Haochen Li, Jiale Li, Xinchu Li, Jialin Li, Dan Chen, Yangxin Zhang, Qiaoming Yu, Fan Yang, Yunxiao Liu, Weidong Dai, Yaqiang Sun, Pengmin Li, M. Eric Schranz, Fengwang Ma, Tao Zhao
{"title":"Genomic investigation of plant secondary metabolism: insights from synteny network analysis of oxidosqualene cyclase flanking genes","authors":"Haochen Li, Jiale Li, Xinchu Li, Jialin Li, Dan Chen, Yangxin Zhang, Qiaoming Yu, Fan Yang, Yunxiao Liu, Weidong Dai, Yaqiang Sun, Pengmin Li, M. Eric Schranz, Fengwang Ma, Tao Zhao","doi":"10.1111/nph.20357","DOIUrl":null,"url":null,"abstract":"Summary<jats:list list-type=\"bullet\"> <jats:list-item>The clustered distribution of genes involved in metabolic pathways within the plant genome has garnered significant attention from researchers. By comparing and analyzing changes in the flanking regions of metabolic genes across a diverse array of species, we can enhance our understanding of the formation and distribution of biosynthetic gene clusters (BGCs).</jats:list-item> <jats:list-item>In this study, we have designed a workflow that uncovers and assesses conserved positional relationships between genes in various species by using synteny neighborhood networks (SNN). This workflow is then applied to the analysis of flanking genes associated with oxidosqualene cyclases (OSCs). The method allows for the recognition and comparison of homologous blocks with unique flanking genes accompanying different subfamilies of OSCs.</jats:list-item> <jats:list-item>The examination of the flanking genes of OSCs in 122 plant species revealed multiple genes with conserved positional relationships with OSCs in angiosperms. Specifically, the earliest adjacency of OSC genes and CYP716 genes first appeared in basal eudicots, and the nonrandom occurrence of CYP716 genes in the flanking region of OSC persists across different lineages of eudicots.</jats:list-item> <jats:list-item>Our study showed the substitution of genes in the flanking region of the OSC varies across different plant lineages, and our approach facilitates the investigation of flanking gene rearrangements in the formation of OSC‐related BGCs.</jats:list-item> </jats:list>","PeriodicalId":214,"journal":{"name":"New Phytologist","volume":"25 1","pages":""},"PeriodicalIF":8.3000,"publicationDate":"2024-12-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":"0","resultStr":null,"platform":"Semanticscholar","paperid":null,"PeriodicalName":"New Phytologist","FirstCategoryId":"99","ListUrlMain":"https://doi.org/10.1111/nph.20357","RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":null,"EPubDate":"","PubModel":"","JCR":"Q1","JCRName":"PLANT SCIENCES","Score":null,"Total":0}
引用次数: 0
Abstract
SummaryThe clustered distribution of genes involved in metabolic pathways within the plant genome has garnered significant attention from researchers. By comparing and analyzing changes in the flanking regions of metabolic genes across a diverse array of species, we can enhance our understanding of the formation and distribution of biosynthetic gene clusters (BGCs).In this study, we have designed a workflow that uncovers and assesses conserved positional relationships between genes in various species by using synteny neighborhood networks (SNN). This workflow is then applied to the analysis of flanking genes associated with oxidosqualene cyclases (OSCs). The method allows for the recognition and comparison of homologous blocks with unique flanking genes accompanying different subfamilies of OSCs.The examination of the flanking genes of OSCs in 122 plant species revealed multiple genes with conserved positional relationships with OSCs in angiosperms. Specifically, the earliest adjacency of OSC genes and CYP716 genes first appeared in basal eudicots, and the nonrandom occurrence of CYP716 genes in the flanking region of OSC persists across different lineages of eudicots.Our study showed the substitution of genes in the flanking region of the OSC varies across different plant lineages, and our approach facilitates the investigation of flanking gene rearrangements in the formation of OSC‐related BGCs.
期刊介绍:
New Phytologist is an international electronic journal published 24 times a year. It is owned by the New Phytologist Foundation, a non-profit-making charitable organization dedicated to promoting plant science. The journal publishes excellent, novel, rigorous, and timely research and scholarship in plant science and its applications. The articles cover topics in five sections: Physiology & Development, Environment, Interaction, Evolution, and Transformative Plant Biotechnology. These sections encompass intracellular processes, global environmental change, and encourage cross-disciplinary approaches. The journal recognizes the use of techniques from molecular and cell biology, functional genomics, modeling, and system-based approaches in plant science. Abstracting and Indexing Information for New Phytologist includes Academic Search, AgBiotech News & Information, Agroforestry Abstracts, Biochemistry & Biophysics Citation Index, Botanical Pesticides, CAB Abstracts®, Environment Index, Global Health, and Plant Breeding Abstracts, and others.