Incidence, complexity and diversity of simple sequence repeats across potexvirus genomes

Abstract

An in-silico analysis of simple sequence repeats (SSRs) in genomes of 32 species of potexviruses was performed wherein a total of 691 SSRs and 33 cSSRs were observed. Though SSRs were present in all the studied genomes their incident frequency ranged from 11 to 30 per genome. Further, 10 potexvirus genomes possessed no cSSRs when extracted at a dMAX of 10 and wherein present, the highest frequency was 3. SSR and cSSR incidence, relative density and relative abundance were non-significantly correlated with genome size and GC content suggesting an ongoing evolutionary and adaptive phase of the virus species. SSRs present primarily ranged from mono- to tri-nucleotide repeat motifs with a greatly skewed distribution across the coding and non-coding regions. Present work is an effort for the undergoing compilation and analysis of incidence, distribution and variation of the viral repeat sequences to understand their evolutionary and functional relevance.

Keywords: CP; Correlation studies; IMEx; Imperfect Microsatellite Extraction; Potexvirus; RA; RD; RDRP; RNA dependent RNA polymerase; SSR; Simple sequence repeats; TGB; cSSR; coat protein; compound simple sequence repeat; relative abundance; relative density; simple sequence repeat; triple gene block.