@article{corredor_apoptotic_2025,
	title = {Apoptotic bodies in phytoplankton suggest evolutionary conservation of cell death mechanisms},
	volume = {16},
	copyright = {2025 The Author(s)},
	issn = {2041-1723},
	url = {https://www.nature.com/articles/s41467-025-63956-4},
	doi = {10.1038/s41467-025-63956-4},
	abstract = {Programmed Cell Death (PCD) in eukaryotes is a regulated process occurring during development, cell differentiation and aging. Apoptosis is a particularly well studied morphotype of PCD, only observed in animal cells (metazoan). Its most definitive hallmark is the formation and release of membrane-enclosed extracellular vesicles called Apoptotic Bodies (ABs). Although apoptotic-like features have been described in plants, yeast, protozoa and phytoplankton, the production of ABs has been thought to be limited to multicellular animals. Here we report the production and release of extracellular ABs in a non-metazoan unicellular eukaryote, the cryptophyte alga Guillardia theta. Morphologies of G. theta cells during aging and pharmacologically-induced cell death confirm the presence of ABs and apoptosis in phytoplankton. G. theta ABs have similar composition to metazoan ABs, carrying DNA, proteins, lipids, carbohydrates, fragments of organelles and cytosol portions. Our results demonstrate that G. theta, a microalga that arose from secondary endosymbiosis, experiences apoptotic cell death in physiological conditions, similar to animal cells. Since secondary endosymbiosis occurred prior to the origin of multicellularity, our discovery questions the evolutionary origin of PCD.},
	language = {en},
	number = {1},
	urldate = {2025-10-03},
	journal = {Nature Communications},
	author = {Corredor, Luisa and Vergou, Georgia Antonia and Skalický, Vladimír and Antoniadi, Ioanna and Wheaton, Benjamin J. and Ljung, Karin and Gorzsás, András and Funk, Christiane},
	month = sep,
	year = {2025},
	note = {Publisher: Nature Publishing Group},
	keywords = {Apoptosis, Cellular microbiology, Plant cell death},
	pages = {8427},
}

Programmed Cell Death (PCD) in eukaryotes is a regulated process occurring during development, cell differentiation and aging. Apoptosis is a particularly well studied morphotype of PCD, only observed in animal cells (metazoan). Its most definitive hallmark is the formation and release of membrane-enclosed extracellular vesicles called Apoptotic Bodies (ABs). Although apoptotic-like features have been described in plants, yeast, protozoa and phytoplankton, the production of ABs has been thought to be limited to multicellular animals. Here we report the production and release of extracellular ABs in a non-metazoan unicellular eukaryote, the cryptophyte alga Guillardia theta. Morphologies of G. theta cells during aging and pharmacologically-induced cell death confirm the presence of ABs and apoptosis in phytoplankton. G. theta ABs have similar composition to metazoan ABs, carrying DNA, proteins, lipids, carbohydrates, fragments of organelles and cytosol portions. Our results demonstrate that G. theta, a microalga that arose from secondary endosymbiosis, experiences apoptotic cell death in physiological conditions, similar to animal cells. Since secondary endosymbiosis occurred prior to the origin of multicellularity, our discovery questions the evolutionary origin of PCD.

@article{ibanez_circadian_2025,
	title = {The circadian clock of {Populus} affects physiological, transcriptional and metabolomic responses to osmotic and ionic components of salt stress},
	volume = {2},
	copyright = {2025 The Author(s)},
	issn = {2948-281X},
	url = {https://www.nature.com/articles/s44323-025-00052-2},
	doi = {10.1038/s44323-025-00052-2},
	abstract = {The circadian oscillator is an innate timing mechanism present in most organisms, including plants. In this study, Populus tremula × P. tremuloides (Populus) trees with reduced expression of circadian clock components were exposed to gradually increases in the osmotic and ionic components of salt stress. Reduced levels of the morning components PttLATE ELONGATED HYPOCOTYL 1 and 2 (PttLHY1,2) or of the evening components PttPSEUDO-RESPONSE REGULATOR 7a and b (PttPRR7a,b) and PttGIGANTEA1,2 (PttGI1,2) affected growth adaptation under stress conditions. PttLHY1,2 regulated growth under NaCl treatment via the control of PttCyclin D3 expression. PttPRR7a,b and PttGI1,2 were instrumental in maintaining growth in roots by enabling effective adaptation of the metabolome. Major changes in the root metabolome under prolonged stress included alterations in carbohydrate, amino acids, and fatty acids. This study places the circadian clock at the centre of adaptation to adverse conditions in trees and will help the development of stress-resistant trees.},
	language = {en},
	number = {1},
	urldate = {2025-10-03},
	journal = {npj Biological Timing and Sleep},
	author = {Ibáñez, Cristian and Vergara, Alexander and Castro, David and Bascunan-Godoy, Luisa and Sjölander, Johan and Jurca, Manuela and Pin, Pierre A. and Nilsson, Ove and Eriksson, Maria E.},
	month = oct,
	year = {2025},
	note = {Publisher: Nature Publishing Group},
	keywords = {Circadian rhythm signalling peptides and proteins, Plant sciences},
	pages = {34},
}

The circadian oscillator is an innate timing mechanism present in most organisms, including plants. In this study, Populus tremula × P. tremuloides (Populus) trees with reduced expression of circadian clock components were exposed to gradually increases in the osmotic and ionic components of salt stress. Reduced levels of the morning components PttLATE ELONGATED HYPOCOTYL 1 and 2 (PttLHY1,2) or of the evening components PttPSEUDO-RESPONSE REGULATOR 7a and b (PttPRR7a,b) and PttGIGANTEA1,2 (PttGI1,2) affected growth adaptation under stress conditions. PttLHY1,2 regulated growth under NaCl treatment via the control of PttCyclin D3 expression. PttPRR7a,b and PttGI1,2 were instrumental in maintaining growth in roots by enabling effective adaptation of the metabolome. Major changes in the root metabolome under prolonged stress included alterations in carbohydrate, amino acids, and fatty acids. This study places the circadian clock at the centre of adaptation to adverse conditions in trees and will help the development of stress-resistant trees.

@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.