@article{zhou_early_2026,
	title = {{EARLY} {ABORTION} 1 is an evolutionarily conserved gene required for plant reproduction},
	issn = {0022-0957},
	url = {https://doi.org/10.1093/jxb/erag142},
	doi = {10.1093/jxb/erag142},
	abstract = {The functions of approximately one-third of the proteins in the model plant Arabidopsis remain unknown. It is likely that some of the genes encoding these proteins are essential, and thus indispensable for the survival of the plant; furthermore, these genes would be included in the minimum viable set required for plant life. Evolutionarily conserved single copy genes in flowering plants are enriched in essential housekeeping functions. Building on this observation, we designed a reverse genetic screen that focuses on evolutionarily conserved single copy Arabidopsis genes of unknown function with predominant expression in meristematic cells. This approach identified a previously uncharacterized essential Arabidopsis gene, named as EARLY ABORTION 1 (EBO1). Mutation of the EBO1 locus disrupts gametophyte and/or early embryo development, resulting in defective ovule or seed development. A functional fluorescent EBO1 fusion protein was found to localize to the nucleus, and co-immunoprecipitation experiments detected an interaction between EBO1 and Nucleolar Protein 58 (NOP58) and proteins involved in RNA metabolism, chromatin modification, and transcription. The presented results open a new line of investigation into an evolutionarily conserved mechanism involved in the development of both male and female gametophytes as well as seeds.},
	urldate = {2026-04-24},
	journal = {Journal of Experimental Botany},
	author = {Zhou, Jingjing and Wang, Wei and Zhang, Li and Bruce, Ylva and Zhu, Shaochun and Mateus, André and Niittylä, Totte},
	month = mar,
	year = {2026},
	pages = {erag142},
}

The functions of approximately one-third of the proteins in the model plant Arabidopsis remain unknown. It is likely that some of the genes encoding these proteins are essential, and thus indispensable for the survival of the plant; furthermore, these genes would be included in the minimum viable set required for plant life. Evolutionarily conserved single copy genes in flowering plants are enriched in essential housekeeping functions. Building on this observation, we designed a reverse genetic screen that focuses on evolutionarily conserved single copy Arabidopsis genes of unknown function with predominant expression in meristematic cells. This approach identified a previously uncharacterized essential Arabidopsis gene, named as EARLY ABORTION 1 (EBO1). Mutation of the EBO1 locus disrupts gametophyte and/or early embryo development, resulting in defective ovule or seed development. A functional fluorescent EBO1 fusion protein was found to localize to the nucleus, and co-immunoprecipitation experiments detected an interaction between EBO1 and Nucleolar Protein 58 (NOP58) and proteins involved in RNA metabolism, chromatin modification, and transcription. The presented results open a new line of investigation into an evolutionarily conserved mechanism involved in the development of both male and female gametophytes as well as seeds.

@article{yang_natural_2026,
	title = {Natural selection and recombination interact to structure genome-wide variation in pines},
	volume = {126},
	copyright = {© 2026 The Author(s). The Plant Journal published by Society for Experimental Biology and John Wiley \& Sons Ltd.},
	issn = {1365-313X},
	url = {https://onlinelibrary.wiley.com/doi/abs/10.1111/tpj.70866},
	doi = {10.1111/tpj.70866},
	abstract = {Genetic differentiation among populations often varies significantly across the genome due to factors such as selection and recombination, resulting in a heterogeneous genomic landscape. However, variation in low-differentiation regions—genomic valleys—remains poorly understood. Moreover, most insights into plant genomic landscapes come from flowering plants, while comparable genome-wide studies in other taxa, such as conifers, remain limited. We analyzed whole-genome sequencing data from 100 individuals of three pine species—Pinus banksiana, Pinus contorta, and Pinus nigra. We found substantial genome-wide variation in recombination rates, with intergenic regions exhibiting higher recombination than genic regions, and rates decreasing with increasing distance from genes. Recombination rate was negatively correlated with gene length, driven primarily by intron length, suggesting that long introns in conifers may promote the retention of exceptionally long genes by maintaining low recombination in these regions. Genomic scans further revealed that genomic valleys are maintained through either balancing, background, or parallel selection. Additionally, multiple forms of selection were strongly associated with local recombination rate variation, highlighting the significant role of recombination in shaping patterns of genomic differentiation. Our findings provide new insight into the evolution and maintenance of extremely long genes in conifers. Moreover, the results indicate that allopatric selection in regions of low recombination is a major force structuring genomic variation in these species.},
	language = {en},
	number = {1},
	urldate = {2026-04-24},
	journal = {The Plant Journal},
	author = {Yang, Chen-Jui and Funda, Tomas and Chaudhary, Rajiv and Chen, Zhi-Qiang and Barcala, Maximiliano Estravis and Wu, Harry},
	year = {2026},
	note = {\_eprint: https://onlinelibrary.wiley.com/doi/pdf/10.1111/tpj.70866},
	keywords = {Pinus, comparative genomics, conifer genome, genomic landscapes, long gene, natural selection, recombination},
	pages = {e70866},
}

Genetic differentiation among populations often varies significantly across the genome due to factors such as selection and recombination, resulting in a heterogeneous genomic landscape. However, variation in low-differentiation regions—genomic valleys—remains poorly understood. Moreover, most insights into plant genomic landscapes come from flowering plants, while comparable genome-wide studies in other taxa, such as conifers, remain limited. We analyzed whole-genome sequencing data from 100 individuals of three pine species—Pinus banksiana, Pinus contorta, and Pinus nigra. We found substantial genome-wide variation in recombination rates, with intergenic regions exhibiting higher recombination than genic regions, and rates decreasing with increasing distance from genes. Recombination rate was negatively correlated with gene length, driven primarily by intron length, suggesting that long introns in conifers may promote the retention of exceptionally long genes by maintaining low recombination in these regions. Genomic scans further revealed that genomic valleys are maintained through either balancing, background, or parallel selection. Additionally, multiple forms of selection were strongly associated with local recombination rate variation, highlighting the significant role of recombination in shaping patterns of genomic differentiation. Our findings provide new insight into the evolution and maintenance of extremely long genes in conifers. Moreover, the results indicate that allopatric selection in regions of low recombination is a major force structuring genomic variation in these species.

@article{wang_recurrent_2026,
	title = {Recurrent sex chromosome turnover mediated by distinct {ARR17} and {PISTILLATA} duplications in willows},
	volume = {27},
	issn = {1474-760X},
	url = {https://doi.org/10.1186/s13059-026-04026-w},
	doi = {10.1186/s13059-026-04026-w},
	abstract = {Sex chromosome turnovers evolve via translocation or duplication of established sex-determining genes, or their replacement by newly evolved ones. Few cases of replacements by new factors have been documented in dioecious plants, but are suspected in Salix, in which both XY and ZW systems occur, with sex-linked regions (SLRs) of different species on various chromosomes. The male-determining genes in XY species’ SLRs are partial duplicates of autosomal ARR17-like genes and regulate the expression of downstream genes involved in stamen development by producing small RNAs that suppress the expression of intact copies.},
	language = {en},
	number = {1},
	urldate = {2026-04-24},
	journal = {Genome Biology},
	author = {Wang, Yuàn and Xue, Zhi-Qing and Zhang, Ren-Gang and Zhu, Zhi-Ying and Hörandl, Elvira and Wang, Xiao-Ru and Mao, Yan-Fei and Charlesworth, Deborah and He, Li},
	month = mar,
	year = {2026},
	keywords = {Pericentromeric regions, Recombination landscape, Salix, Sex chromosome turnovers, Sex determination, Translocation},
	pages = {137},
}

Sex chromosome turnovers evolve via translocation or duplication of established sex-determining genes, or their replacement by newly evolved ones. Few cases of replacements by new factors have been documented in dioecious plants, but are suspected in Salix, in which both XY and ZW systems occur, with sex-linked regions (SLRs) of different species on various chromosomes. The male-determining genes in XY species’ SLRs are partial duplicates of autosomal ARR17-like genes and regulate the expression of downstream genes involved in stamen development by producing small RNAs that suppress the expression of intact copies.

@article{pravdova_rapid_2026,
	title = {Rapid {Analysis} of {NAD} and {Other} {Phosphorylated} {Metabolites} in {Complex} {Biological} {Samples} by {Hydrophilic} {Interaction} {Liquid} {Chromatography} {Coupled} with {Tandem} {Mass} {Spectrometry}},
	volume = {98},
	issn = {0003-2700},
	url = {https://doi.org/10.1021/acs.analchem.6c00721},
	doi = {10.1021/acs.analchem.6c00721},
	abstract = {Nucleotides and coenzymes play critical roles in energy metabolism and cellular signaling and as building blocks of nucleic acids. This work addresses the challenges in the measurement of the phosphorylated metabolites using hydrophilic interaction liquid chromatography coupled with mass spectrometry, which facilitates the separation and detection of polar metabolites. Here, we present optimized HILIC-MS/MS methods for rapid analysis of polar metabolites including nucleotides and their derivatives in complex biological matrices, such as murine adipose, skeletal, and liver tissues, human plasma, and bacteria. The developed methodologies enable separation of key nucleotides and other phosphorylated metabolites within 6 min and cofactors such as NAD+, NADH, NADP+, and NADPH within 4 min. Validation of these methods demonstrated high accuracy, precision, and sensitivity and stresses the substantial impact of matrix effects. The applicability of the methods was also tested on 13C-labeling experiments with mouse pluripotent stem cells. Additionally, sample pretreatment techniques, such as liquid–liquid extraction and solid-phase extraction, were evaluated as a tool to decrease the negative impact of matrix effects in complex samples. This work enhances the analytical capabilities for nucleotide quantification in metabolomics, facilitating the study of metabolic pathways and disease markers.},
	number = {15},
	urldate = {2026-04-24},
	journal = {Analytical Chemistry},
	publisher = {American Chemical Society},
	author = {Pravdova, Adela and Kleinert, Maximilian and Henderson, John and Kafkia, Eleni and Pladevall-Morera, David and Yonamine, Caio Y. and Treebak, Jonas T. and Brodiazhenko, Tetiana and Terenin, Ilya and Zylicz, Jan Jakub and Moritz, Thomas and Hodek, Ondrej},
	month = apr,
	year = {2026},
	pages = {11428--11437},
}

Nucleotides and coenzymes play critical roles in energy metabolism and cellular signaling and as building blocks of nucleic acids. This work addresses the challenges in the measurement of the phosphorylated metabolites using hydrophilic interaction liquid chromatography coupled with mass spectrometry, which facilitates the separation and detection of polar metabolites. Here, we present optimized HILIC-MS/MS methods for rapid analysis of polar metabolites including nucleotides and their derivatives in complex biological matrices, such as murine adipose, skeletal, and liver tissues, human plasma, and bacteria. The developed methodologies enable separation of key nucleotides and other phosphorylated metabolites within 6 min and cofactors such as NAD+, NADH, NADP+, and NADPH within 4 min. Validation of these methods demonstrated high accuracy, precision, and sensitivity and stresses the substantial impact of matrix effects. The applicability of the methods was also tested on 13C-labeling experiments with mouse pluripotent stem cells. Additionally, sample pretreatment techniques, such as liquid–liquid extraction and solid-phase extraction, were evaluated as a tool to decrease the negative impact of matrix effects in complex samples. This work enhances the analytical capabilities for nucleotide quantification in metabolomics, facilitating the study of metabolic pathways and disease markers.

@article{nagahage_arabidopsis_2026,
	title = {The {Arabidopsis} thaliana {METACASPASE} {IIf} {Regulates} {Sugar} {Metabolism} and {Delays} {Dark}-{Induced} {Leaf} {Senescence}},
	volume = {178},
	copyright = {© 2026 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.70888},
	doi = {10.1111/ppl.70888},
	abstract = {The Arabidopsis thaliana METACASPASE IIf (AtMCA-IIf) is expressed during both developmental cell death and leaf senescence in Arabidopsis thaliana. It has been shown to contribute to developmental cell death but its role in regulating leaf senescence has remained unclear. To investigate this, we conducted dark-induced senescence assays using atmca-IIf mutant lines, which exhibited an accelerated senescence phenotype accompanied by increased levels of glycolytic sugars in light and slow degradation of starch in dark-incubated leaves. Our findings therefore support AtMCA-IIf function in leaf senescence through modulation of sugar metabolism. We propose, on the basis of both in vitro and in vivo data, that one of the proteolytic targets of AtMCA-IIf in this process is PFPβ1, a subunit of the pyrophosphate-dependent fructose-6-phosphate phosphotransferase β1 (PFPβ1), a key enzyme in the glycolytic pathway. Accordingly, pfpβ1 mutants displayed accelerated senescence of dark-incubated leaves. Together, our results suggest that AtMCA-IIf mitigates leaf senescence through targeted modulation of sugar metabolism, thereby delaying the progression of senescence under dark conditions.},
	language = {en},
	number = {2},
	urldate = {2026-04-24},
	journal = {Physiologia Plantarum},
	author = {Nagahage, Isura Sumeda Priyadarshana and Carrio-Segui, Angela and Pandey, Shashank K. and Tuominen, Hannele},
	year = {2026},
	note = {\_eprint: https://onlinelibrary.wiley.com/doi/pdf/10.1111/ppl.70888},
	keywords = {Arabidopsis thaliana, leaf senescence, metacaspase, metacaspase-dependent proteolysis, sugar metabolism},
	pages = {e70888},
}

The Arabidopsis thaliana METACASPASE IIf (AtMCA-IIf) is expressed during both developmental cell death and leaf senescence in Arabidopsis thaliana. It has been shown to contribute to developmental cell death but its role in regulating leaf senescence has remained unclear. To investigate this, we conducted dark-induced senescence assays using atmca-IIf mutant lines, which exhibited an accelerated senescence phenotype accompanied by increased levels of glycolytic sugars in light and slow degradation of starch in dark-incubated leaves. Our findings therefore support AtMCA-IIf function in leaf senescence through modulation of sugar metabolism. We propose, on the basis of both in vitro and in vivo data, that one of the proteolytic targets of AtMCA-IIf in this process is PFPβ1, a subunit of the pyrophosphate-dependent fructose-6-phosphate phosphotransferase β1 (PFPβ1), a key enzyme in the glycolytic pathway. Accordingly, pfpβ1 mutants displayed accelerated senescence of dark-incubated leaves. Together, our results suggest that AtMCA-IIf mitigates leaf senescence through targeted modulation of sugar metabolism, thereby delaying the progression of senescence under dark conditions.