@article{giubilei_clearing_2026,
	title = {Clearing the {Noise}: {Seasonal} {Dynamics} of {Endophytic} {Bacteria} in {Fagus} sylvatica {Leaves} {Revealed} by {Application} of {PNA} {Clamps}},
	volume = {178},
	issn = {1399-3054},
	shorttitle = {Clearing the {Noise}},
	url = {https://onlinelibrary.wiley.com/doi/abs/10.1111/ppl.70897},
	doi = {10.1111/ppl.70897},
	abstract = {The characterization of the seasonal dynamics of endophytic bacteria in beech leaves can be hindered by co-amplification of chloroplast and mitochondrial plant DNA. This study applies established peptide nucleic acid (PNA) clamps to suppress host-derived amplification while resolving bacterial succession across the vegetative season. Chloroplast- and mitochondrion-specific PNAs inverted the proportion of host to bacterial reads, enabled the recovery of bacterial sequence variants, and increased alpha diversity accordingly. Beta-diversity analyses showed that, once host contamination was removed, samples displayed a clear seasonal trajectory. Early-season leaves contained high abundances of Pseudomonas together with taxa likely introduced through plant–insect–microbe interactions. As leaves matured, the microbiome shifted toward a more stable composition dominated by well-established genera. The transition from early transient taxa to the later enrichment of phyllosphere-adapted and nutrient-cycling genera demonstrates that beech leaves host a temporally structured microbiome shaped by leaf development and seasonal environmental stress.},
	language = {en},
	number = {3},
	urldate = {2026-04-27},
	journal = {Physiologia Plantarum},
	author = {Giubilei, Irene and Turco, Silvia and Cardacino, Antonella and Mahawar, Lovely and Albrectsen, Benedicte Riber and Mazzaglia, Angelo},
	year = {2026},
	note = {\_eprint: https://onlinelibrary.wiley.com/doi/pdf/10.1111/ppl.70897},
	keywords = {Fagus sylvatica, PNA clamps, endophytes, metabarcoding, microbiome},
	pages = {e70897},
}

The characterization of the seasonal dynamics of endophytic bacteria in beech leaves can be hindered by co-amplification of chloroplast and mitochondrial plant DNA. This study applies established peptide nucleic acid (PNA) clamps to suppress host-derived amplification while resolving bacterial succession across the vegetative season. Chloroplast- and mitochondrion-specific PNAs inverted the proportion of host to bacterial reads, enabled the recovery of bacterial sequence variants, and increased alpha diversity accordingly. Beta-diversity analyses showed that, once host contamination was removed, samples displayed a clear seasonal trajectory. Early-season leaves contained high abundances of Pseudomonas together with taxa likely introduced through plant–insect–microbe interactions. As leaves matured, the microbiome shifted toward a more stable composition dominated by well-established genera. The transition from early transient taxa to the later enrichment of phyllosphere-adapted and nutrient-cycling genera demonstrates that beech leaves host a temporally structured microbiome shaped by leaf development and seasonal environmental stress.

@article{tiziani_deciphering_2026,
	title = {Deciphering underexplored rhizosphere processes: root acquisition of citric acid and its metabolic journey in tomato},
	issn = {0022-0957},
	shorttitle = {Deciphering underexplored rhizosphere processes},
	url = {https://doi.org/10.1093/jxb/erag066},
	doi = {10.1093/jxb/erag066},
	abstract = {Root-exuded organic acids are crucial in mitigating iron (Fe) and phosphorus (P) deficiencies, and their biosynthesis and secretion require significant metabolic investment. Recent studies have shown that roots can also uptake exudates. We hypothesized that citric acid uptake increases under Fe and P deficiencies, declines over time, and contributes to primary metabolism. We investigated citric acid uptake, translocation, and metabolization in Fe- and P-deficient tomato plants grown hydroponically using 13C-labelling with bulk stable-isotope and compound-specific stable-isotope analysis. Physiological parameters, root morphology, and elemental composition were also assessed. Deficient plants showed reduced P and Fe contents, reduced photosynthesis, altered root morphology, and an altered citric acid uptake that could not be attributed to morphological differences. Iron deficiency reduced citric acid uptake, indicating its role in rhizospheric Fe mobilization, while P deficiency increased the uptake, enhancing resource use efficiency. Unexpectedly, citric acid uptake increased with plant development. In Fe deficiency, citric acid-derived carbon was allocated to secondary metabolites, while in P deficiency it supported the tricarboxylic acid and GS-GOGAT cycles. This study is the first to demonstrate that citric acid uptake is a multifunctional process, underscoring its critical role in plant responses to nutrient starvation, especially under P deficiency.},
	urldate = {2026-04-24},
	journal = {Journal of Experimental Botany},
	author = {Tiziani, Raphael and Trevisan, Fabio and Hodek, Ondřej and Jämtgård, Sandra and Moritz, Thomas and Bouaicha, Oussama and Chibesa, Mirriam C and Fracasso, Ilaria and Mimmo, Tanja},
	month = feb,
	year = {2026},
	pages = {erag066},
}

Root-exuded organic acids are crucial in mitigating iron (Fe) and phosphorus (P) deficiencies, and their biosynthesis and secretion require significant metabolic investment. Recent studies have shown that roots can also uptake exudates. We hypothesized that citric acid uptake increases under Fe and P deficiencies, declines over time, and contributes to primary metabolism. We investigated citric acid uptake, translocation, and metabolization in Fe- and P-deficient tomato plants grown hydroponically using 13C-labelling with bulk stable-isotope and compound-specific stable-isotope analysis. Physiological parameters, root morphology, and elemental composition were also assessed. Deficient plants showed reduced P and Fe contents, reduced photosynthesis, altered root morphology, and an altered citric acid uptake that could not be attributed to morphological differences. Iron deficiency reduced citric acid uptake, indicating its role in rhizospheric Fe mobilization, while P deficiency increased the uptake, enhancing resource use efficiency. Unexpectedly, citric acid uptake increased with plant development. In Fe deficiency, citric acid-derived carbon was allocated to secondary metabolites, while in P deficiency it supported the tricarboxylic acid and GS-GOGAT cycles. This study is the first to demonstrate that citric acid uptake is a multifunctional process, underscoring its critical role in plant responses to nutrient starvation, especially under P deficiency.

@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.