Journal of Integrative Plant Biology最新文献_第4页

An integrative framework reveals widespread gene flow during the early radiation of oaks and relatives in Quercoideae (Fagaceae). 综合框架揭示了橡树和栎科（Fagaceae）近缘植物早期辐射过程中广泛的基因流动。

IF 9.3 1区生物学

Journal of Integrative Plant Biology Pub Date : 2024-09-19 DOI: 10.1111/jipb.13773

Shui-Yin Liu, Ying-Ying Yang, Qin Tian, Zhi-Yun Yang, Shu-Feng Li, Paul J Valdes, Alex Farnsworth, Heather R Kates, Carolina M Siniscalchi, Robert P Guralnick, Douglas E Soltis, Pamela S Soltis, Gregory W Stull, Ryan A Folk, Ting-Shuang Yi

{"title":"An integrative framework reveals widespread gene flow during the early radiation of oaks and relatives in Quercoideae (Fagaceae).","authors":"Shui-Yin Liu, Ying-Ying Yang, Qin Tian, Zhi-Yun Yang, Shu-Feng Li, Paul J Valdes, Alex Farnsworth, Heather R Kates, Carolina M Siniscalchi, Robert P Guralnick, Douglas E Soltis, Pamela S Soltis, Gregory W Stull, Ryan A Folk, Ting-Shuang Yi","doi":"10.1111/jipb.13773","DOIUrl":"https://doi.org/10.1111/jipb.13773","url":null,"abstract":"Although the frequency of ancient hybridization across the Tree of Life is greater than previously thought, little work has been devoted to uncovering the extent, timeline, and geographic and ecological context of ancient hybridization. Using an expansive new dataset of nuclear and chloroplast DNA sequences, we conducted a multifaceted phylogenomic investigation to identify ancient reticulation in the early evolution of oaks (Quercus). We document extensive nuclear gene tree and cytonuclear discordance among major lineages of Quercus and relatives in Quercoideae. Our analyses recovered clear signatures of gene flow against a backdrop of rampant incomplete lineage sorting, with gene flow most prevalent among major lineages of Quercus and relatives in Quercoideae during their initial radiation, dated to the Early-Middle Eocene. Ancestral reconstructions including fossils suggest ancestors of Castanea + Castanopsis, Lithocarpus, and the Old World oak clade probably co-occurred in North America and Eurasia, while the ancestors of Chrysolepis, Notholithocarpus, and the New World oak clade co-occurred in North America, offering ample opportunity for hybridization in each region. Our study shows that hybridization-perhaps in the form of ancient syngameons like those seen today-has been a common and important process throughout the evolutionary history of oaks and their relatives. Concomitantly, this study provides a methodological framework for detecting ancient hybridization in other groups.","PeriodicalId":195,"journal":{"name":"Journal of Integrative Plant Biology","volume":" ","pages":""},"PeriodicalIF":9.3,"publicationDate":"2024-09-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142277672","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}

引用次数: 0

Transcriptional regulation of phospholipid transport in cotton fiber elongation by GhMYB30D04–GhHD1 interaction complex GhMYB30D04-GhHD1相互作用复合物对棉纤维伸长过程中磷脂运输的转录调控

IF 11.4 1区生物学

Journal of Integrative Plant Biology Pub Date : 2024-09-17 DOI: 10.1111/jipb.13776

Qingwei Song, Chuanhui Du, Yiyang Xu, Jin Wang, Min Lin, Kaijing Zuo

{"title":"Transcriptional regulation of phospholipid transport in cotton fiber elongation by GhMYB30D04–GhHD1 interaction complex","authors":"Qingwei Song, Chuanhui Du, Yiyang Xu, Jin Wang, Min Lin, Kaijing Zuo","doi":"10.1111/jipb.13776","DOIUrl":"https://doi.org/10.1111/jipb.13776","url":null,"abstract":"Cotton fiber length is basically determined by well‐coordinated gene expression and phosphatidylinositol phosphates (PIPs) accumulation during fiber elongation but the regulatory mechanism governing PIPs transport remains unknown. Here, we report a MYB transcription factor GhMYB30D04 in Gossypium hirsutum that promotes fiber elongation through modulating the expression of PIP transporter gene GhLTPG1. Knockout of GhMYB30D04 gene in cotton (KO) results in a reduction of GhLTPG1 transcripts with lower accumulation of PIPs, leading to shorter fibers and lower fiber yield. Conversely, GhMYB30D04 overexpression (GhMYB30D04‐OE) causes richer PIPs and longer cotton fibers, mimicking the effects of exogenously applying PIPs on the ovules of GhMYB30D04‐KO and wild type. Furthermore, GhMYB30D04 interacts with GhHD1, the crucial transcription factor of fiber initiation, to form an activation complex stabilized by PIPs, both of which upregulate GhLTPG1 expression. Comparative omics‐analysis revealed that higher and extended expressions of LTPG1 in fiber elongation mainly correlate with the variations of the GhMYB30D04 gene between two cotton allotetraploids, contributing to longer fiber in G. babardense. Our work clarifies a mechanism by which GhHD1–GhMYB30D04 form a regulatory module of fiber elongation to tightly control PIP accumulation. Our work still has an implication that GhMYB30D04–GhHD1 associates with development transition from fiber initiation to elongation.","PeriodicalId":195,"journal":{"name":"Journal of Integrative Plant Biology","volume":"9 1","pages":""},"PeriodicalIF":11.4,"publicationDate":"2024-09-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142266992","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}

引用次数: 0

OsFAD1-OsMYBR22 modulates clustered spikelet through regulating BRD3 in rice. OsFAD1-OsMYBR22 通过调控 BRD3 调节水稻的丛生小穗。

IF 9.3 1区生物学

Journal of Integrative Plant Biology Pub Date : 2024-09-16 DOI: 10.1111/jipb.13775

Mingxing Cheng, Huanran Yuan, Ruihua Wang, Fengfeng Fan, Fengfeng Si, Xiong Luo, Wei Liu, Shaoqing Li

引用次数: 0

MetMiner: A user‐friendly pipeline for large‐scale plant metabolomics data analysis MetMiner：用于大规模植物代谢组学数据分析的用户友好型管道

IF 11.4 1区生物学

Journal of Integrative Plant Biology Pub Date : 2024-09-10 DOI: 10.1111/jipb.13774

Xiao Wang, Shuang Liang, Wenqi Yang, Ke Yu, Fei Liang, Bing Zhao, Xiang Zhu, Chao Zhou, Luis A. J. Mur, Jeremy A. Roberts, Junli Zhang, Xuebin Zhang

{"title":"MetMiner: A user‐friendly pipeline for large‐scale plant metabolomics data analysis","authors":"Xiao Wang, Shuang Liang, Wenqi Yang, Ke Yu, Fei Liang, Bing Zhao, Xiang Zhu, Chao Zhou, Luis A. J. Mur, Jeremy A. Roberts, Junli Zhang, Xuebin Zhang","doi":"10.1111/jipb.13774","DOIUrl":"https://doi.org/10.1111/jipb.13774","url":null,"abstract":"The utilization of metabolomics approaches to explore the metabolic mechanisms underlying plant fitness and adaptation to dynamic environments is growing, highlighting the need for an efficient and user‐friendly toolkit tailored for analyzing the extensive datasets generated by metabolomics studies. Current protocols for metabolome data analysis often struggle with handling large‐scale datasets or require programming skills. To address this, we present MetMiner (https://github.com/ShawnWx2019/MetMiner), a user‐friendly, full‐functionality pipeline specifically designed for plant metabolomics data analysis. Built on R shiny, MetMiner can be deployed on servers to utilize additional computational resources for processing large‐scale datasets. MetMiner ensures transparency, traceability, and reproducibility throughout the analytical process. Its intuitive interface provides robust data interaction and graphical capabilities, enabling users without prior programming skills to engage deeply in data analysis. Additionally, we constructed and integrated a plant‐specific mass spectrometry database into the MetMiner pipeline to optimize metabolite annotation. We have also developed MDAtoolkits, which include a complete set of tools for statistical analysis, metabolite classification, and enrichment analysis, to facilitate the mining of biological meaning from the datasets. Moreover, we propose an iterative weighted gene co‐expression network analysis strategy for efficient biomarker metabolite screening in large‐scale metabolomics data mining. In two case studies, we validated MetMiner's efficiency in data mining and robustness in metabolite annotation. Together, the MetMiner pipeline represents a promising solution for plant metabolomics analysis, providing a valuable tool for the scientific community to use with ease.","PeriodicalId":195,"journal":{"name":"Journal of Integrative Plant Biology","volume":"63 1","pages":""},"PeriodicalIF":11.4,"publicationDate":"2024-09-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142194385","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}

引用次数: 0

A highly efficient soybean transformation system using GRF3-GIF1 chimeric protein. 使用 GRF3-GIF1 嵌合蛋白的高效大豆转化系统。

IF 9.3 1区生物学

Journal of Integrative Plant Biology Pub Date : 2024-09-06 DOI: 10.1111/jipb.13767

Ying Zhao, Peng Cheng, Ying Liu, Chunyan Liu, Zhenbang Hu, Dawei Xin, Xiaoxia Wu, Mingliang Yang, Qingshan Chen

引用次数: 0

Cover Image: 封面图片：

IF 9.3 1区生物学

Journal of Integrative Plant Biology Pub Date : 2024-09-05 DOI: 10.1111/jipb.13527

引用次数: 0

Issue information page 发行信息页面

IF 9.3 1区生物学

Journal of Integrative Plant Biology Pub Date : 2024-09-05 DOI: 10.1111/jipb.13526

引用次数: 0

Profiling of Phakopsora pachyrhizi transcriptome revealed co-expressed virulence effectors as prospective RNA interference targets for soybean rust management. Phakopsora pachyrhizi 转录组分析表明，共同表达的毒力效应因子是大豆锈病管理的前瞻性 RNA 干扰靶标。

IF 9.3 1区生物学

Journal of Integrative Plant Biology Pub Date : 2024-09-03 DOI: 10.1111/jipb.13772

Haibing Ouyang, Guangzheng Sun, Kainan Li, Rui Wang, Xiaoyu Lv, Zhichao Zhang, Rong Zhao, Ying Wang, Haidong Shu, Haibin Jiang, Sicong Zhang, Jinbin Wu, Qi Zhang, Xi Chen, Tengfei Liu, Wenwu Ye, Yan Wang, Yuanchao Wang

{"title":"Profiling of Phakopsora pachyrhizi transcriptome revealed co-expressed virulence effectors as prospective RNA interference targets for soybean rust management.","authors":"Haibing Ouyang, Guangzheng Sun, Kainan Li, Rui Wang, Xiaoyu Lv, Zhichao Zhang, Rong Zhao, Ying Wang, Haidong Shu, Haibin Jiang, Sicong Zhang, Jinbin Wu, Qi Zhang, Xi Chen, Tengfei Liu, Wenwu Ye, Yan Wang, Yuanchao Wang","doi":"10.1111/jipb.13772","DOIUrl":"https://doi.org/10.1111/jipb.13772","url":null,"abstract":"Soybean rust (SBR), caused by an obligate biotrophic pathogen Phakopsora pachyrhizi, is a devastating disease of soybean worldwide. However, the mechanisms underlying plant invasion by P. pachyrhizi are poorly understood, which hinders the development of effective control strategies for SBR. Here we performed detailed histological characterization on the infection cycle of P. pachyrhizi in soybean and conducted a high-resolution transcriptional dissection of P. pachyrhizi during infection. This revealed P. pachyrhizi infection leads to significant changes in gene expression with 10 co-expressed gene modules, representing dramatic transcriptional shifts in metabolism and signal transduction during different stages throughout the infection cycle. Numerous genes encoding secreted protein are biphasic expressed, and are capable of inhibiting programmed cell death triggered by microbial effectors. Notably, three co-expressed P. pachyrhizi apoplastic effectors (PpAE1, PpAE2, and PpAE3) were found to suppress plant immune responses and were essential for P. pachyrhizi infection. Double-stranded RNA coupled with nanomaterials significantly inhibited SBR infection by targeting PpAE1, PpAE2, and PpAE3, and provided long-lasting protection to soybean against P. pachyrhizi. Together, this study revealed prominent changes in gene expression associated with SBR and identified P. pachyrhizi virulence effectors as promising targets of RNA interference-based soybean protection strategy against SBR.","PeriodicalId":195,"journal":{"name":"Journal of Integrative Plant Biology","volume":" ","pages":""},"PeriodicalIF":9.3,"publicationDate":"2024-09-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142118564","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}

引用次数: 0

Tradeoff between productivity and stability across above- and below-ground communities. 地面和地下群落生产力与稳定性之间的权衡。

IF 9.3 1区生物学

Journal of Integrative Plant Biology Pub Date : 2024-08-29 DOI: 10.1111/jipb.13771

Zonghao Hu, Haiyan Liu, Junjie Yang, Bin Hua, Michael Bahn, Shuang Pang, Tingting Li, Wei Yang, Honghui Wu, Xingguo Han, Ximei Zhang

引用次数: 0

The METHYLTRANSFERASE B-SERRATE interaction mediates the reciprocal regulation of microRNA biogenesis and RNA m⁶A modification. METHYLTRANSFERASE B-SERRATE 相互作用介导了 microRNA 生物发生和 RNA m6A 修饰的相互调控。

IF 9.3 1区生物学

Journal of Integrative Plant Biology Pub Date : 2024-08-29 DOI: 10.1111/jipb.13770

Haiyan Bai, Yanghuan Dai, Panting Fan, Yiming Zhou, Xiangying Wang, Jingjing Chen, Yuzhe Jiao, Chang Du, Zhuoxi Huang, Yuting Xie, Xiaoyu Guo, Xiaoqiang Lang, Yongqing Ling, Yizhen Deng, Qi Liu, Shengbo He, Zhonghui Zhang

{"title":"The METHYLTRANSFERASE B-SERRATE interaction mediates the reciprocal regulation of microRNA biogenesis and RNA m6A modification.","authors":"Haiyan Bai, Yanghuan Dai, Panting Fan, Yiming Zhou, Xiangying Wang, Jingjing Chen, Yuzhe Jiao, Chang Du, Zhuoxi Huang, Yuting Xie, Xiaoyu Guo, Xiaoqiang Lang, Yongqing Ling, Yizhen Deng, Qi Liu, Shengbo He, Zhonghui Zhang","doi":"10.1111/jipb.13770","DOIUrl":"https://doi.org/10.1111/jipb.13770","url":null,"abstract":"In eukaryotes, RNA N6-methyladenosine (m6A) modification and microRNA (miRNA)-mediated RNA silencing represent two critical epigenetic regulatory mechanisms. The m6A methyltransferase complex (MTC) and the microprocessor complex both undergo liquid-liquid phase separation to form nuclear membraneless organelles. Although m6A methyltransferase has been shown to positively regulate miRNA biogenesis, a mechanism of reciprocal regulation between the MTC and the microprocessor complex has remained elusive. Here, we demonstrate that the MTC and the microprocessor complex associate with each other through the METHYLTRANSFERASE B (MTB)-SERRATE (SE) interacting module. Knockdown of MTB impaired miRNA biogenesis by diminishing microprocessor complex binding to primary miRNAs (pri-miRNAs) and their respective MIRNA loci. Additionally, loss of SE function led to disruptions in transcriptome-wide m6A modification. Further biochemical assays and fluorescence recovery after photobleaching (FRAP) assay indicated that SE enhances the liquid-liquid phase separation and solubility of the MTC. Moreover, the MTC exhibited enhanced retention on chromatin and diminished binding to its RNA substrates in the se mutant background. Collectively, our results reveal the substantial regulatory interplay between RNA m6A modification and miRNA biogenesis.","PeriodicalId":195,"journal":{"name":"Journal of Integrative Plant Biology","volume":" ","pages":""},"PeriodicalIF":9.3,"publicationDate":"2024-08-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142102691","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}

引用次数: 0