加权基因共表达网络分析挖掘老鸦瓣芽茎发育关键基因

目的 利用老鸦瓣Amana edulis各部位及芽茎不同发育时期RNA-Seq及基因表达量数据，挖掘老鸦瓣芽茎发育过程关键基因。方法 通过加权基因共表达网络分析（weighted gene co-expression network analysis,WGCNA）法构建网络，根据模块功能富集分析及基因表达模式进行共表达模块和核心基因的筛选。结果 通过基因表达量相关性进一步将网络划分为15个模块，将共表达模块与老鸦瓣芽茎3个发育时期相关联，鉴定到与芽茎发生高度相关的3个模块，即T1MEplum1模块、T2 MEdarkturquoise模块和T3 MElightcyan模块。对3个模块内的基因进行动态基因本体（gene ontology,GO）和京都基因与基因组百科全书（Kyoto encyclopedia of genes and genomes,KEGG）功能富集分析并绘制网络关系图，挖掘出4个与芽茎发育过程相关核心基因（Te＿c1647、Te＿c3695、Te＿c23305、Te＿c52282），涉及蛋白质合成、次生代谢产物的糖基化修饰、植物激素调节等。结论 挖掘出的3个共表达模块...

Key Genes involving in stolon development of Amana edulis with weighted gene co-expression network analysis

Objective To detect the hub genes of the stolon development process in Amana edulis by using the RNA-Seq and gene expression data from various parts of A. edulis and bud stems at different developmental periods. Methods The network was constructed by weighted gene co-expression network analysis (WGCNA) method, and co-expression modules and core genes were screened based on module functional enrichment analysis and gene expression patterns. Results Fifteen modules were divided through the correlation of gene expression, the co-expression module was associated with the three developmental stages of A. edulis stolon, and three modules were identified to be highly related to stolon development, namely T1 MEplum1 module, T2 MEdarkturquoise module and T3 MElightcyan module, respectively. The analysis of gene ontology (GO) and Kyoto encyclopedia of genes and genomes (KEGG) function enrichment of the three modules and network relationship diagrams found that four hub genes related to the stolon development process, namely Te_c1647, Te_c3695, Te_c23305, Te_c52282, which were involved in protein synthesis, glycosylation modification of secondary metabolites, plant hormone regulation etc. Conclusion The identification of three co-expression modules and four hub genes mined will be helpful for further elucidating the mechanism about A. edulis stolon development.