普通丝瓜幼苗响应低温弱光核心基因共表达网络的WGCNA鉴定

Identification of Luffa Under Low Temperature and Weak Light Stress Gene Co-expression Modules by WGCNA

为研究普通丝瓜[Luffa cylindrica(L.)Roem.]在低温弱光胁迫下基因共表达网络,引入权重基因共表达分析网络的方法(weighted gene co-expression network analysis,WGCNA),筛选出响应低温弱光的核心基因。以普通丝瓜低温弱光处理的15个转录组测序样本为基础,以低温弱光样本为处理性状,创建表型矩阵,聚类分成了29个板块,其中有13个板块与低温弱光处理性状相关。对正向相关性最高的3个板块进行预测,得到108个转录因子,其中占比前3类的分别是ERF(18个)、MYB(10个)、NAC(10个)。通过KEGG通路富集发现,3个板块分别涉及到过氧化物酶体、植物激素信号转导、光合作用以及MAPK信号通路等途径。根据TOM值(topological overlap matrix)、MM值(module member-ship)和连通度(K.in)在板块中筛选出3个核心基因,并经蛋白质同源性分析鉴定为ATPβ、G6PDH、PER5;对3个核心基因的上、下游差异表达基因(DEG)分析发现在G6PDH下游基因中下调表达基因数量占比达到93.97%,G6PDH基因被低温弱光诱导上调表达后可能会抑制下游关联基因表达;3个核心基因的启动子中具有低温响应、茉莉酸甲酯响应、赤霉素响应以及光响应等元件;3个核心基因的共表达网络都预测到了ERF转录因子。

To study coexpression network of Luffa cylindrica(L.)Roem under low temperature and weak light stress,weighted gene co-expression network analysis was introduced.WGCNA to screen out the core genes that respond to low temperature and weak light.Based on 15 transcript sequencing samples of common Luffa treated with low temperature and weak light,phenotypic matrix was created with low temperature and weak light samples as processing traits,and 29 module were clustered,among which 13 module were correlated with low temperature and weak light treatment traits.The three module with the highest positive correlation were predicted and 108 transcription factors were obtained,among which the top three types were ERF(18),MYB(10)and NAC(10).According to the enrichment of KEGG pathway,the three module are involved in peroxisome,plant hormone signal transduction,photosynthesis and MAPK signal pathway,respectively.Three core genes were screened from the module according to topological overlap matrix(TOM),module member-ship(MM)and connectivity(K.in),and identified as ATPβ,G6PDH and PER5 by protein homology analysis.The analysis of up-expression and down-expression differentially expressed genes(DEG)of the three core genes showed that 93.97%of down-expression genes of G6PDH were down-regulated in the downstream genes,and the up-expression expression of G6PDH gene induced by low temperature and weak light might inhibit the expression of downstream associated genes.The promoters of the three core genes had elements such as low temperature response,methyl jasmonate response,gibberellin response and light response.The co-expression networks of the three core genes predicted ERF transcription.