New Phytologist最新文献

{"title":"The baldcypress genome provides insights into the adaptive evolution of flooding stress tolerance.","authors":"Ying Yang,Chaoguang Yu,Jianfeng Hua,Ziyang Wang,Tingting Chen,Qinglin Zhu,Hui You,Lei Xuan,Chengyi Tang,Yunlong Yin","doi":"10.1111/nph.70230","DOIUrl":"https://doi.org/10.1111/nph.70230","url":null,"abstract":"The evolutionary history of gymnosperms suggests that most species struggle in wet environments. However, baldcypress (Taxodium distichum var. distichum) thrives in wetlands, making it a prime candidate for studying flood tolerance in gymnosperms. Our study aimed to explore the genetic basis of this flood tolerance. We accomplished the first chromosome-level genome assembly of baldcypress. Using Oryza sativa, Arabidopsis thaliana, baldcypress, and Taxus wallichiana, we compared gene expression, regulatory elements, and gene expansions between flood-tolerant and flood-intolerant plants. The baldcypress genome spans c. 7.82 Gb, containing 44 010 protein-coding genes. We identified 409 commonly upregulated and 668 commonly downregulated orthogroups, representing conserved flood-stress responses. Additionally, 352 orthogroups contained more upregulated genes in tolerant plants. Baldcypress appears to employ different evolutionary strategies than rice to withstand flooding. Both strategies involve the evolution of ERF-VII transcriptional activation and antioxidant pathways. However, each species expanded distinct nodes within these pathways. Additionally, the evolution of spliceosome genes in baldcypress and energy-producing genes in rice further reflects their differing evolutionary strategies. This study underscores the diversity and commonality of mechanisms underlying plant flood responses and tolerance, providing theoretical guidance for research on the genetic improvement of plant flooding tolerance.","PeriodicalId":214,"journal":{"name":"New Phytologist","volume":"57 1","pages":""},"PeriodicalIF":9.4,"publicationDate":"2025-05-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144122300","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":"Hygroscopic stem reshaping promotes long-distance plant dispersal.","authors":"Yuhong Luo,Zhenjie Guo,Jiquan Chen,Wenyuan Ruan,Xingliang Xu,Le Li,Yufan Bao,Nuo Xu,Xiaoping Xin,Keke Yi,David J Eldridge,Yuchun Yan","doi":"10.1111/nph.70225","DOIUrl":"https://doi.org/10.1111/nph.70225","url":null,"abstract":"Cleistogenes squarrosa is a pioneer tumble plant widely distributed across the Eurasian steppes. It achieves long-distance wind dispersal through stem reshaping. However, the underlying ecological adaptation mechanisms of this dispersal strategy remain unexplored. Combining with field and laboratory observations, we revealed that four coordinated processes - plant phenology, cell wall development, water supplies, and aerodynamic adaptations - interactively facilitate the anemochory of this endemic species in the Eurasian steppes. Specifically, the development of the cell wall with heterogeneous microfibril arrangement plays a critical role in hygroscopic stem reshaping, which occurs in synchrony with seed maturation. Remarkably, the subsequently dry and windy season perfectly follows these two synchronized processes, providing ideal dehydration conditions for stem reshaping and enhancing aerodynamic efficiency for long-distance dispersal. This model for long-distance dispersal innovatively showcases how microscopic cell wall structure propels macroscopic dispersal capabilities and environmental adaptation, ultimately enhancing ecosystem resilience to environmental changes. Collectively, these results indicate the potential for promoting the introduction and cultivation of C. squarrosa to support the restoration of degraded and arid ecosystems. Moreover, this newly identified mechanism provides a valuable direction for future research aimed at developing herbaceous plant varieties with improved dispersal capabilities through molecular breeding techniques.","PeriodicalId":214,"journal":{"name":"New Phytologist","volume":"137 1","pages":""},"PeriodicalIF":9.4,"publicationDate":"2025-05-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144122307","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 novel approach for detecting molecular O2 at the subcellular level in plants.","authors":"Ole Pedersen","doi":"10.1111/nph.70248","DOIUrl":"https://doi.org/10.1111/nph.70248","url":null,"abstract":"","PeriodicalId":214,"journal":{"name":"New Phytologist","volume":"137 1","pages":""},"PeriodicalIF":9.4,"publicationDate":"2025-05-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144122308","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":"Receptor-like kinases BIR1 and BIR3 modulate antiviral resistance by different mechanisms","authors":"Carmen Robinson, Irene Guzmán-Benito, Ana Rocío Sede, Laura Elvira-González, Chenlei Hua, Malgorzata Ciska, Thorsten Nürnberger, Manfred Heinlein, César Llave","doi":"10.1111/nph.70216","DOIUrl":"https://doi.org/10.1111/nph.70216","url":null,"abstract":"<h2> Introduction</h2>\u0000<p>Innate immunity in plants is the first line of defense against pathogens, such as microbes and herbivores, and comprises the so-called pathogen-associated molecular pattern (PAMP)-triggered immunity (PTI) and effector-triggered immunity (ETI; Jones <i>et al</i>., <span>2024</span>). PTI prevents nonadapted microbes from infecting the host and restricts the infection of adapted pathogens in susceptible hosts, while ETI provides resistance against adapted pathogens (Zhou & Zhang, <span>2020</span>). PTI uses cell surface receptors to sense immunogenic PAMPs, while ETI deploys nucleotide-binding domain leucine-rich repeat (LRR) intracellular immune receptors (NLRs) encoded by resistance (<i>R</i>) genes to sense pathogen-effector proteins or effector-induced manipulations of host proteins. NLRs are classified as TOLL/INTERLEUKIN RECEPTOR (TIR)-NLRs (TNLs) and coiled-coil domain containing NLRs (CNLs; Saijo <i>et al</i>., <span>2018</span>; Duxbury <i>et al</i>., <span>2021</span>; Yu <i>et al</i>., <span>2021</span>). PTI and ETI function synergistically and interdependently in plants and share common downstream responses including the production of apoplastic reactive oxygen species (ROS), cytosolic calcium (Ca<sup>+2</sup>) influx, activation of mitogen-activated protein kinases (MAPK) and Ca<sup>+2</sup>-dependent protein kinases (CPK), generation of the signal molecule salicylic acid (SA), differential expression of genes, callose deposition, and stomatal closure (Jones & Dangl, <span>2006</span>; Ngou <i>et al</i>., <span>2021</span>; Pruitt <i>et al</i>., <span>2021</span>; Tian <i>et al</i>., <span>2021</span>; Yuan <i>et al</i>., <span>2021</span>). Besides, NLR-mediated resistance is often accompanied by a form of programmed cell death at the infection site known as hypersensitive response (HR; Coll <i>et al</i>., <span>2011</span>).</p>\u0000<p>While RNA silencing has been traditionally regarded as the primary defense against viruses in plants (Lopez-Gomollon & Baulcombe, <span>2022</span>), viral infections also trigger canonical immune responses, such as MAPK activation, increased production of SA and ethylene, callose deposition, or the upregulation of PTI-related genes (Korner <i>et al</i>., <span>2013</span>; Nicaise, <span>2014</span>; Calil & Fontes, <span>2017</span>). Recently, growing evidence points toward an active role of several PTI and ETI signal transducers in the antiviral response. A role for the receptor-like kinase (RLK) BRASSINOSTEROID INSENSITIVE1-ASSOCIATED RECEPTOR KINASE 1 (BAK1), a member of the SOMATIC EMBRYOGENESIS RECEPTOR KINASE (SERK) family, and its closest homolog BAK1-LIKE1 (BKK1) in antiviral resistance has been reported using <i>bak1</i> and <i>bak1 bkk1</i> Arabidopsis mutants, which show increased susceptibility to several RNA viruses, including turnip crinkle virus (TCV), oilseed rape mosaic virus (ORMV), tobacco mosaic virus (TMV), plum pox virus, and tobacco ratt","PeriodicalId":214,"journal":{"name":"New Phytologist","volume":"38 1","pages":""},"PeriodicalIF":9.4,"publicationDate":"2025-05-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144122552","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":"HSFA2D-LAZY6-LAZY1 module regulates shoot gravitropism and tiller angle in rice.","authors":"Yan Liang,Yundong Yuan,Yueyue Cai,Mei Ma,Xue Lin,Xiaobin Sun,Han Zhao,Junfeng Zhai,Ningpei Han,Jie Zhou,Wenguang Wang,Yonghong Wang,Ning Zhang","doi":"10.1111/nph.70237","DOIUrl":"https://doi.org/10.1111/nph.70237","url":null,"abstract":"Tiller angle is a critical architectural trait in rice (Oryza sativa), affecting planting density, light interception, and grain yield. While HEAT STRESS TRANSCRIPTION FACTOR 2D (HSFA2D) has been shown to regulate tiller angle via LAZY1 (LA1)-mediated auxin distribution, the precise mechanisms governing this pathway remain elusive. We identified and characterized LA6, which encodes a heat shock protein 70-interacting protein, through mutant screening and the MutMap strategy. Biochemical, molecular, and genetic studies were used to elucidate the functional relationship of LA6 with HSFA2D and LA1 in mediating shoot gravitropism and tiller angle. The la6 mutant exhibited impaired shoot gravitropism and increased tiller angle due to reduced lateral auxin transport and disrupted asymmetric auxin distribution. The LA6 gene was highly expressed in shoot bases, and the LA6 protein was localized to the nucleus, cytoplasm, and plasma membrane. Intriguingly, LA6 physically interacted with HSFA2D and LA1. Genetic analyses showed that LA6 acts downstream of HSFA2D and upstream of LA1 within the same regulatory pathway. Our findings reveal that the HSFA2D-LA6-LA1 module orchestrates shoot gravitropism and tiller angle in rice, which not only advances our understanding of plant architecture regulation but also provides potential targets for yield improvement.","PeriodicalId":214,"journal":{"name":"New Phytologist","volume":"237 1","pages":""},"PeriodicalIF":9.4,"publicationDate":"2025-05-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144122253","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":"Corrigendum to Genetic and epigenetic reprogramming in response to internal and external cues by induced transposon mobilization in Moso bamboo.","authors":"","doi":"10.1111/nph.70222","DOIUrl":"https://doi.org/10.1111/nph.70222","url":null,"abstract":"","PeriodicalId":214,"journal":{"name":"New Phytologist","volume":"50 1","pages":""},"PeriodicalIF":9.4,"publicationDate":"2025-05-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144122185","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":"Exploring the untapped potential of single‐cell and spatial omics in plant biology","authors":"Tatsuya Nobori","doi":"10.1111/nph.70220","DOIUrl":"https://doi.org/10.1111/nph.70220","url":null,"abstract":"SummaryAdvances in single‐cell and spatial omics technologies have revolutionised biology by revealing the diverse molecular states of individual cells and their spatial organization within tissues. The field of plant biology has widely adopted single‐cell transcriptome and chromatin accessibility profiling and spatial transcriptomics, which extend traditional cell biology and genomics analyses and provide unique opportunities to reveal molecular and cellular dynamics of tissues. Using these technologies, comprehensive cell atlases have been generated in several model plant species, providing valuable platforms for discovery and tool development. Other emerging technologies related to single‐cell and spatial omics, such as multiomics, lineage tracing, molecular recording, and high‐content genetic and chemical perturbation phenotyping, offer immense potential for deepening our understanding of plant biology yet remain underutilised due to unique technical challenges and resource availability. Overcoming plant‐specific barriers, such as cell wall complexity and limited antibody resources, alongside community‐driven efforts in developing more complete reference atlases and computational tools, will accelerate progress. The synergy between technological innovation and targeted biological questions is poised to drive significant discoveries, advancing plant science. This review highlights the current applications of single‐cell and spatial omics technologies in plant research and introduces emerging approaches with the potential to transform the field.","PeriodicalId":214,"journal":{"name":"New Phytologist","volume":"8 1","pages":""},"PeriodicalIF":9.4,"publicationDate":"2025-05-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144113685","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":"Role of LEAFLESS, an AP2/ERF family transcription factor, in the regulation of trichome specialized metabolism","authors":"Sabyasachi Mandal, Yohannes H. Rezenom, Thomas D. McKnight","doi":"10.1111/nph.70198","DOIUrl":"https://doi.org/10.1111/nph.70198","url":null,"abstract":"Summary<jats:list list-type=\"bullet\"> <jats:list-item>Acylsugars, specialized metabolites produced by trichomes of many solanaceous species, provide protection against biotic and abiotic stresses. Many acylsugar metabolic enzymes have been identified; however, regulatory factors remain unknown.</jats:list-item> <jats:list-item>Our multidisciplinary approaches identified LEAFLESS (APETALA 2/ ETHYLENE RESPONSE FACTOR (AP2/ERF) family member) as a positive regulator of acylsugar biosynthesis.</jats:list-item> <jats:list-item>Virus‐induced gene silencing (VIGS) of <jats:italic>LEAFLESS</jats:italic> in <jats:italic>Solanum pennellii</jats:italic> (<jats:italic>SpLFS</jats:italic>/<jats:italic>Sopen05g008450</jats:italic>) revealed its distinct roles in two related but separate processes: acylsugar biosynthesis and trichome development. Most acylsugar (and several flavonoid) metabolic genes were downregulated in <jats:italic>SpLFS</jats:italic>‐silenced plants and showed strong co‐expression with <jats:italic>SpLFS</jats:italic>. Phylogenetic and additional data analyses indicated trichome‐enriched expression of <jats:italic>SpLFS</jats:italic> orthologs in other acylsugar‐producing solanaceous species, and VIGS of <jats:italic>SpLFS</jats:italic> orthologs in <jats:italic>Nicotiana benthamiana</jats:italic> reduced acylsugar production. Transcriptional reporter showed expression of <jats:italic>SpLFS</jats:italic> in type I/IV trichome tip cells, the site of acylsugar biosynthesis. Electrophoretic mobility shift assays indicated that SpLFS directly binds to promoters of several acylsugar (and flavonoid) metabolic genes. Additionally, data mining suggested remarkable spatiotemporal functional diversity: from coordinating leaf initiation at incipient primordia (previously reported for the <jats:italic>S. lycopersicum</jats:italic> ortholog SlLFS/Solyc05g013540) to regulating trichome specialized metabolism (acylsugar and flavonoid).</jats:list-item> <jats:list-item>Our work highlights a critical role of LEAFLESS in trichome specialized metabolism, paving the way to disentangle the acylsugar regulatory network.</jats:list-item> </jats:list>","PeriodicalId":214,"journal":{"name":"New Phytologist","volume":"35 1","pages":""},"PeriodicalIF":9.4,"publicationDate":"2025-05-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144113686","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":"BAF60/SWP73 subunits define subclasses of SWI/SNF chromatin remodelling complexes in Arabidopsis.","authors":"Sebastian P Sacharowski,Szymon Kubala,Pawel Cwiek,Jaroslaw Steciuk,Dominika Gratkowska-Zmuda,Paulina Oksinska,Ernest Bucior,Anna T Rolicka,Monika Ciesla,Klaudia Nowicka,Saleh Alseekh,Takayuki Tohge,Patrick Giavalisco,Dorota L Zugaj,Sara C Stolze,Anne Harzen,Rainer Franzen,Bruno Huettel,Elzbieta Grzesiuk,Mohammad-Reza Hajirezaei,Hirofumi Nakagami,Csaba Koncz,Alisdair R Fernie,Tomasz J Sarnowski","doi":"10.1111/nph.70182","DOIUrl":"https://doi.org/10.1111/nph.70182","url":null,"abstract":"Evolutionarily conserved switch-defective/sucrose nonfermentable (SWI/SNF) ATP-dependent chromatin remodelling complexes (CRCs) alter nucleosome positioning and chromatin states, affecting gene expression to regulate important processes such as proper development and hormonal signalling pathways. We employed transcript profiling, chromatin immunoprecipitation (ChIP), mass spectrometry, yeast two-hybrid and bimolecular fluorescence complementation protein-protein interaction studies, along with hormone and metabolite profiling and phenotype assessments, to distinguish the SWP73A and SWP73B subunit functions in Arabidopsis. We identified a novel subclass of SWI/SNF CRCs defined by the presence of the SWP73A subunit. Therefore, we propose a refined classification of SWI/SNF CRCs in Arabidopsis, introducing BRM-associated SWI/SNF (BAS)-A (containing SWP73A) and BAS-B (containing SWP73B) subclasses. The SWP73A- and SWP73B-carrying SWI/SNF CRCs exhibit differential properties, demonstrated by distinct chromatin binding patterns and divergent effects on hormone biosynthesis and metabolism. We additionally found that SWP73A plays a specific role in the regulation of auxin signalling, root development, metabolism and germination that cannot be fully compensated by SWP73B. We recognised that some atypical subclasses of SWI/SNF CRCs may be likely formed in mutant lines with inactivated SWP73 subunits. Our study reveals that the duplication of the SWP73 subunit genes contributes to unique and shared functions of SWI/SNF CRC subclasses in the regulation of various processes in Arabidopsis.","PeriodicalId":214,"journal":{"name":"New Phytologist","volume":"20 1","pages":""},"PeriodicalIF":9.4,"publicationDate":"2025-05-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144122107","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":"The uORF-HsfA1a-WOX11 module controls crown root development in rice.","authors":"Ting Zhang,Yimeng Xiang,Miaomiao Ye,Meng Yuan,Guoyong Xu,Dao-Xiu Zhou,Yu Zhao","doi":"10.1111/nph.70214","DOIUrl":"https://doi.org/10.1111/nph.70214","url":null,"abstract":"OsWOX11 is a key essential determinant of crown root development in rice. However, either overexpression or downregulation of OsWOX11 results in pleiotropic developmental defects, including dwarfism and reduced yield. Therefore, it is necessary to ensure an optimal level of OsWOX11 expression for balancing the subterranean root system and aerial organ development. OsHsfA1a activates OsWOX11 expression by directly binding to heat stress element-like elements within its promoter. Genetic evidence demonstrated that OsHsfA1a overexpressing or knockout transgenic plants phenocopied the crown root growth in OsWOX11 transgenic plants. Additionally, increased expression of OsWOX11 in OsHsfA1a RNAi background could partially complement the defective crown root phenotypes. A uORF (uORFHsfA1a) was identified within the 5'-untranslated region of OsHsfA1a. Transient expression assays coupled with ribosome profiling revealed that uORFHsfA1a attenuated the translation efficiency of OsHsfA1a mRNA. Furthermore, HsfA1aP:uORFHsfA1a-HsfA1a-GFP plants exhibited wild-type crown root phenotypes, whereas uORFHsfA1a knockout transgenic plants displayed similar crown root phenotypes to OsWOX11 overexpressing plants. These findings suggest that uORFHsfA1a fine-tunes the crown root development by repressing OsHsfA1a translation, thereby indirectly modulating OsWOX11 transcript levels. Our study demonstrated a novel uORFHsfA1a-HsfA1a-WOX11 regulatory module that coordinated transcriptional and translational control to maintain optimal OsWOX11 expression. This mechanism ensures the trade-off between root and shoot development. Importantly, targeting uORFHsfA1a regulatory elements provided a new strategy for engineering robust root system architecture without compromising agronomic traits, thereby addressing a critical challenge in cereal crop improvement.","PeriodicalId":214,"journal":{"name":"New Phytologist","volume":"18 1","pages":""},"PeriodicalIF":9.4,"publicationDate":"2025-05-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144103694","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}