Genomic investigation of plant secondary metabolism: insights from synteny network analysis of oxidosqualene cyclase flanking genes

IF 8.3 1区生物学 Q1 PLANT SCIENCES

New Phytologist Pub Date : 2024-12-27 DOI:10.1111/nph.20357

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

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引用次数: 0

Abstract

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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植物次生代谢的基因组研究：来自氧化角鲨烯环化酶侧翼基因的合成网络分析

植物基因组中参与代谢途径的基因的聚类分布已经引起了研究人员的极大关注。通过比较和分析不同物种代谢基因侧翼区域的变化，我们可以加深对生物合成基因簇（bgc）形成和分布的理解。在这项研究中，我们设计了一个工作流程，利用synteny neighborhood network （SNN）发现和评估不同物种中基因之间的保守位置关系。然后将此工作流程应用于与氧化角鲨烯环化酶（OSCs）相关的侧翼基因的分析。该方法允许识别和比较同源块与独特的侧翼基因伴随不同亚家族的OSCs。通过对122种植物中OSCs侧翼基因的分析，发现被子植物中有多个与OSCs具有保守定位关系的基因。具体来说，最早的OSC基因与CYP716基因的邻接最早出现在基底柱中，而CYP716基因在OSC侧翼区域的非随机出现在不同谱系的异株中持续存在。我们的研究表明，在不同的植物谱系中，盐碳侧翼区域的基因替代是不同的，我们的方法有助于研究盐碳相关bgc形成过程中侧翼基因重排。

本文章由计算机程序翻译，如有差异，请以英文原文为准。

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来源期刊

New Phytologist 生物-植物科学

自引率

5.30%

发文量

728

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.