Systems Biology of the Microsatellite Signature in 156 Genomes of the Viral Family Rhabdoviridae

Simple Sequence Repeats (SSR) or microsatellites are composed of 1-6 nucleotide motifs present as tandem repeat sequences across the genome in viruses, prokaryotes and eukaryotes. In this study, we analyze the incidence, composition, and complexity of microsatellites in 156 genomes of the family Rhabdoviridae. The Rhabdoviridae genome may be single or double stranded, 45-100 nm in diameter, 10-16 kb in length. The viruses infect a wide range of land and aquatic animals including humans, birds, reptiles, fish, and plants. The full-length genome sequences were assessed from NCBI ( http://www.ncbi.nlm.nih.gov/ ) and analyzed using IMEx software. A total of 10,058 SSRs and 536 cSSRs (compound SSR: two or more SSRs separated by a distance of < dMAX) were extracted from the Rhabdoviridae genomes. The SSR incidence frequency ranged from 38 to 120 and for cSSR it lay between 0 and 10. The incidence of mono, di and tri nucleotide SSRs is 3042, 4796 and 1663 respectively. The most prevalent mono-nucleotide repeat was "A" comprising of around 21% (2095 of 10058) followed by "T" (567 of 10058). The incidence, distribution, location and clustering of SSR are not constant and fail to follow any rule or pattern, which might be contributing to the viral diversity and evolution. Based on phylogenetic analysis and distribution of SSRs, we propose the mono-nucleotide distribution in A/T region of the genome as a potential parameter for host divergence to humans and related species. This needs to be ascertained in a wider range of viruses.