Journal of Integrative Plant Biology最新文献

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":null,"pages":null},"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":null,"pages":null},"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":null,"pages":null},"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

Regulation of cryptochrome-mediated blue light signaling by the ABI4-PIF4 module. ABI4-PIF4 模块对隐色素介导的蓝光信号转导的调控。

IF 9.3 1区生物学

Journal of Integrative Plant Biology Pub Date : 2024-08-26 DOI: 10.1111/jipb.13769

Pengyu Song, Zidan Yang, Huaichang Wang, Fangfang Wan, Dingming Kang, Wenming Zheng, Zhizhong Gong, Jigang Li

{"title":"Regulation of cryptochrome-mediated blue light signaling by the ABI4-PIF4 module.","authors":"Pengyu Song, Zidan Yang, Huaichang Wang, Fangfang Wan, Dingming Kang, Wenming Zheng, Zhizhong Gong, Jigang Li","doi":"10.1111/jipb.13769","DOIUrl":"https://doi.org/10.1111/jipb.13769","url":null,"abstract":"ABSCISIC ACID-INSENSITIVE 4 (ABI4) is a pivotal transcription factor which coordinates multiple aspects of plant growth and development as well as plant responses to environmental stresses. ABI4 has been shown to be involved in regulating seedling photomorphogenesis; however, the underlying mechanism remains elusive. Here, we show that the role of ABI4 in regulating photomorphogenesis is generally regulated by sucrose, but ABI4 promotes hypocotyl elongation of Arabidopsis seedlings under blue (B) light under all tested sucrose concentrations. We further show that ABI4 physically interacts with PHYTOCHROME INTERACTING FACTOR 4 (PIF4), a well-characterized growth-promoting transcription factor, and post-translationally promotes PIF4 protein accumulation under B light. Further analyses indicate that ABI4 directly interacts with the B light photoreceptors cryptochromes (CRYs) and inhibits the interactions between CRYs and PIF4, thus relieving CRY-mediated repression of PIF4 protein accumulation. In addition, while ABI4 could directly activate its own expression, CRYs enhance, whereas PIF4 inhibits, ABI4-mediated activation of the ABI4 promoter. Together, our study demonstrates that the ABI4-PIF4 module plays an important role in mediating CRY-induced B light signaling in Arabidopsis.","PeriodicalId":195,"journal":{"name":"Journal of Integrative Plant Biology","volume":null,"pages":null},"PeriodicalIF":9.3,"publicationDate":"2024-08-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142054392","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

Generation of humidity-sensitive genic male sterility in maize and wheat for hybrid seed production. 在玉米和小麦中产生对湿度敏感的基因雄性不育，以生产杂交种子。

IF 9.3 1区生物学

Journal of Integrative Plant Biology Pub Date : 2024-08-26 DOI: 10.1111/jipb.13768

Xingchen Xiong, Dan Wang, Changfeng Guo, Guiqiang Fan, Yingchun Zhang, Bo Song, Binzhu Hou, Yuanyuan Yan, Chuanxiao Xie, Xiaoduo Lu, Chunyi Zhang, Xiaoquan Qi

引用次数: 0

A PpEIL2/3-PpNAC1-PpWRKY14 module regulates fruit ripening by modulating ethylene production in peach. PpEIL2/3-PpNAC1-PpWRKY14 模块通过调节乙烯的产生来调控桃的果实成熟。

IF 9.3 1区生物学

Journal of Integrative Plant Biology Pub Date : 2024-08-26 DOI: 10.1111/jipb.13761

Yudi Liu, Wen Xiao, Liao Liao, Beibei Zheng, Yunpeng Cao, Yun Zhao, Ruo-Xi Zhang, Yuepeng Han

{"title":"A PpEIL2/3-PpNAC1-PpWRKY14 module regulates fruit ripening by modulating ethylene production in peach.","authors":"Yudi Liu, Wen Xiao, Liao Liao, Beibei Zheng, Yunpeng Cao, Yun Zhao, Ruo-Xi Zhang, Yuepeng Han","doi":"10.1111/jipb.13761","DOIUrl":"https://doi.org/10.1111/jipb.13761","url":null,"abstract":"WRKY transcription factors play key roles in plant resistance to various stresses, but their roles in fruit ripening remain largely unknown. Here, we report a WRKY gene PpWRKY14 involved in the regulation of fruit ripening in peach. The expression of PpWRKY14 showed an increasing trend throughout fruit development. PpWRKY14 was a target gene of PpNAC1, a master regulator of peach fruit ripening. PpWRKY14 could directly bind to the promoters of PpACS1 and PpACO1 to induce their expression, and this induction was greatly enhanced when PpWRKY14 formed a dimer with PpNAC1. However, the transcription of PpNAC1 could be directly suppressed by two EIN3/EIL1 genes, PpEIL2 and PpEIL3. The PpEIL2/3 genes were highly expressed at the early stages of fruit development, but their expression was programmed to decrease significantly during the ripening stage, thus derepressing the expression of PpNAC1. These results suggested a PpEIL2/3-PpNAC1-PpWRKY14 module that regulates fruit ripening by modulating ethylene production in peach. Our results provided an insight into the regulatory roles of EIN3/EIL1 and WRKY genes in fruit ripening.","PeriodicalId":195,"journal":{"name":"Journal of Integrative Plant Biology","volume":null,"pages":null},"PeriodicalIF":9.3,"publicationDate":"2024-08-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142054389","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