{"title":"Simulating the pathway from life history to phylogeny.","authors":"Kieran N Althaus,Andrew L Hipp","doi":"10.1111/nph.70881","DOIUrl":"https://doi.org/10.1111/nph.70881","url":null,"abstract":"","PeriodicalId":214,"journal":{"name":"New Phytologist","volume":"21 1","pages":""},"PeriodicalIF":9.4,"publicationDate":"2026-01-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145937701","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"Do interspecific hybrids lead to new evolutionary avenues in the plant family Lemnaceae?","authors":"K Sowjanya Sree,Klaus-J Appenroth","doi":"10.1111/nph.70904","DOIUrl":"https://doi.org/10.1111/nph.70904","url":null,"abstract":"","PeriodicalId":214,"journal":{"name":"New Phytologist","volume":"39 1","pages":""},"PeriodicalIF":9.4,"publicationDate":"2026-01-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145937725","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Summary Heterosis, widely used in plant breeding to enhance yield and quality, is not yet fully understood at the allelic level, particularly in woody plants such as Camellia sinensis , the tea plant. In this study, the first haplotype (HA)‐resolved genome of JGY, the most widely cultivated hybrid oolong tea cultivar in China, is presented, and the contribution of its epigenetic and 3D genomic features to heterosis is explored. It was revealed that CHG methylation in gene bodies serves as a key epigenetic predictor of allele‐specific expression (ASE), as identified by machine learning models. Additionally, it was shown that allele‐specific chromatin accessibility plays a significant role in regulating ASE, with specific chromatin regions in the promoter of CsDXS2 , a key enzyme in the methylerythritol phosphate (MEP) terpene biosynthesis pathway, being responsible for the modulation of its expression through CsBZIP48 . Furthermore, HA‐resolved Hi–C analysis uncovered large‐scale chromatin reorganization in the hybrid, including A/B compartment switching and topologically associating domain (TAD) reorganization, which are linked to changes in gene expression, particularly in aroma‐related genes. These findings highlight the coordinated reprogramming of parental epigenetic and 3D genomic features during hybridization and provide new insights into the molecular mechanisms underlying heterosis in woody plants.
{"title":"Haplotype‐resolved genome reveals allele‐aware epigenetic and 3D chromatin regulation of heterosis in the tea hybrid","authors":"Wenlong Lei, Yingao Zhang, Yibin Wang, Jiaxin Yu, Huike Li, Xinru Hou, Wenmin Fan, Yezi Xiao, Jiawei Yan, Xiaomei Lei, Shuai Chen, Weidong Wang, Qingshan Xu, Naixing Ye, Youben Yu, Xingtan Zhang, Pengjie Wang","doi":"10.1111/nph.70908","DOIUrl":"https://doi.org/10.1111/nph.70908","url":null,"abstract":"Summary <jats:list list-type=\"bullet\"> <jats:list-item> Heterosis, widely used in plant breeding to enhance yield and quality, is not yet fully understood at the allelic level, particularly in woody plants such as <jats:italic>Camellia sinensis</jats:italic> , the tea plant. </jats:list-item> <jats:list-item> In this study, the first haplotype (HA)‐resolved genome of JGY, the most widely cultivated hybrid oolong tea cultivar in China, is presented, and the contribution of its epigenetic and 3D genomic features to heterosis is explored. </jats:list-item> <jats:list-item> It was revealed that CHG methylation in gene bodies serves as a key epigenetic predictor of allele‐specific expression (ASE), as identified by machine learning models. Additionally, it was shown that allele‐specific chromatin accessibility plays a significant role in regulating ASE, with specific chromatin regions in the promoter of <jats:italic>CsDXS2</jats:italic> , a key enzyme in the methylerythritol phosphate (MEP) terpene biosynthesis pathway, being responsible for the modulation of its expression through <jats:italic>CsBZIP48</jats:italic> . Furthermore, HA‐resolved Hi–C analysis uncovered large‐scale chromatin reorganization in the hybrid, including A/B compartment switching and topologically associating domain (TAD) reorganization, which are linked to changes in gene expression, particularly in aroma‐related genes. </jats:list-item> <jats:list-item> These findings highlight the coordinated reprogramming of parental epigenetic and 3D genomic features during hybridization and provide new insights into the molecular mechanisms underlying heterosis in woody plants. </jats:list-item> </jats:list>","PeriodicalId":214,"journal":{"name":"New Phytologist","volume":"47 1","pages":""},"PeriodicalIF":9.4,"publicationDate":"2026-01-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145920156","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Nitrogen (N) enrichment is expected to exacerbate plant phosphorus (P) limitation, yet this assumption has seldom been empirically tested. We investigated the effects of 7-9 yr of N and P addition on grassland aboveground net primary productivity (ANPP), leaf N : P, and P fractions. Nitrogen addition more than doubled ANPP and increased community leaf N : P from 9.3 to 17.2, a shift traditionally interpreted as indicating N-induced P limitation under the stoichiometric framework. However, subsequent P addition following N enrichment did not increase ANPP, despite decreasing leaf N : P, directly challenging the predicted P limitation. Plants in N-enriched communities exhibited increased nucleic acid P and residual P concentrations. Phosphorus addition following N enrichment increased metabolic P and lipid P concentrations, but not nucleic acid P or residual P. Allocation to nucleic acid P was more tightly linked to plant growth, indicating that plants in N-enriched communities can adapt to low total P by reallocating P toward nucleic acid P. Our results provide a novel mechanism that explains the uncertainties of leaf N : P as a sole indicator of nutrient limitation for primary productivity, and highlight the critical role of leaf P fraction allocation in mediating plant adaptation to stoichiometric imbalance.
{"title":"Why leaf N : P is not reliable for diagnosing nutrient limitation of productivity: answer from leaf phosphorus fractions.","authors":"Xiao-Sa Liang,Yu Ning,Hong-Yi Wang,Zheng-Wen Wang,Cong Ding,Xiao-Ru Zhang,Yuan-Xiu Wu,Zhi-Wei Zhang,Jordi Sardans,Josep Peñuelas,Xiao-Tao Lü","doi":"10.1111/nph.70893","DOIUrl":"https://doi.org/10.1111/nph.70893","url":null,"abstract":"Nitrogen (N) enrichment is expected to exacerbate plant phosphorus (P) limitation, yet this assumption has seldom been empirically tested. We investigated the effects of 7-9 yr of N and P addition on grassland aboveground net primary productivity (ANPP), leaf N : P, and P fractions. Nitrogen addition more than doubled ANPP and increased community leaf N : P from 9.3 to 17.2, a shift traditionally interpreted as indicating N-induced P limitation under the stoichiometric framework. However, subsequent P addition following N enrichment did not increase ANPP, despite decreasing leaf N : P, directly challenging the predicted P limitation. Plants in N-enriched communities exhibited increased nucleic acid P and residual P concentrations. Phosphorus addition following N enrichment increased metabolic P and lipid P concentrations, but not nucleic acid P or residual P. Allocation to nucleic acid P was more tightly linked to plant growth, indicating that plants in N-enriched communities can adapt to low total P by reallocating P toward nucleic acid P. Our results provide a novel mechanism that explains the uncertainties of leaf N : P as a sole indicator of nutrient limitation for primary productivity, and highlight the critical role of leaf P fraction allocation in mediating plant adaptation to stoichiometric imbalance.","PeriodicalId":214,"journal":{"name":"New Phytologist","volume":"1 1","pages":""},"PeriodicalIF":9.4,"publicationDate":"2026-01-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145937726","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"A mitochondrial gatekeeper for cold resilience: deciphering the importance of a structural variant of VDAC1/3a in Solanum habrochaites.","authors":"Federico Vita,Vasileios Fotopoulos","doi":"10.1111/nph.70902","DOIUrl":"https://doi.org/10.1111/nph.70902","url":null,"abstract":"","PeriodicalId":214,"journal":{"name":"New Phytologist","volume":"57 1","pages":""},"PeriodicalIF":9.4,"publicationDate":"2026-01-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145937721","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Dario Zappone,Peter Michael Schröder,Ivan Petřík,Xiao Dong,Rudi Schäufele,Korbinian Schneeberger,Ondřej Novák,Claus Schwechheimer
We hypothesized that B-GATA family transcription factors have important roles in growth regulation in moss. We analyzed B-GATA family transcription factor mutants from Physcomitrium patens and Arabidopsis thaliana to assess growth, gene expression, and cytokinin-related processes under varying nitrogen conditions. We found that nitrogen-dependent growth and transcriptional regulation are strongly impaired in mutants from Physcomitrium and Arabidopsis. We detected altered cytokinin homeostasis or signaling in the mutants, linking hormonal imbalance to growth and transcription defects. We demonstrated a conserved, critical role of B-GATAs in plant nitrogen-responsive growth. Results suggest that B-GATAs influence nitrogen-regulated transcription downstream from cytokinin, supporting an ancient, evolutionarily conserved mechanism connecting nutrient signaling to growth. We provided experimental evidence for the long-speculated but as-yet not demonstrated role of GATA transcription factors in nitrogen-dependent growth in land plants.
{"title":"B-GATA factors are required for nitrogen-responsive growth in Physcomitrium patens and Arabidopsis thaliana.","authors":"Dario Zappone,Peter Michael Schröder,Ivan Petřík,Xiao Dong,Rudi Schäufele,Korbinian Schneeberger,Ondřej Novák,Claus Schwechheimer","doi":"10.1111/nph.70887","DOIUrl":"https://doi.org/10.1111/nph.70887","url":null,"abstract":"We hypothesized that B-GATA family transcription factors have important roles in growth regulation in moss. We analyzed B-GATA family transcription factor mutants from Physcomitrium patens and Arabidopsis thaliana to assess growth, gene expression, and cytokinin-related processes under varying nitrogen conditions. We found that nitrogen-dependent growth and transcriptional regulation are strongly impaired in mutants from Physcomitrium and Arabidopsis. We detected altered cytokinin homeostasis or signaling in the mutants, linking hormonal imbalance to growth and transcription defects. We demonstrated a conserved, critical role of B-GATAs in plant nitrogen-responsive growth. Results suggest that B-GATAs influence nitrogen-regulated transcription downstream from cytokinin, supporting an ancient, evolutionarily conserved mechanism connecting nutrient signaling to growth. We provided experimental evidence for the long-speculated but as-yet not demonstrated role of GATA transcription factors in nitrogen-dependent growth in land plants.","PeriodicalId":214,"journal":{"name":"New Phytologist","volume":"244 1","pages":""},"PeriodicalIF":9.4,"publicationDate":"2026-01-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145937723","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Trichomes develop as outward projections from the epidermal surface. By contrast, as subepidermal secretory cavities, citrus oil glands originate from epidermal cells and develop into specialized hollow structures. During the development of these epidermis-derived structures in vascular plants, transcription factors, such as the homeodomain-leucine zipper and APETALA2/Ethylene responsive factor families, regulate their initiation and morphogenesis. Subsequent biosynthesis of secondary metabolites within these secretory structures is often mediated by jasmonic acid signaling and basic helix-loop-helix proteins, particularly MYC transcription factors. Here, we compare the regulatory mechanisms governing the development of glandular trichomes and secretory cavities, along with the biosynthesis of secondary metabolites. These insights provide the basic knowledge for harnessing these secretory structures as chassis in synthetic biology applications.
{"title":"Plant epidermis-derived secretory structures: from glandular trichomes to secretory cavities.","authors":"Shu Xiang,Shiyun Zhou,Xiuxin Deng,Fei Zhang","doi":"10.1111/nph.70892","DOIUrl":"https://doi.org/10.1111/nph.70892","url":null,"abstract":"Trichomes develop as outward projections from the epidermal surface. By contrast, as subepidermal secretory cavities, citrus oil glands originate from epidermal cells and develop into specialized hollow structures. During the development of these epidermis-derived structures in vascular plants, transcription factors, such as the homeodomain-leucine zipper and APETALA2/Ethylene responsive factor families, regulate their initiation and morphogenesis. Subsequent biosynthesis of secondary metabolites within these secretory structures is often mediated by jasmonic acid signaling and basic helix-loop-helix proteins, particularly MYC transcription factors. Here, we compare the regulatory mechanisms governing the development of glandular trichomes and secretory cavities, along with the biosynthesis of secondary metabolites. These insights provide the basic knowledge for harnessing these secretory structures as chassis in synthetic biology applications.","PeriodicalId":214,"journal":{"name":"New Phytologist","volume":"86 1","pages":""},"PeriodicalIF":9.4,"publicationDate":"2026-01-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145937724","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Arno S Schaveling,Dennie M Te Molder,Paul Heeres,Joris J M van Steenbrugge,Stefan J S van de Ruitenbeek,Casper C van Schaik,Sven van den Elsen,Geert Smant,Mark G Sterken
Globodera pallida poses a major threat to potato production, with management strategies primarily relying on genetic resistance. However, increasing virulence in field populations across Western Europe raises major concerns for G. pallida control. To investigate the evolutionary mechanisms driving this rise in virulence, we propagated 13 field populations on 30 commercial potato varieties. Our findings indicate that the genetic basis of resistance in potatoes is small, with the major resistance conferred by GpaV from Solanum vernei. The wide application of GpaVvrn has led to continuous selection on standing genetic variation in G. pallida. To map virulence, we propagated two field populations on a GpaVvrn-resistant variety for five generations. High-coverage whole-genome sequencing of each generation revealed that GpaVvrn-mediated selection acted on a single locus of a newly assembled G. pallida Rookmaker reference genome. Examination of this virulence-associated locus identified Gp-pat-1 as a candidate gene. Silencing Gp-pat-1 increased virulence on a GpaVvrn-resistant variety but had no effect on nematode virulence on a susceptible variety, classifying Gp-pat-1 as an avirulence gene. Our findings show that GpaVvrn-mediated negative selection on Gp-pat-1 is driving the emergence of virulence and improves our understanding of resistance breakdown and the evolutionary dynamics of nematode adaptation in the field.
{"title":"The potato cyst nematode Globodera pallida overcomes major potato resistance through selection on standing variation at a single locus.","authors":"Arno S Schaveling,Dennie M Te Molder,Paul Heeres,Joris J M van Steenbrugge,Stefan J S van de Ruitenbeek,Casper C van Schaik,Sven van den Elsen,Geert Smant,Mark G Sterken","doi":"10.1111/nph.70886","DOIUrl":"https://doi.org/10.1111/nph.70886","url":null,"abstract":"Globodera pallida poses a major threat to potato production, with management strategies primarily relying on genetic resistance. However, increasing virulence in field populations across Western Europe raises major concerns for G. pallida control. To investigate the evolutionary mechanisms driving this rise in virulence, we propagated 13 field populations on 30 commercial potato varieties. Our findings indicate that the genetic basis of resistance in potatoes is small, with the major resistance conferred by GpaV from Solanum vernei. The wide application of GpaVvrn has led to continuous selection on standing genetic variation in G. pallida. To map virulence, we propagated two field populations on a GpaVvrn-resistant variety for five generations. High-coverage whole-genome sequencing of each generation revealed that GpaVvrn-mediated selection acted on a single locus of a newly assembled G. pallida Rookmaker reference genome. Examination of this virulence-associated locus identified Gp-pat-1 as a candidate gene. Silencing Gp-pat-1 increased virulence on a GpaVvrn-resistant variety but had no effect on nematode virulence on a susceptible variety, classifying Gp-pat-1 as an avirulence gene. Our findings show that GpaVvrn-mediated negative selection on Gp-pat-1 is driving the emergence of virulence and improves our understanding of resistance breakdown and the evolutionary dynamics of nematode adaptation in the field.","PeriodicalId":214,"journal":{"name":"New Phytologist","volume":"84 1","pages":""},"PeriodicalIF":9.4,"publicationDate":"2026-01-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145907871","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Robert D. Hill, Sean M. Robertson, Abir U. Igamberdiev, Mohammed M. Mira, Olivia Wilkins, Claudio Stasolla
With the intensification of unpredictable flooding events because of global warming, there is a need to understand how root cells perceive and respond to oxygen deprivation. The use of high-throughput single-nuclei RNA-sequencing (snRNA-Seq) allows the examination of gene expression profiles in discrete cell types. Root tip segments of Arabidopsis seedlings subjected to normoxic (21% oxygen) or hypoxic (4% oxygen) treatments for 4 h were analyzed by snRNA-Seq. Hypoxia induces a major transcriptome rewiring, most prominent in the meristematic root cells, with the exclusion of the quiescent center (QC), which is vulnerable to low oxygen. Changes in carbon and nitrogen metabolism by low oxygen were centered around increasing demand for carbohydrate to drive glycolytic fermentation, reduction of nitrate to sustain energetic processes, and the bypass of the TCA cycle via aspartate aminotransferase upregulation. The reduction of nitrate and nitrite in hypoxic cells contributes to amino acid metabolism and the utilization of NO in the phytoglobin–nitric oxide cycle to decrease the redox level and sustain energy production. In conclusion, the use of snRNA-Seq provides a high-resolution atlas of gene expression events defining root cell-specific responses to low oxygen.
{"title":"Discrete and cell-specific hypoxic responses in Arabidopsis roots resolved by single-nuclei transcriptomics","authors":"Robert D. Hill, Sean M. Robertson, Abir U. Igamberdiev, Mohammed M. Mira, Olivia Wilkins, Claudio Stasolla","doi":"10.1111/nph.70874","DOIUrl":"https://doi.org/10.1111/nph.70874","url":null,"abstract":"With the intensification of unpredictable flooding events because of global warming, there is a need to understand how root cells perceive and respond to oxygen deprivation. The use of high-throughput single-nuclei RNA-sequencing (snRNA-Seq) allows the examination of gene expression profiles in discrete cell types. Root tip segments of Arabidopsis seedlings subjected to normoxic (21% oxygen) or hypoxic (4% oxygen) treatments for 4 h were analyzed by snRNA-Seq. Hypoxia induces a major transcriptome rewiring, most prominent in the meristematic root cells, with the exclusion of the quiescent center (QC), which is vulnerable to low oxygen. Changes in carbon and nitrogen metabolism by low oxygen were centered around increasing demand for carbohydrate to drive glycolytic fermentation, reduction of nitrate to sustain energetic processes, and the bypass of the TCA cycle via aspartate aminotransferase upregulation. The reduction of nitrate and nitrite in hypoxic cells contributes to amino acid metabolism and the utilization of NO in the phytoglobin–nitric oxide cycle to decrease the redox level and sustain energy production. In conclusion, the use of snRNA-Seq provides a high-resolution atlas of gene expression events defining root cell-specific responses to low oxygen.","PeriodicalId":214,"journal":{"name":"New Phytologist","volume":"44 1","pages":""},"PeriodicalIF":9.4,"publicationDate":"2026-01-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145903586","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Summary The Bryopsidales, a group of siphonous green algae, are of particular evolutionary interest due to their unusual cellular organization and striking morphological and ecological diversity. There are indications of genome duplication, but low taxon sampling has limited our insights into these processes and how they may contribute to these traits. The relationships among certain bryopsidalean lineages remain unresolved, even with plastid genome‐scale datasets. Nuclear genomes offer promise for resolving phylogenetic uncertainties and pinpointing duplication events, but progress has been hindered by the limited availability of such datasets. Here, we present new nuclear genome data for 44 taxa sampled across the phylogenetic breadth of Bryopsidales, and conduct phylogenomic analyses of 708 nuclear genes with coalescent and concatenation approaches. Our results significantly advance the resolution of Bryopsidales relationships, including confident placement of previously hard‐to‐resolve lineages like Pseudobryopsis , Ostreobineae, and the Halimedineae tribes. We identified many ancient gene duplications across the Bryopsidales tree, including potential whole‐genome duplications in the Ostreobiaceae and Caulerpaceae. Our work presents the most highly resolved phylogeny of Bryopsidales to date and offers an extensive framework for the exploration of the potential roles of genome duplications that may have facilitated niche adaptations and invasive trait development.
{"title":"Extensive nuclear datasets resolve the phylogeny of siphonous green algae and identify genome duplications as a contributing factor to evolutionary adaptations","authors":"Riyad Hossen, Saelin Bjornson, Trevor Bringloe, Heroen Verbruggen","doi":"10.1111/nph.70813","DOIUrl":"https://doi.org/10.1111/nph.70813","url":null,"abstract":"Summary <jats:list list-type=\"bullet\"> <jats:list-item> The Bryopsidales, a group of siphonous green algae, are of particular evolutionary interest due to their unusual cellular organization and striking morphological and ecological diversity. There are indications of genome duplication, but low taxon sampling has limited our insights into these processes and how they may contribute to these traits. The relationships among certain bryopsidalean lineages remain unresolved, even with plastid genome‐scale datasets. Nuclear genomes offer promise for resolving phylogenetic uncertainties and pinpointing duplication events, but progress has been hindered by the limited availability of such datasets. </jats:list-item> <jats:list-item> Here, we present new nuclear genome data for 44 taxa sampled across the phylogenetic breadth of Bryopsidales, and conduct phylogenomic analyses of 708 nuclear genes with coalescent and concatenation approaches. </jats:list-item> <jats:list-item> Our results significantly advance the resolution of Bryopsidales relationships, including confident placement of previously hard‐to‐resolve lineages like <jats:italic>Pseudobryopsis</jats:italic> , Ostreobineae, and the Halimedineae tribes. We identified many ancient gene duplications across the Bryopsidales tree, including potential whole‐genome duplications in the Ostreobiaceae and Caulerpaceae. </jats:list-item> <jats:list-item> Our work presents the most highly resolved phylogeny of Bryopsidales to date and offers an extensive framework for the exploration of the potential roles of genome duplications that may have facilitated niche adaptations and invasive trait development. </jats:list-item> </jats:list>","PeriodicalId":214,"journal":{"name":"New Phytologist","volume":"259 1","pages":""},"PeriodicalIF":9.4,"publicationDate":"2026-01-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145897337","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
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