Genome-wide in silico analysis of SOD genes in common bean (Phaseolus vulgaris L.)

Abstract

Superoxide dismutases (SODs) are a group of enzymes that play essential roles in catalyzing the dismutation of superoxide radicals to protect cells from oxidative damage caused by various adverse conditions. SODs are classified into three types based on their metal cofactors: Cu/ZnSOD, FeSOD, and MnSOD. This study presents the first genome-wide identification of SOD genes in Phaseolus vulgaris L. Eight SOD genes were identified in the genome of P. vulgaris L., including four Cu/ZnSODs (CSD), three FeSODs (FSD) and one MnSOD (MSD). The protein sequence ranged between 166 and 312 amino acids with 5–8 introns each. Most PvSOD genes are in chromosome 7. The syntenic analysis revealed that PvFSD1 and PvFSD2 genes were derived from segmental duplication. As expected, phylogenetic analyses grouped the PvSOD proteins into three classes based on their metal cofactors: copper/zinc (Cu/Zn)SOD, manganese (Mn)SOD, and iron (Fe)SOD. Expression pattern analysis using RNAseq data indicated that three of the PvSOD genes (PvMSD1, PvCSD3, and PvFSD1) were detected in majority of tissues and developmental stages. This study provides a comprehensive analysis about SOD genes in P. vulgaris L. and new resources for future studies on the functional analysis of PvSOD genes in this species of great agronomic importance.