Microsatellites in different Potyvirus genomes: survey and analysis

Abstract

Simple sequence repeats (SSRs) have been extensively used for various genetic and evolutionary studies in eukaryotic and prokaryotic organisms, while few relevant researches have been made in viruses. The Potyvirus is a fine system to study roles and evolution of SSRs in viruses. The densities, relative abundances, compositions and evolutionary inferences of SSRs in 45 different Potyvirus genomes have been analyzed in this study. Results showed that the densities and relative abundances of SSRs are similar in all those Potyvirus genomes. The number of SSRs decreases with an increase in the length of repeat unit. Dinucleotide repeats are the most abundant and followed by trinucleotide repeats, and the numbers of tetra-, penta- and hexanucleotide repeats are very small. Repeats of AC/CA, AG/GA and AAG/GAA predominate, whereas repeats of CG/GC, ATA and CAC are rare. The genome sizes of the Potyvirus species have little influence on the total number and relative abundance of SSRs. Our study suggested that the variety of SSRs may be related to the genome diversity of Potyvirus. Maybe Potyvirus and HIV genomes have the similar evolution mode and parallel evolution level.