Common bean pan-genome reveals abundant variation patterns and relationships of stress response genes and pathways.

IF 3.5 2区 生物学 Q2 BIOTECHNOLOGY & APPLIED MICROBIOLOGY
Xu Wang, Ming Yan, Shanshan Cui, Fang Li, Qingqing Zhao, Qingnan Wang, Bin Jiang, Yixin Huang, Yang Sun, Xiangdong Kong
{"title":"Common bean pan-genome reveals abundant variation patterns and relationships of stress response genes and pathways.","authors":"Xu Wang, Ming Yan, Shanshan Cui, Fang Li, Qingqing Zhao, Qingnan Wang, Bin Jiang, Yixin Huang, Yang Sun, Xiangdong Kong","doi":"10.1186/s12864-025-11662-2","DOIUrl":null,"url":null,"abstract":"<p><p>Long-term geographical isolation and the different directions of domestication can cause a large number of genome variations. Population genetic analysis based on a single reference genome cannot capture all the variation information. Pan-genome construction is an effective way to overcome this problem. Resequencing data from 683 common bean landraces and breeding lines provided a pan-genome construction data resource. For the first time, for common bean pan-genome construction, 305 Mb non-reference contigs and 10,452 novel genes were identified. Among these new genes, 373 resistance gene analogs containing 372 variable genes were identified and used to narrow down the candidate genes in Pseudomonas syringae pv. phaseolicola resistance quantitative trait locus interval of the common bean. Transcriptome analysis of multiple biotic and abiotic stresses reveals that gene expression patterns are organ-, stress-, and gene conservation-specific. Core and shell genes may be co-expressed in all samples and may have functional complementarity to maintain the stability of plant growth. Within pathways, 8990 and 30,272 mutual exclusivity and co-occurrence gene presence-absence variations (PAVs) were discovered respectively, providing further insights into the functional complementarity of genes. In conclusion, our study provides a comprehensive genome resource, which will be useful for further common bean breeding and study.</p>","PeriodicalId":9030,"journal":{"name":"BMC Genomics","volume":"26 1","pages":"495"},"PeriodicalIF":3.5000,"publicationDate":"2025-05-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12084947/pdf/","citationCount":"0","resultStr":null,"platform":"Semanticscholar","paperid":null,"PeriodicalName":"BMC Genomics","FirstCategoryId":"99","ListUrlMain":"https://doi.org/10.1186/s12864-025-11662-2","RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":null,"EPubDate":"","PubModel":"","JCR":"Q2","JCRName":"BIOTECHNOLOGY & APPLIED MICROBIOLOGY","Score":null,"Total":0}
引用次数: 0

Abstract

Long-term geographical isolation and the different directions of domestication can cause a large number of genome variations. Population genetic analysis based on a single reference genome cannot capture all the variation information. Pan-genome construction is an effective way to overcome this problem. Resequencing data from 683 common bean landraces and breeding lines provided a pan-genome construction data resource. For the first time, for common bean pan-genome construction, 305 Mb non-reference contigs and 10,452 novel genes were identified. Among these new genes, 373 resistance gene analogs containing 372 variable genes were identified and used to narrow down the candidate genes in Pseudomonas syringae pv. phaseolicola resistance quantitative trait locus interval of the common bean. Transcriptome analysis of multiple biotic and abiotic stresses reveals that gene expression patterns are organ-, stress-, and gene conservation-specific. Core and shell genes may be co-expressed in all samples and may have functional complementarity to maintain the stability of plant growth. Within pathways, 8990 and 30,272 mutual exclusivity and co-occurrence gene presence-absence variations (PAVs) were discovered respectively, providing further insights into the functional complementarity of genes. In conclusion, our study provides a comprehensive genome resource, which will be useful for further common bean breeding and study.

普通豆类泛基因组揭示了丰富的胁迫反应基因和途径的变异模式和关系。
长期的地理隔离和驯化方向的不同会导致大量的基因组变异。基于单个参考基因组的群体遗传分析无法捕获所有的变异信息。泛基因组构建是克服这一问题的有效途径。683个菜豆地方品种和育种品系的重测序数据为构建泛基因组提供了数据资源。在普通豆泛基因组构建中,首次鉴定出305mb的非参考contigs和10452个新基因。在这些新基因中,鉴定出373个抗性基因类似物,包含372个可变基因,并用于缩小丁香假单胞菌pv的候选基因范围。菜豆抗油菜病数量性状的位点间隔。多种生物和非生物胁迫的转录组分析表明,基因表达模式是器官特异性、胁迫特异性和基因保守特异性的。核和壳基因可能在所有样品中共表达,并且可能具有功能互补,以维持植物生长的稳定性。在这些通路中,分别发现了8990个和30272个互排他性和共发生基因存在-缺失变异(pav),进一步揭示了基因的功能互补性。本研究为今后蚕豆的育种和研究提供了较为全面的基因组资源。
本文章由计算机程序翻译,如有差异,请以英文原文为准。
求助全文
约1分钟内获得全文 求助全文
来源期刊
BMC Genomics
BMC Genomics 生物-生物工程与应用微生物
CiteScore
7.40
自引率
4.50%
发文量
769
审稿时长
6.4 months
期刊介绍: BMC Genomics is an open access, peer-reviewed journal that considers articles on all aspects of genome-scale analysis, functional genomics, and proteomics. BMC Genomics is part of the BMC series which publishes subject-specific journals focused on the needs of individual research communities across all areas of biology and medicine. We offer an efficient, fair and friendly peer review service, and are committed to publishing all sound science, provided that there is some advance in knowledge presented by the work.
×
引用
GB/T 7714-2015
复制
MLA
复制
APA
复制
导出至
BibTeX EndNote RefMan NoteFirst NoteExpress
×
提示
您的信息不完整,为了账户安全,请先补充。
现在去补充
×
提示
您因"违规操作"
具体请查看互助需知
我知道了
×
提示
确定
请完成安全验证×
copy
已复制链接
快去分享给好友吧!
我知道了
右上角分享
点击右上角分享
0
联系我们:info@booksci.cn Book学术提供免费学术资源搜索服务,方便国内外学者检索中英文文献。致力于提供最便捷和优质的服务体验。 Copyright © 2023 布克学术 All rights reserved.
京ICP备2023020795号-1
ghs 京公网安备 11010802042870号
Book学术文献互助
Book学术文献互助群
群 号:481959085
Book学术官方微信