Journal of Integrative Plant Biology最新文献

{"title":"Nuclear phylogenomics provide evidence to clarify key morphological evolution and whole-genome duplication across rosids.","authors":"Yiyong Zhao, Di Yu, Wenyu Kuo, Jie Huang, Jing Guo, Miao Sun, Yi Hu, Douglas E Soltis, Pamela S Soltis, Hong Ma, Chien-Hsun Huang","doi":"10.1111/jipb.13972","DOIUrl":"https://doi.org/10.1111/jipb.13972","url":null,"abstract":"<p><p>Rosids, comprising 90,000-120,000 species, form a large clade of angiosperms, including extensively studied families with many economically and scientifically important plants. They are also ecologically important, dominating many temperate and tropical ecosystems. Great progress in understanding rosid phylogenetic relationships has facilitated evolutionary studies, but phylogenetic uncertainties remain. To construct a more comprehensive nuclear phylogeny with expanded taxon coverage at the familial levels, we generated 203 new transcriptomes and two shotgun genomes. Along with other available data sets, our sample includes 419 eudicots, including 316 rosids, representing 83 families and all 16 rosid orders. Compared to the 1KP study, our highly resolved rosid phylogeny provides strongly supported internal relationships for one additional order and 16 families. We uncovered cytoplasmic-nuclear discordance for several deep rosid relationships with possible evidence of hybridization/gene flow and incomplete lineage sorting. By tracing ancestral states of morphological characters, we revealed putative floral evolutionary trends in some major clades. We detected strong evidence for 27 putative whole-genome duplication (WGD) events distributed across 20 rosid families, including five novel WGDs. Additionally, our expanded taxon sampling allowed for revised phylogenetic positions of several previously reported WGD events. Most of the supported WGDs correspond to origins of families or large subclades and occurred near times of geological and global climate upheavals, including those at the Cretaceous-Paleogene boundary. Our findings support the idea that large-scale genomic changes and key morphological innovations might have contributed to adaptive evolution and increased biodiversity in rosids.</p>","PeriodicalId":195,"journal":{"name":"Journal of Integrative Plant Biology","volume":" ","pages":""},"PeriodicalIF":9.3,"publicationDate":"2025-07-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144648092","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":"Long-term climate warming and nitrogen deposition increase leaf epiphytic and endophytic bacterial diversity.","authors":"Lu Bai, Yunzhuo Wen, Guodong Han, Jinglei Tang, Zhuwen Xu, Zhongwu Wang, Lin Jiang, Haiyan Ren","doi":"10.1111/jipb.13965","DOIUrl":"https://doi.org/10.1111/jipb.13965","url":null,"abstract":"<p><p>Plant microbiome plays a vital role in plant fitness and ecosystem functioning, yet its response to global environmental change remains poorly understood. Using an 18-year field experiment, we investigated the effects of climate warming and nitrogen deposition on the diversity of leaf epiphytic and endophytic bacterial communities in two dominant plant species (Stipa breviflora and Cleistogenes songorica) of a temperate desert steppe. We found that warming and nitrogen addition increased both epiphytic and endophytic bacterial diversity, but via different mechanisms. Specifically, epiphytic diversity increased with leaf temperature and transpiration rate, whereas greater endophyte diversity was linked to higher leaf carbon and nitrogen concentrations. Structural equation modeling revealed that both epiphytic and endophytic diversity were negatively associated with plant diversity. Our results demonstrate different mechanisms driving similar responses of leaf epiphytic and endophytic bacterial diversity to global change, and point to a negative feedback loop between phyllosphere bacterial and plant diversity.</p>","PeriodicalId":195,"journal":{"name":"Journal of Integrative Plant Biology","volume":" ","pages":""},"PeriodicalIF":9.3,"publicationDate":"2025-07-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144635811","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":"Integrating morphological, anatomical, and physiological traits to explain elevational distributions in Himalayan steppe and alpine plants.","authors":"Jan Binter, Martin Macek, Jiri Dolezal","doi":"10.1111/jipb.13971","DOIUrl":"https://doi.org/10.1111/jipb.13971","url":null,"abstract":"<p><p>Understanding plant adaptive strategies that determine species distributions and ecological optima is crucial for predicting responses to global change drivers. While functional traits provide mechanistic insights into distribution patterns, the specific trait syndromes that best predict elevational optima, particularly in less-studied regions such as the Himalayas, remain unclear. This study employs a novel hierarchical framework integrating morphological, anatomical, and physiological traits to explain elevational distributions among 310 plant species across a 3,500-m gradient (2,650-6,150 m). We analyzed 95,000 floristic records collected from 4,062 localities spanning 80,000 km² in Ladakh, NW Himalayas, India, to define elevational optima and link them with 17 functional traits from over 7,800 individuals. We assessed the roles of moisture and cold limitations on trait-optima relationships by comparing two contrasting habitats (dry steppe and wetter, colder alpine). The predictive power of functional traits was more pronounced in the alpine species facing more extreme abiotic stress than the steppe species. Our results indicate that conservative life history strategies strongly predict elevational optima in alpine areas, while drought avoidance and competitive dominance are key in steppe habitats. Trait syndromes combining short stature, compact growth forms, enhanced storage tissues, and features promoting water-use efficiency (δ¹³C), freezing resistance (fructan levels), and nutrient retention (high root nitrogen and leaf phosphorus) explained 61% of the variation in alpine species' optima. Conversely, lifespan and clonal propagation determined the optima of steppe species at lower elevations. The study emphasizes the importance of functional trait combinations in determining elevational optima, highlighting that alpine species prioritize resource conservation and stress tolerance, while steppe species focus on competitive growth strategies. This multi-trait approach contrasts with previous research focusing on single trait-elevation relationships, providing novel insights into the diverse mechanisms shaping elevational distributions and offering valuable predictive power for assessing vegetation responses to future climate change.</p>","PeriodicalId":195,"journal":{"name":"Journal of Integrative Plant Biology","volume":" ","pages":""},"PeriodicalIF":9.3,"publicationDate":"2025-07-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144635810","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":"MORF proteins: A small family regulating organellar RNA editing and beyond.","authors":"Jialong Li, Jiarui Yuan, Yanjun Jing, Rongcheng Lin","doi":"10.1111/jipb.13967","DOIUrl":"https://doi.org/10.1111/jipb.13967","url":null,"abstract":"<p><p>In the chloroplasts/plastids and mitochondria of flowering plants, RNA editing alters hundreds of cytidines to uridines at specific sites mediated by the editosome. Over the past decade, Multiple Organellar RNA Editing Factor (MORF) proteins have emerged as essential regulators that affect the editing efficiency of most editing sites in plastids and mitochondria. In Arabidopsis, the MORF family consists of nine members, each possessing a single conserved MORF-box that is distributed among flowering plants. Accumulating studies have demonstrated that MORF proteins interact with many other factors, including the PPR proteins and enzymes in different biosynthetic pathways, indicating that the MORF proteins play a more extensive role in regulating organellar development than RNA editing. Recent studies reveal that MORF2 and MORF9 possess holdase activity and may act as chaperones and that MORF8 undergoes heat-dependent phase separation to inhibit RNA editing in chloroplasts. In this review, we provide an overview of our current knowledge of the MORF family proteins and discuss the biological and molecular functions of this family in plants.</p>","PeriodicalId":195,"journal":{"name":"Journal of Integrative Plant Biology","volume":" ","pages":""},"PeriodicalIF":9.3,"publicationDate":"2025-07-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144635812","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":"Development of cytosine and adenine base editors for maize precision breeding.","authors":"Xiao Fu, Nan Wang, Lina Li, Dexin Qiao, Xiantao Qi, Changlin Liu, Zhaoxu Gao, Chuanxiao Xie, Jinjie Zhu","doi":"10.1111/jipb.13964","DOIUrl":"https://doi.org/10.1111/jipb.13964","url":null,"abstract":"<p><p>Base editing technologies can improve crops, but their efficiency in maize remains suboptimal. This study attempts to overcome these limitations by examining optimized cytosine and adenine base editors (CBEs and ABEs), namely evoAPOBEC1, evoFERNY, evoCDA1, TadA8.20, and TadA8e, for precise genome editing in transient and stable expression maize cells. Employing a seed fluorescence reporter (SFR) system for rapid screening of BE transformants and transgene-free progenies, we enhanced editing efficiencies and heritability. Notably, TadA8.20 and evoCDA1 attained multiplexed editing efficiencies of up to 100.0% and 79.0% at the tested loci, respectively, with some homozygous and bi-allelic mutants exceeding 72.4% and 73.7%. Precise editing of ZmACC1/2 (acetyl-CoA carboxylase) improved herbicide resistance, with ZmACC2 mutants displaying improved performance. This study advances crop genetic engineering by facilitating robust, multi-locus modifications without altered agronomic performance, enhancing herbicide tolerance in maize. The successful utilization of these BE is a significant step forward in agricultural biotechnology and precision breeding.</p>","PeriodicalId":195,"journal":{"name":"Journal of Integrative Plant Biology","volume":" ","pages":""},"PeriodicalIF":9.3,"publicationDate":"2025-07-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144606952","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":"Identifying rubber-related genes through developing a sense/antisense RNA expression mutant library of Taraxacum kok-saghyz Rodin.","authors":"Xiuli Fan, Qingwen Chen, Lianlian Hu, Chunyan Hai, Zepeng Hu, Junhui Zhang, Liquan Kou, Guodong Wang, Xiaoguang Song, Hong Yu, Xia Xu, Jiayang Li","doi":"10.1111/jipb.13969","DOIUrl":"https://doi.org/10.1111/jipb.13969","url":null,"abstract":"<p><p>Taraxacum kok-saghyz Rodin (TKS) is a promising alternative crop source for producing high-quality natural rubber (NR) and has become an ideal model plant for studying NR biosynthesis, regulation mechanisms, and production. So far, only a very limited number of functional genes related to NR biosynthesis have been identified in TKS. To achieve a systematic identification of its novel functional genes, we developed a mutant system denoted sense/antisense RNA expression (SARE) and have generated more than 8,000 transgenic TKS plants. A series of mutants with altered phenotypes, particularly changes in NR contents, were identified. To evaluate the efficiency of this library, we chose one mutant, c112, which exhibits a significant increase in NR content, for in-depth characterization. The c112 mutant arose from the sense insertion of a dormancy-associated gene1 (DRM1)/auxin repressed protein (ARP) gene, which we named high natural rubber content1 (HRC1). In the c112 mutant, the concentrations of NR precursors isopentenyl pyrophosphate and dimethylallyl diphosphate decreased, while geranylgeranyl diphosphate increased, suggesting that HRC1 regulates metabolic flux in NR biosynthesis. In summary, the developed TKS SARE mutant library provides valuable genetic resources for identifying key functional genes to accelerate the domestication of TKS from wild species to economic crops through molecular breeding.</p>","PeriodicalId":195,"journal":{"name":"Journal of Integrative Plant Biology","volume":" ","pages":""},"PeriodicalIF":9.3,"publicationDate":"2025-07-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144606953","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":"Rice black-streaked dwarf virus-encoded P6 protein impairs OsPelota-mediated antiviral RNA decay defense via promoting OsSCE1b ubiquitination and degradation in rice.","authors":"Yi Xie, Ming Zeng, Dan Wang, Shi-Bo Gao, Liyan Li, Lianshun Zheng, Yunge Zhang, Shifang Fei, Cui Zhang, Yaqin Wang, Xueping Zhou, Jianxiang Wu","doi":"10.1111/jipb.13966","DOIUrl":"https://doi.org/10.1111/jipb.13966","url":null,"abstract":"<p><p>Rice black-streaked dwarf virus (RBSDV) is a major viral pathogen threatening rice production worldwide. However, the molecular mechanisms underlying the arms race between RBSDV and its host remain largely elusive. Here, we demonstrate that RBSDV infection, or the expression of viral RNA-silencing suppressor protein P6, promotes the ubiquitination and degradation of rice small ubiquitin-like modifiers (SUMO) conjugating enzyme 1b (OsSCE1b). OsSCE1b catalyzes the SUMOylation of OsPelota, a protein involved in plant antiviral RNA decay. Furthermore, RBSDV P6 enhances the interaction between rice ubiquitin E3 ligases SINAT3/4/5 and OsSCE1b in the cytoplasm, leading to increased ubiquitination and degradation of OsSCE1b. Rice plants overexpressing OsSCE1b exhibited reduced susceptibility to RBSDV infection. Conversely, OsSCE1b knockdown and knockout lines, as well as OsPelota knockout lines, were more susceptible, indicating that both OsSCE1b and OsPelota negatively regulate RBSDV infection. Additionally, our findings show that OsSCE1b-catalyzed SUMOylated OsPelota interacts with the Hsp70 subfamily B suppressor OsHBS1, forming a complex that degrades RBSDV genomic RNAs containing one or more GA₆ motifs. Taken together, our data demonstrate that OsSCE1b negatively regulates RBSDV infection by promoting OsPelota SUMOylation and activating the antiviral RNA decay activity of the OsPelota-OsHBS1 complex. Conversely, RBSDV P6 promotes viral infection by enhancing OsSCE1b ubiquitination and degradation, thereby suppressing OsPelota SUMOylation and the rice antiviral RNA decay defense response.</p>","PeriodicalId":195,"journal":{"name":"Journal of Integrative Plant Biology","volume":" ","pages":""},"PeriodicalIF":9.3,"publicationDate":"2025-07-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144606954","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":"Cover Image:","authors":"","doi":"10.1111/jipb.13697","DOIUrl":"https://doi.org/10.1111/jipb.13697","url":null,"abstract":"<p>The cover illustrates serotonin's role in safeguarding plants from stress-induced damage. In the classic Chinese novel “Journey to the West”, the Monkey King embodies divine power, mirroring the role of serotonin in plant stress responses. The cover illustration depicts serotonin as the Monkey King, battling plant stress, represented by the White Bone Demon, to protect the plant. Sun <i>et al.</i> (pages 1706–1724) provide a comprehensive review of the multifaceted roles of serotonin in plant stress responses, highlighting its potential as a key regulator in enhancing plant resilience.</p>","PeriodicalId":195,"journal":{"name":"Journal of Integrative Plant Biology","volume":"67 7","pages":""},"PeriodicalIF":9.3,"publicationDate":"2025-07-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1111/jipb.13697","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144537199","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":"The horizontally transferred gene, CsMTAN, rewired purine traffic to build caffeine factories in tea leaves.","authors":"Xinxin Jia, Xiaoliang Zhang, Xueli Chen, Alisdair R Fernie, Weiwei Wen","doi":"10.1111/jipb.13957","DOIUrl":"https://doi.org/10.1111/jipb.13957","url":null,"abstract":"<p><p>Purine-related metabolites are central to primary metabolic pathways in plants and serve as precursors for purine alkaloid biosynthesis in caffeinated species such as tea plants (Camellia sinensis). In this study, metabolite profiling of two tissues (young and mature leaves) was performed across 183 genetically diverse tea accessions, identifying and quantifying 10 purine alkaloid-related metabolites. Metabolite genome-wide association studies revealed 17 significant loci associated with these metabolites, including both known loci such as caffeine synthase and 16 novel loci (P < 1.05 × 10^-5). Through functional annotation and in vitro enzymatic assay, we characterized 5'-methylthioadenosine/S-adenosylhomocysteine nucleosidase (CsMTAN) as the causal gene underlying natural variation in adenosine and adenine content. CsMTAN can catalyze the degradation of both 5'-methylthioadenosine and S-adenosylhomocysteine to release adenine. The T → A nucleotide substitution at SNP55151898, which leads to a phenylalanine → tyrosine substitution at residue 179 (F179Y), resulted in a significant alteration of enzyme activity in vitro, as evidenced by an approximately 50% reduction in adenine abundance (P < 0.05). Transient overexpression of CsMTAN-A and CsMTAN-T in Nicotiana benthamiana both significantly increased adenine content and dramatically decreased adenosine content, providing direct evidence for the functional involvement of CsMTAN in plant purine metabolism. CsMTAN-T overexpression resulted in significantly lower adenosine level than CsMTAN-A (P < 0.05). Phylogenetic analysis across 115 species and protein structural modeling revealed a distinct evolutionary divergence between plant MTAN evolution and species phylogeny, strongly suggesting the occurrence of horizontal gene transfer events in the evolutionary history of plant MTANs. This study thus furthered our understanding of the genetics and molecular mechanisms regulating purine metabolism and purine alkaloid biosynthesis in tea plants and provided novel targets for molecular breeding and synthetic biology applications.</p>","PeriodicalId":195,"journal":{"name":"Journal of Integrative Plant Biology","volume":" ","pages":""},"PeriodicalIF":9.3,"publicationDate":"2025-07-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144551528","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":"Issue information page","authors":"","doi":"10.1111/jipb.13696","DOIUrl":"https://doi.org/10.1111/jipb.13696","url":null,"abstract":"","PeriodicalId":195,"journal":{"name":"Journal of Integrative Plant Biology","volume":"67 7","pages":"1687-1688"},"PeriodicalIF":9.3,"publicationDate":"2025-07-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1111/jipb.13696","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144537200","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}