The Plant Journal最新文献

{"title":"Riboflavin in phloem sap helps wild tomato combat whiteflies","authors":"Gwendolyn K. Kirschner","doi":"10.1111/tpj.70474","DOIUrl":"10.1111/tpj.70474","url":null,"abstract":"<p>The whitefly <i>Bemisia tabaci</i> feeds on vegetable and ornamental crops including chilli, okra, potato, tobacco and tomato, causing global annual losses of up to billions of US dollars (Sani et al., <span>2020</span>). As phloem-feeding insects, <i>B. tabaci</i> feed on host plants by inserting their mouthpart, the stylet, directly into the phloem. During that process, they inject RNA and protein that suppress the plant immune system. Additionally, they can transfer viruses such as the tomato yellow leaf curl virus (Jones, <span>2003</span>). Whitefly is a rapidly adapting pest that has evolved resistance to even the most potent chemical treatments (Barman et al., <span>2022</span>). Sustainable whitefly management requires integrating multiple defence layers—including genetic resistance—into comprehensive integrated pest management strategies. Some wild relatives of cultivated tomato are resistant to whitefly damage. Identifying the mechanisms and genes underlying whitefly resistance in wild tomato can equip the vegetable breeding industry with genetic tools to introgress this trait into cultivated varieties.</p><p>Most of these resistance mechanisms in wild tomato are based on the production of specialised metabolites in glandular trichomes that are bioactive against <i>B. tabaci</i> (Kortbeek et al., <span>2021</span>). Lissy-Anne Denkers, first author of the highlighted publication, did a research internship in Petra Bleeker's lab at the University of Amsterdam, in which she worked on this resistance mechanism. This sparked her interest in tomato and the role of specialised metabolites in biotic interactions. She was fascinated by the tomato–whitefly interaction as a research system because it presents complex yet tangible questions that can be approached from multiple disciplines, including plant physiology, biochemistry, insect physiology and behaviour, ecotoxicology and broader ecology. Although the different tomato species with their large variation in appearance, chemistry and resistances were what captured her initial interest, she could not help but develop some secret appreciation for whiteflies, especially the clumsily walking first instar nymphs.</p><p>For her PhD project, Denkers analysed a defence mechanism that was independent of trichome repellents. The wild tomato accession <i>Solanum chmielewskii</i> was found to be susceptible to adult whiteflies; however, the whiteflies deposited fewer eggs on its leaves, and the development of juvenile whitefly stages was hampered (de Almeida et al., <span>2023</span>). The team hypothesised that this resistance in <i>S. chmielewskii</i> might be due to something in the phloem that specifically targets young stages of whiteflies, the nymphs, which rely on constant feeding from the phloem (Denkers et al., <span>2025</span>).</p><p>Whiteflies deposit their eggs on host plant leaves, then the first instar nymph hatches and searches for a feeding site towards the leaf vasculature. There, ","PeriodicalId":233,"journal":{"name":"The Plant Journal","volume":"123 5","pages":""},"PeriodicalIF":5.7,"publicationDate":"2025-09-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1111/tpj.70474","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145068759","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"RNA processing/modifying enzymes play key roles in the response to thermospermine in Arabidopsis thaliana","authors":"Mitsuru Saraumi,&nbsp;Takahiro Tanaka,&nbsp;Daiki Koyama,&nbsp;Yoshitaka Nishi,&nbsp;Yoshihiro Takahashi,&nbsp;Hiroyasu Motose,&nbsp;Taku Takahashi","doi":"10.1111/tpj.70476","DOIUrl":"https://doi.org/10.1111/tpj.70476","url":null,"abstract":"<p>Thermospermine is involved in negative regulation of xylem differentiation by enhancing the translation of mRNAs of the <i>SAC51</i> gene family in Arabidopsis (<i>Arabidopsis thaliana</i>). These mRNAs contain conserved upstream open reading frames (uORFs) that interfere with the translation of the main ORF. To investigate the mechanism by which thermospermine acts in this process, we isolated mutants insensitive to thermospermine, named ‘<i>its</i>’. We show that the four genes responsible for these mutants, <i>its1</i> to <i>its4</i>, encode: (i) a homolog of SPOUT RNA methyltransferase, (ii) an rRNA pseudouridine synthase CBF5/NAP57, (iii) a putative spliceosome disassembly factor STIPL1/NTR1, and (iv) a plant-specific RNA-binding protein PHIP1. These four mutants were found to have much higher levels of thermospermine than the wild-type. While all these mutants except <i>its1</i> appear almost normal, they enhance the dwarf phenotype of a mutant of <i>ACL5,</i> which encodes thermospermine synthase, resulting in tiny plants resembling a double knockout of <i>ACL5</i> and <i>SACL3</i>, a member of the <i>SAC51</i> family. Reporter assays revealed that GUS activity from the CaMV 35S promoter-<i>SAC51</i> 5′-GUS fusion construct was significantly reduced in <i>its1</i> and <i>its4</i> or not affected in <i>its2</i> and <i>its3</i>, while it was slightly increased in <i>its1</i>, <i>its3</i>, and <i>its4</i>, or not changed in <i>its2</i> by thermospermine. These findings underscore the critical role of RNA processing and modification in the thermospermine-dependent translational regulation of uORF-containing transcripts.</p>","PeriodicalId":233,"journal":{"name":"The Plant Journal","volume":"123 5","pages":""},"PeriodicalIF":5.7,"publicationDate":"2025-09-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1111/tpj.70476","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145057814","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Whole-tissue 3D immunostaining of shoot apical meristems in rice at single-cell resolution","authors":"Yurika Morishita,&nbsp;Ryosuke Takata,&nbsp;Asuka Higo,&nbsp;Aya Yoshida,&nbsp;Hiroyuki Tsuji","doi":"10.1111/tpj.70470","DOIUrl":"https://doi.org/10.1111/tpj.70470","url":null,"abstract":"<div>\u0000 \u0000 <p>The shoot apical meristem (SAM) produces all above-ground organs of plants and is thus a central focus of plant developmental biology. Developmental processes in the SAM are regulated by various factors that control gene expression at the cellular level. Key among these are the chemical modifications of the N-terminal tails of histones, which are essential components of nucleosomes and chromatin that play crucial roles in these processes. While immunostaining is a valuable method for the spatial analysis of histone modifications, its application to the SAM has posed technical challenges. Here, we developed a three-dimensional immunostaining method for rice (<i>Oryza sativa</i>) SAMs at single-cell resolution using a permeabilization process with specific cell wall degrading enzymes, along with the iTOMEI clearing technique (Sakamoto et al. [2022] <i>Communications Biology</i>, 5, 12). We detected clear signals throughout the deeper tissue layers, allowing us to visualize histone modifications associated with both active and repressive chromatin states, as well as M phase–specific modifications localized on chromosomes. The repressive modifications H3K9me2 and H3K27me3 exhibited punctate patterns within the nuclei, whereas the modifications linked to transcriptional activity were more diffusely distributed. Double staining showed that H3K9me2 forms a peripheral layer around a central domain enriched in H3K4me1. A comparative analysis of SAMs during the vegetative and reproductive phases indicated that active modifications persisted across both phases, whereas repressive modifications increased during the reproductive phase. Our protocol facilitates the three-dimensional visualization of chromatin states in the SAM, offering a robust tool for exploring the spatial regulation of plant development at the single-cell level.</p>\u0000 </div>","PeriodicalId":233,"journal":{"name":"The Plant Journal","volume":"123 5","pages":""},"PeriodicalIF":5.7,"publicationDate":"2025-09-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145057929","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":"Multi-omics analysis of ubiquitin E2 genes in Setaria: evidence for the roles of E2 genes in various aspects of plant development, stress tolerance, and domestication","authors":"Zaixu Zhou,&nbsp;Linlin Zhang,&nbsp;Yannan Wang,&nbsp;Yang Zhang,&nbsp;Han Jia,&nbsp;Hui Zhi,&nbsp;Guanqing Jia,&nbsp;Yuanhuai Han,&nbsp;Xianmin Diao,&nbsp;Sha Tang","doi":"10.1111/tpj.70473","DOIUrl":"https://doi.org/10.1111/tpj.70473","url":null,"abstract":"<div>\u0000 \u0000 <p>Ubiquitin E2 enzymes (E2s) are critical mediators in the ubiquitination cascade, a post-translational modification process that regulates protein stability, activity, localization, and degradation. Here, we analyzed the <i>E2</i> gene family in foxtail millet (<i>Setaria italica</i>), integrating comparative genomics, transcriptomics, and functional studies. A total of 52 <i>E2</i> genes were identified and classified into four subfamilies (UBC, UEV, SCE, and RCE) based on phylogenetic analysis across 49 species. Notably, foxtail millet exhibited significant gene expansion. Tissue-specific expression profiling revealed distinct roles of <i>E2</i> genes in growth and development. Haplotype and quantitative trait loci analyses demonstrated that several <i>E2</i> genes, including <i>SiUBC39</i>, are associated with key agronomic traits, such as plant height, flowering time, and stress tolerance. Using CRISPR/Cas9, we validated the functional role of <i>SiUBC39</i>, finding that its disruption led to phenotypes resembling wild species (<i>Setaria viridis</i>), such as early flowering and reduced plant height and grain yield. IP-MS and transcriptome analysis revealed <i>SiUBC39</i>'s involvement in growth and development regulation, drought stress response, and immune response. SiPIP2;1 and SiEhd2 were identified as interactors of SiUBC39, explaining its roles in blast resistance and flowering time control. Furthermore, domestication analysis identified an A/G mutation in the <i>SiUBC39</i> promoter TATA box, distinguishing domesticated and wild haplotypes and highlighting its role in domestication selection. This study underscores the essential roles of <i>E2</i> genes in regulating crop agronomic traits and stress responses, providing valuable insights for genetic improvement in foxtail millet and other cereals.</p>\u0000 </div>","PeriodicalId":233,"journal":{"name":"The Plant Journal","volume":"123 5","pages":""},"PeriodicalIF":5.7,"publicationDate":"2025-09-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145038078","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 fire blight pathogen Erwinia amylovora enters apple leaves through naturally occurring wounds from the abscission of trichomes","authors":"Felicia Millett,&nbsp;James Standish,&nbsp;Jules Scanley,&nbsp;Katelyn Miller,&nbsp;John Inguagiato,&nbsp;Nubia Zuverza-Mena,&nbsp;Maritza Abril,&nbsp;Victoria Robinson,&nbsp;Yan Li,&nbsp;George W. Sundin,&nbsp;Quan Zeng","doi":"10.1111/tpj.70472","DOIUrl":"https://doi.org/10.1111/tpj.70472","url":null,"abstract":"<div>\u0000 \u0000 <p>The plant epidermis is a single layer of cells covering all plant organs. How pathogens overcome this barrier and enter plants is an important aspect of plant–pathogen interactions. For bacterial plant pathogens, known entry points include natural openings, such as stomata, hydathodes, and mechanical injuries caused by insect feeding, wind damage, or hailstorms. Here, we report that the fire blight pathogen <i>Erwinia amylovora</i> enters apple leaves through naturally occurring wounds caused by the abscission of trichomes during the course of leaf development. Through macroscopic and microscopic observations, we depicted a clear invasion path for <i>E. amylovora</i> cells, from epiphytic growth on glandular trichomes (GT) and non-glandular trichomes (NT) to entry through wounds caused by abscised trichomes, into the epithem, and subsequent spread through xylem. We further observed that GT and NT undergo an abscission process, and that the amount of naturally occurring wounds during abscission is associated with the increase in <i>E. amylovora</i> population. Key genes important for the colonization of GT and NT were identified. The contribution of the type III secretion system and amylovoran biosynthesis during GT colonization was validated. Our findings propose a novel host entry mechanism of plant pathogenic bacteria through naturally occurring wounds during the abscission of plant surface structures.</p>\u0000 </div>","PeriodicalId":233,"journal":{"name":"The Plant Journal","volume":"123 5","pages":""},"PeriodicalIF":5.7,"publicationDate":"2025-09-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145038080","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":"Beyond parental lines: multi-omics analyses reveal epigenetic and transcriptional mechanisms underlying heterosis in Oryza sativa × Oryza rufipogon hybrids","authors":"Xin Peng,&nbsp;Yahui Wu,&nbsp;Yuli Gan,&nbsp;Jiantao Tan,&nbsp;Qian Qian,&nbsp;MengYuan Shen,&nbsp;Kangli Sun,&nbsp;Xing Huo,&nbsp;Degui Zhou,&nbsp;Qi Liu","doi":"10.1111/tpj.70471","DOIUrl":"https://doi.org/10.1111/tpj.70471","url":null,"abstract":"<div>\u0000 \u0000 <p>Heterosis, or hybrid vigor, refers to the superior phenotypes of a hybrid compared with their parents and is widely exploited in agriculture. Interspecific hybrids within the <i>Oryza</i> genus demonstrate significant potential for the systematic improvement of rice varieties. Nevertheless, the mechanistic basis underlying heterosis in interspecific <i>Oryza</i> hybrids remains poorly understood. Here, we systematically performed phenotypic characterization, whole-genome bisulfite sequencing, RNA sequencing, and small RNA profiling using <i>Oryza sativa</i> L. ssp. <i>japonica</i> cv. <i>Nipponbare</i> (NIP), <i>Oryza rufipogon</i> Griff. acc. CWR, and their resulting F₁ hybrid (named as NC). NIP and CWR showed distinct phenotypic and molecular differences. The interspecific hybrid, NC, exhibited significant yield heterosis. In the hybrid, most epigenetic and transcriptional features displayed additive inheritance patterns relative to parental lines. Analysis revealed that domestication-selected genes maintained relatively low DNA methylation coupled with high expression levels in both hybrid and parental lines. Additionally, we identified that non-additive miRNAs were potentially involved in regulating fertility, cell growth, and cell division processes in the hybrid. A significant negative correlation was observed between DNA methylation level and gene expression. Functional enrichment analysis revealed that hybrid-MPV DEGs were significantly associated with flowering time regulation, carbohydrate metabolism, photosynthesis, protein phosphorylation, seed development, and defense responses. Through weighted gene co-expression network analysis, we identified 102 functional gene modules, six of which were significantly associated with yield-related heterosis. Collectively, our results provide a multi-omics framework for understanding interspecific hybridization between elite cultivars and wild rice relatives, highlighting CWR as an untapped genetic reservoir for rice improvement.</p>\u0000 </div>","PeriodicalId":233,"journal":{"name":"The Plant Journal","volume":"123 5","pages":""},"PeriodicalIF":5.7,"publicationDate":"2025-09-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145038277","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 miR396b-MsGRF1c module positively associates with alfalfa nodule senescence","authors":"Jianping Yan,&nbsp;Yanrong Liu,&nbsp;Yanan Gao,&nbsp;Mingzhi Xu,&nbsp;Kangning Zhang,&nbsp;Yaling Liu,&nbsp;Wanjun Zhang","doi":"10.1111/tpj.70468","DOIUrl":"https://doi.org/10.1111/tpj.70468","url":null,"abstract":"<div>\u0000 \u0000 <p>The miR396-GRF module plays a vital role in the growth and development of plant organs. However, its function in the development of leguminous nodules remains unclear. Here, we observed significant upregulation of miR396b in alfalfa (<i>Medicago sativa</i> L.) senescent nodules, especially in the upper part of the nitrogen fixation region. Transgenic lines overexpressing or sequestering miR396b were generated to examine its role in nodule senescence. Here, we report that miR396b acts as a positive regulator in nodule senescence by affecting the accumulation of reactive oxygen species (ROS) in different regions of a nodule. Among the 10 miR396b-targeted <i>MsGRFs</i>, <i>MsGRF1c</i> showed the most significant transcriptional suppression by miR396b in nodules. By overexpressing <i>rMsGRF1c</i> (a synonymous mutation of <i>MsGRF1c</i> resistant to miR396b cleavage) and suppression of MsGRF1c activity via <i>MsGRF1c-SRDX</i> overexpression in alfalfa, we confirmed that <i>MsGRF1c</i> delayed nodule senescence by regulating ROS distribution and promoted alfalfa above-ground biomass yield after sinorhizobium inoculation. A glutamine synthetase gene (<i>MsGS2</i>), which showed differentially expressed in the RNA sequencing data, was markedly upregulated in the nodule senescent region and repressed by <i>MsGRF1c.</i> Then, <i>MsGS2</i> was experimentally validated as a direct transcriptional target of MsGRF1c. Transient interference of <i>MsGS2</i> expression in nodules via antisense oligodeoxynucleotide treatment proved its essential role in regulating ROS distribution and nitrogen fixation efficiency in alfalfa nodules. Our results shed light on the miR396b-<i>MsGRF1c</i>-<i>MsGS2</i> pathway that plays a vital role in regulating alfalfa nodule senescence by affecting ROS distribution, and we propose an alternative way to create new alfalfa germplasm with enhanced nitrogen fixation capacity and biomass yield.</p>\u0000 </div>","PeriodicalId":233,"journal":{"name":"The Plant Journal","volume":"123 5","pages":""},"PeriodicalIF":5.7,"publicationDate":"2025-09-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145037595","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":"RNA-binding proteins orchestrating immunity in plants","authors":"Marcel Bach-Pages,&nbsp;Athira Menon,&nbsp;Brett Wadley,&nbsp;Alfredo Castello,&nbsp;Gail M. Preston","doi":"10.1111/tpj.70433","DOIUrl":"https://doi.org/10.1111/tpj.70433","url":null,"abstract":"<p>RNA-binding proteins (RBPs) direct the function and fate of RNA throughout the RNA lifecycle and play important roles in plant immunity, orchestrating the post-transcriptional reprogramming of the transcriptome following induction of plant immune responses, a process that we term ‘RBP-mediated immunity’. Although the importance of specific RBPs in plant immunity has been known for many years, this field of research is rapidly expanding as new techniques for global profiling of protein–RNA interactions, together with techniques such as ribosomal profiling and metabolic profiling to monitor mRNA translation and turnover and advanced imaging techniques to study RNA and protein structure and localisation, are uncovering new RBPs and providing new insight into the role of RBPs in plant–microbe interactions. Here we discuss the regulatory roles of RBPs during the RNA lifecycle, with a particular focus on post-transcriptional processes and how RBP functions alter plants' immunological profile in response to cellular pathogens, drawing both on studies of specific RBPs and insights from global profiling approaches. Unsurprisingly, given their central role in plant immune responses, RBPs can also be targeted by pathogens and therefore represent one of the plant's Achilles' heels. We therefore also review emerging evidence for RBP-mediated susceptibility in plants. Together, knowledge regarding the regulation, specificity and function of immune-related RBPs can inform plant-breeding programmes to generate crops with increased disease resistance.</p>","PeriodicalId":233,"journal":{"name":"The Plant Journal","volume":"123 5","pages":""},"PeriodicalIF":5.7,"publicationDate":"2025-09-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1111/tpj.70433","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145037897","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Genome imbalance modulates the expression of long non-coding RNAs in maize","authors":"Wenjie Yue,&nbsp;Chuang Yu,&nbsp;Hua Yang,&nbsp;Shiqi Lin,&nbsp;Shuyi Liu,&nbsp;James A. Birchler,&nbsp;Xiaowen Shi","doi":"10.1111/tpj.70464","DOIUrl":"https://doi.org/10.1111/tpj.70464","url":null,"abstract":"<div>\u0000 \u0000 <p>Genome imbalance, resulting from varying the dosage of individual chromosomes (aneuploidy), has a more detrimental effect than changes in complete sets of chromosomes (haploidy/polyploidy). This imbalance is likely due to disruptions in stoichiometry and interactions among macromolecular assemblies. Previous research has shown that aneuploidy causes global modulation of protein-coding genes (PCGs), microRNAs, and transposable elements (TEs), affecting both the varied chromosome (<i>cis</i>-located) and unvaried genome regions (<i>trans</i>-located) across various taxa. While long non-coding RNAs (lncRNAs) are important gene expression regulators, their roles in the context of genomic imbalance remain largely unexplored. In this study, we analyzed and compared the impact of aneuploidy and haploidy/polyploidy on lncRNA expression using RNA-seq data from maize mature leaf tissue. Our results indicate that <i>cis</i>-located lncRNAs are modulated from dosage compensation to a gene dosage effect, while <i>trans</i>-located lncRNAs exhibit trends ranging from an inverse effect to a positive correlation with chromosomal dosage. Remarkably, the ploidy series showed a lesser degree of lncRNA modulation. LncRNAs and TEs display a similar trend of inverse modulation but exhibit greater sensitivity to dosage changes compared to PCGs. The construction of <i>cis</i>-acting and <i>trans</i>-acting lncRNA co-expression networks indicates that lncRNAs likely function as dosage-sensitive regulators of gene expression under conditions of genomic imbalance. Overall, this study not only elucidates the dosage effect of plant lncRNAs but also serves as a valuable resource for exploring potential regulators of PCGs that play significant biological functions.</p>\u0000 </div>","PeriodicalId":233,"journal":{"name":"The Plant Journal","volume":"123 5","pages":""},"PeriodicalIF":5.7,"publicationDate":"2025-09-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145022012","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":"Genomic resequencing unravels species differentiation and polyploid origins in the aquatic plant genus Trapa","authors":"Xiangrong Fan,&nbsp;Minghao Qu,&nbsp;Nancy Rybicki,&nbsp;Lynde L. Dodd,&nbsp;Jie Min,&nbsp;Yuanyuan Chen,&nbsp;Lei Gao","doi":"10.1111/tpj.70463","DOIUrl":"https://doi.org/10.1111/tpj.70463","url":null,"abstract":"<div>\u0000 \u0000 <p><i>Trapa</i> L. is a non-cereal aquatic crop with significant economic and ecological value. However, debates over its classification have caused uncertainties in species differentiation and the mechanisms of polyploid speciation. This study employed whole-genome resequencing together with the fruit morphology of 229 <i>Trapa</i> accessions (153 Asian and 76 North American samples) to elucidate species differentiation and polyploidization events in <i>Trapa</i>. For the species with AA genome and large fruits, clear genetic differentiation was found between two clades with different geographic origins, that is, from the Yangtze River and Amur River basins. The invasive AA species in North America (<i>T. natans</i>) was identified as originating from the Amur River based on genetic and morphological similarities, while all the cultivated accessions were AA species originating from the Yangtze River with severe genetic impoverishment. The separation of the two BB species with small seeds, that is, <i>T. incisa</i> and <i>T. maximowiczii</i>, was strongly supported by both morphological and genetic evidence. For the tetraploids, Asian and North American tetraploids were revealed to have distinct evolutionary origins. Asian allotetraploids (AABB) originated through hybridization between AA diploids from the Yangtze River Basin and BB diploids <i>T. maximowiczii</i>, supported by nuclear and chloroplast evidence. In contrast, the invasive North American tetraploids (<i>T. bispinosa</i> var. <i>iinumai</i>) exhibited an AACC-like genome, suggesting an independent polyploidization involving an unknown “CC” diploid. These findings provide critical insights into <i>Trapa</i>'s complex evolutionary history, polyploidizations, and invasive origins, offering a genomic foundation for the conservation and sustainable utilization of the underutilized aquatic crop amid global environmental challenges.</p>\u0000 </div>","PeriodicalId":233,"journal":{"name":"The Plant Journal","volume":"123 5","pages":""},"PeriodicalIF":5.7,"publicationDate":"2025-09-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145022013","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}