Mining and analysis of simple sequence repeats in the chloroplast genomes of genus Vigna

Abstract

The genus Vigna is distributed throughout the world and it is phylogenetically closely related to agriculturally important crops. Simple sequence repeats (SSRs) are defined as sequence repeat units that occur between 1 and 6 bp and found in both coding and non-coding regions of genome. The availability of organelle genome sequence helps in understanding the organization of SSRs in them. In this study, chloroplast genome sequences of the genus Vigna were screened for the identification of chloroplast simple sequence repeats (cpSSRs). A total of 21, 24 and 25 cpSSRs in Vigna angularis, Vigna radiata and Vigna unguiculata, respectively, were mined computationally. The density of ∼1SSR/6.1–7.2 kb was observed. Depending on the different repeat units, the length of SSRs ranged from 12 to 24 bp. Mononucleotides were the most abundant repeats followed by dinucleotide repeats. Hexanucleotide repeats were completely absent in the chloroplast genomes of genus Vigna. Seven cpSSRs were selected on the basis of repeats to study transferability. The transferable markers can be employed in genome mapping and comparative mapping among Vigna species in future studies.