WheatCENet: A Database for Comparative Co-expression Networks Analysis of Allohexaploid Wheat and Its Progenitors

IF 11.5 2区 生物学 Q1 GENETICS & HEREDITY Genomics, Proteomics & Bioinformatics Pub Date : 2023-04-01 DOI:10.1016/j.gpb.2022.04.007
Zhongqiu Li , Yiheng Hu , Xuelian Ma , Lingling Da , Jiajie She , Yue Liu , Xin Yi , Yaxin Cao , Wenying Xu , Yuannian Jiao , Zhen Su
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引用次数: 6

Abstract

Genetic and epigenetic changes after polyploidization events could result in variable gene expression and modified regulatory networks. Here, using large-scale transcriptome data, we constructed co-expression networks for diploid, tetraploid, and hexaploid wheat species, and built a platform for comparing co-expression networks of allohexaploid wheat and its progenitors, named WheatCENet. WheatCENet is a platform for searching and comparing specific functional co-expression networks, as well as identifying the related functions of the genes clustered therein. Functional annotations like pathways, gene families, protein–protein interactions, microRNAs (miRNAs), and several lines of epigenome data are integrated into this platform, and Gene Ontology (GO) annotation, gene set enrichment analysis (GSEA), motif identification, and other useful tools are also included. Using WheatCENet, we found that the network of WHEAT ABERRANT PANICLE ORGANIZATION 1 (WAPO1) has more co-expressed genes related to spike development in hexaploid wheat than its progenitors. We also found a novel motif of CCWWWWWWGG (CArG) specifically in the promoter region of WAPO-A1, suggesting that neofunctionalization of the WAPO-A1 gene affects spikelet development in hexaploid wheat. WheatCENet is useful for investigating co-expression networks and conducting other analyses, and thus facilitates comparative and functional genomic studies in wheat. WheatCENet is freely available at http://bioinformatics.cpolar.cn/WheatCENet and http://bioinformatics.cau.edu.cn/WheatCENet.

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小麦CENet:一个用于异六倍体小麦及其祖先比较共表达网络分析的数据库。
多倍体化事件后的遗传和表观遗传学变化可能导致可变的基因表达和修饰的调控网络。在这里,利用大规模转录组数据,我们构建了二倍体、四倍体和六倍体小麦物种的共表达网络,并建立了一个比较异六倍体麦及其祖先共表达网络的平台,名为WheatCENet。WheatCENet是一个用于搜索和比较特定功能共表达网络以及鉴定其中聚集的基因的相关功能的平台。将通路、基因家族、蛋白质-蛋白质相互作用、微小RNA(miRNA)和几行表观基因组数据等功能注释集成到该平台中,还包括基因本体论(GO)注释、基因集富集分析(GSEA)、基序鉴定和其他有用工具。利用WheatCENet,我们发现在六倍体小麦中,小麦异常小穗组织1(WAPO1)网络比其祖先具有更多与穗发育相关的共表达基因。我们还在WAPO-A1的启动子区发现了一个新的CCWWWWWWGG基序(CArG),这表明WAPO-A1基因的新功能化影响了六倍体小麦的小穗发育。小麦CENet有助于研究共表达网络和进行其他分析,从而促进小麦的比较和功能基因组研究。WheatCENet可在http://bioinformatics.cpolar.cn/WheatCENet和http://bioinformatics.cau.edu.cn/WheatCENet.
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来源期刊
Genomics, Proteomics & Bioinformatics
Genomics, Proteomics & Bioinformatics Biochemistry, Genetics and Molecular Biology-Biochemistry
CiteScore
14.30
自引率
4.20%
发文量
844
审稿时长
61 days
期刊介绍: Genomics, Proteomics and Bioinformatics (GPB) is the official journal of the Beijing Institute of Genomics, Chinese Academy of Sciences / China National Center for Bioinformation and Genetics Society of China. It aims to disseminate new developments in the field of omics and bioinformatics, publish high-quality discoveries quickly, and promote open access and online publication. GPB welcomes submissions in all areas of life science, biology, and biomedicine, with a focus on large data acquisition, analysis, and curation. Manuscripts covering omics and related bioinformatics topics are particularly encouraged. GPB is indexed/abstracted by PubMed/MEDLINE, PubMed Central, Scopus, BIOSIS Previews, Chemical Abstracts, CSCD, among others.
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