黄瓜共表达基因模块的识别及其特点分析  

Identification and Characterization Analysis of Co- expression Gene Modules in Cucumber(Cucumis sativus L.)

作　　者：林行众 张忠华[2] 杨清[1] 黄三文[1,2] 

机构地区：[1]南京农业大学生命科学学院,南京210095 [2]中国农业科学研究院蔬菜花卉研究所/农业部园艺作物生物学与种质创制重点实验室/中-荷园艺作物基因组分析实验室,北京100081

出　　处：《农业生物技术学报》2015年第9期1121-1130,共10页Journal of Agricultural Biotechnology

基　　金：国家重点基础研究发展计划(973)项目(No.2012CB113900);国家自然科学基金(No.31225025;No.31322047和No.11171155);中国农业科学院科技创新工程

摘　　要：共表达网络分析是利用海量生物学数据研究基因与性状关系的重要方法.本研究利用黄瓜（Cucumis sativus L.）10份不同组织的转录组数据计算各个基因在不同组织中表达丰度,去除在10个组织中表达量最大值小于5的基因,然后利用R语言中的权重共表达网络分析（weighted gene co-expression network analysis,WGCNA）软件包构建了共表达网络,获得1 134个共表达模块,一共16 924个基因.去除模块内基因之间相关系数平均值小于0.9的模块,最后得到839个共表达模块,一共11 844个基因.由于不同组织细胞转录本产生的差异,导致不同组织产生结构和功能上的差异,在839个模块中,有323个与组织特异性相关联的模块,涉及5 784个基因.利用R语言中的topGO软件对特异性模块进行GO（Gene Ontology）富集分析,结果表明,10个组织中除了卷须,有9个组织的特异性模块存在功能富集,富集的这些生物学过程（biological process）大多与组织结构和功能存在一定的关系.此外还发现一些模块中存在基因簇现象,一般有2～5个基因,其中2个基因成簇的现象最为普遍.成簇基因在染色体上的物理距离在25 kb以内.黄瓜苦味合成代谢相关模块在叶和茎中分别有3和1个,共有10个已经发表的相关基因,这些模块在苦味合成的前体——萜类的生物合成途径富集存在.以上10个基因中有7个在模块M107中,而且这7个基因分布在模块M107中的两个基因簇中,说明功能相关的基因经常在染色体上相邻分布.本研究结合了转录组和网络分析的方法,发现了许多重要的共表达基因模块,为黄瓜基因的共表达分析提供了非常重要的研究基础和数据支持.Co-expression analysis is an important approach to explore the genes responsible for different traits in large biological data set. In this study, we calculated the expression abundance of genes in 10 different tissues of cucumber （Cucumis sativus L.） using RNA-Seq data and removed the genes whose maximal fragments per kilobase of exon per million fragments mapped （FPKM） values were less than 5 across 10 different tissues. Then, co-expression modules were detected according to the correlation and TO （Tooological Overlap） value between genes by applying WGCNA package in R project. Finally, 1 134 modules were obtained including 16 924 genes, of which 839 modules were selected for their mean correlation coefficients more than 0.9, getting 11 844 genes in total. The great functional and morphological variation in plant tissue types arises from the differential regulation of a finite set of genomic transcripts. The relationship analysis between modules and tissue types found 323 tissue-correlated modules including 5 784 genes. These modules highly correlated with tissues （r〉0.65）. Using the topGO package in R project, we identified Gene Ontology （GO） terms that appeared in modules more frequently than expected. Nine of the 10 tissues had correlated- modules highly enriched in GO biological processes respectively （Fisher＇s exact test, P〈0.000 1）, except tendril. GO enrichment analysis （Fisher＇s exact test, P〈0.000 1） of tissue-specific modules showed some specific genes were related to different tissues. The overrepresented GO biological processes in tissue-specific modules was often consistent with known tissue attributes. Positional clusters were also found in the modules with size ranging from 2 to 5 genes, most of which contained 2 genes. The physical distance between clustered genes in one module on the chromosome was less than 25 kb. The clustered genes often had similar structure or function. As an example, we got 3 modules in leaf and 1 module in stem correlated to the bios

关 键 词：黄瓜 转录组 权重共表达网络分析(WGCNA) 共表达 

分 类 号：Q78[生物学—分子生物学]