mitochondria from guard cells also had a much lower abundance of proteins involved in the translation machinery, thus raising questions about the efficiency of the mitochondrial protein turnover in these cells. In a second step, we carried out the same comparative analysis, but with plants that were subjected to carbon starvation by placing them in prolonged darkness for three or 6 days. For all cell types studied, an increased abundance of proteins involved in branched-chain amino acid metabolism was detected. However, while guard cell mitochondria underwent a drastic reduction in proteins involved in respiration, translation, and RNA editing, suggesting a sharp downregulation of mitochondrial functions, mitochondrial proteomes from mesophyll and vascular cells did not show many differences, except for an increased arginine/proline/glutamate metabolism. Together, the results reported here support a differential regulation of the mitochondrial metabolism among the cell types constituting a leaf, a difference that is exacerbated upon stress.},
	language = {en},
	number = {5},
	urldate = {2025-09-05},
	journal = {Physiologia Plantarum},
	author = {Boussardon, Clément and Hussain, Shah and Keech, Olivier},
	year = {2025},
	note = {\_eprint: https://onlinelibrary.wiley.com/doi/pdf/10.1111/ppl.70465},
	keywords = {cell-specific, glutamate, mitochondria, proteome, translation},
	pages = {e70465},
}

A leaf is an organ composed of different tissues that fulfill specific functions. We hypothesized that since cells in vascular or mesophyll tissues as well as in stoma are developmentally tuned to operate their functions, mitochondria from these cells could exhibit significant metabolic differences. Using the IMTACT method, mitochondria were isolated from these three specific cell types, and the subsequent proteomes were analyzed. At steady state, mitochondria from vascular and guard cells had a significantly higher abundance of proteins associated with the mtETC, the TCA cycle, and the metabolic use of amino acids (glutamate, proline, isoleucine, leucine, and valine) as alternative substrates. Intriguingly, the mitochondria from guard cells also had a much lower abundance of proteins involved in the translation machinery, thus raising questions about the efficiency of the mitochondrial protein turnover in these cells. In a second step, we carried out the same comparative analysis, but with plants that were subjected to carbon starvation by placing them in prolonged darkness for three or 6 days. For all cell types studied, an increased abundance of proteins involved in branched-chain amino acid metabolism was detected. However, while guard cell mitochondria underwent a drastic reduction in proteins involved in respiration, translation, and RNA editing, suggesting a sharp downregulation of mitochondrial functions, mitochondrial proteomes from mesophyll and vascular cells did not show many differences, except for an increased arginine/proline/glutamate metabolism. Together, the results reported here support a differential regulation of the mitochondrial metabolism among the cell types constituting a leaf, a difference that is exacerbated upon stress.