Genome wide survey and analysis of microsatellites in Tombusviridae family

Abstract

Microsatellites are small repetitive sequences found in all kingdoms of life including viruses. Members of the Tombusviridae family severely affect growth of wide range of plants and reduce economic yield in diverse cropping systems worldwide. Here, we analyzed the nature and distribution of both simple and complex microsatellites present in complete genome of 47 species of Tombusviridae family. Our results showed, in all analyzed genomes, genome size and GC content had a weak influence on number, relative abundance and relative density of microsatellites, respectively. For each genome, dinucleotide repeats followed by mononucleotide repeats were found to be highly predominant. Mononucleotide repeats were found to be underrepresented in majority of Tombusviridae genomes. Poly G and Poly C repeats were more abundant as compared to poly A or poly T nucleotides. TG/GT and AG/CA was the most abundant dinucleotide repeat motif observed in Tombusviridae genomes. Repeats larger than trinucleotide were never found in these viral genomes. Comparative study of relative abundance and density of microsatellite among available RNA and DNA viral genomes indicated that simple repeats were lower than many RNA virus genomes. To our knowledge, this is the first analysis of microsatellites occurring in Tombusviridae genomes. Characterization of such variations in repeat sequences would be important in deciphering the origin, mutational processes, and role of repeat sequences in viral genomes.