柳枝稷Hsp70家族基因鉴定与生物信息学分析

Genome-wide identification and bioinformatics analysis of Hsp70 family genes in switchgrass

热激蛋白70 (Hsp70)是生物体内分布最广和研究最多的一类蛋白,在植物非生物胁迫响应中发挥着重要调控作用。柳枝稷(Panicum virgatum)是多年生暖季型能饲兼用草,且被视为生物能源模式植物。本研究利用隐马尔科夫模型文件PF00012鉴定到了柳枝稷41个Hsp70基因,分别将属于Dank亚家族的33个基因命名为PvHsp70-1~PvHsp70-33(包括4个分子伴侣BiP基因),将属于Hsp110/SSE亚家族的8个基因命名为PvHsp110-1~PvHsp110-8。41个Hsp70基因不均衡地分布在柳枝稷12条染色体上,在09K染色体上分布最多(11个),04K和04N染色体上分布最少(1个)。应用系统进化树进化分析表明,41个基因可聚类为6个组,每组基因的结构、基序(数量、类型、顺序)相似。柳枝稷、水稻(Oryza sativa)和拟南芥(Arabidopsis thaliana)的91个直系同源Hsp70基因聚类分析显示,共聚为4类,分别定位于细胞质、内质网、线粒体和质体。此外,32个PvHsp70基因具有基因组共线性关系,存在一对串联复制基因PvHsp110-4和PvHsp110-5。PvHsp70基因的启动子区主要是包含HSE等响应非生物胁迫相关作用元件和激素应答顺式作用元件。在柳枝稷不同组织的不同发育时期,PvHsp70s基因的表达水平也存在差异。镉胁迫下,有29个PvHsp70基因上调表达。本研究结果为理清PvHsp70基因在柳枝稷响应逆境胁迫中的功能奠定了基础。

The heat shock protein 70(Hsp70) family of proteins is among the most widely distributed and intensively studied proteins in organisms. The proteins have vital regulatory roles in plant responses to abiotic stress. Switchgrass(Panicum virgatum) is a perennial warm-season bioenergy and forage grass species. It is a model bioenergy plant. In this study, a total of 41 Hsp70 family genes were identified in switchgrass using the Hsp70 hidden Markov model(PF00012). Thirty-three of the genes classified in the Dank subfamily were designated PvHsp70-1~PvHsp70-33(including four chaperone BiP genes)and eight in the Hsp110/SSE subfamily were designated PvHsp110-1~ PvHsp110-8. Forty-one PvHsp70 genes were unequally distributed in 12 chromosomes of switchgrass, with a maximum(n = 11) of the PvHsp70 genes on chromosome09K. Only one gene was located each on chromosome 04K and 04N. Gene structure and phylogenetic analyses classified the 41 Pv Hsp70 genes into six groups. The type, order, and number of motifs were similar among proteins within the same group, but differed among different groups. Combined phylogenetic analysis that included 91 orthologous Hsp70 genes of switchgrass, Arabidopsis, and rice clustered their encoding proteins into four classes that were subcellularly located in the cytosol, endoplasmic reticulum, mitochondria, and plastids. In addition, genomic collinearity analysis revealed that 32PvHsp70 genes were collinear, with a pair of tandem replicated genes(PvHsp110-4 and PvHsp110-5). Promoter analysis revealed multiple abiotic stress-related cis-elements and hormone-responsive cis-elements(e.g., HSE elements) in the promoters of the PvHsp70 genes. The expression levels of PvHsp70 genes were different at different developmental stages in different tissues. Upon cadmium stress, 29 PvHsp70 genes were upregulated. The results of this study provide support for understanding the role of PvHsp70 genes in the regulation of switchgrass stress responses.