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

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 chromosome 09K. Only one gene was located each on chromosome 04K and 04N. Gene structure and phylogenetic analyses classified the 41 PvHsp70 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 32 PvHsp70 genes were collinear, with a pair of tandem replicated genes (PvHsp110-4 andPvHsp110-5). 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 ofPvHsp70 genes in the regulation of switchgrass stress responses.