Genomic investigation of plant secondary metabolism: insights from synteny network analysis of oxidosqualene cyclase flanking genes
文献类型： 外文期刊
作者： Li, Haochen 1 ; Li, Jiale 1 ; Li, Xinchu 1 ; Li, Jialin 1 ; Chen, Dan 1 ; Zhang, Yangxin 1 ; Yu, Qiaoming 1 ; Yang, Fan 1 ; Liu, Yunxiao 1 ; Dai, Weidong 2 ; Sun, Yaqiang 1 ; Li, Pengmin 1 ; Schranz, M. Eric 3 ; Ma, Fengwang 1 ; Zhao, Tao 1 ;
作者机构： 1.Northwest A&F Univ, Coll Hort, State Key Lab Crop Stress Resistance & High Effici, Shaanxi Key Lab Apple, Yangling 712100, Peoples R China
2.Chinese Acad Agr Sci, Tea Res Inst, Hangzhou 310008, Zhejiang, Peoples R China
3.Wageningen Univ & Res, Biosystemat Grp, NL-6708 PB Wageningen, Netherlands
关键词： biosynthetic gene cluster; CYP716; genomic flanking genes; oxidosqualene cyclase; synteny neighborhood network
期刊名称：NEW PHYTOLOGIST （ 影响因子：8.1； 五年影响因子：10.3 ）
ISSN： 0028-646X
年卷期： 2025 年 245 卷 5 期
页码：
收录情况： SCI
摘要： 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). 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.
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