Genome wide identification and analysis of microsatellite repeats in the largest DNA viruses (Poxviridae Family): An in silico approach

Abstract

Background: Microsatellites also known as simple sequence repeats (SSRs), which is also called as junk DNA, mainly used as a neutral genetic marker, presented across coding and non-coding regions of prokaryotes, eukaryotes, and viruses. They are subjects of different fields, such as gene mapping, population genetics, DNA fingerprinting, forensic studies and evolution.Aim: The presented study is focused on the evolutionary relationship between poxviruses for the identification and systematic analysis of the nature and distribution of complex microsatellites, presenting in large DNA viral genomes of poxviruses (Poxviridae family) in vertebrates and invertebrates. Materials and Methods: Genome sequences of seventeen species from the Poxviridae family were assessed by the National Center for Biotechnology (NCBI). The microsatellite was extracted using IMEx software, and statistical analysis was performed using Microsoft office Excel 2007. Furthermore, the molecular evolutionary analyses of poxviruses were conducted using MEGA6. Results: In the current study, we screened 17 vertebrate and invertebrates of pox viral genomes and a total of 8539 SSRs which revealed a total of 2387 cSSRs distributed across all the genomes. From the sequences, poly A or poly T mononucleotide prevailed over a poly G or poly C. Among the identified motifs dinucleotides 51.73% which were the most common types of repeats followed by mononucleotides 36.12%, trinucleotides 11.28%, tetranucleotides 0.56%, pentanucleotides 0.10%, and hexanucleotides 0.21%. Polymorphism increases with genome length and decreasing GC content of repeat motifs for dinucleotides, trinucleotides, and tetranucleotides. This result may help genome-wide evolutionary and quantitative analysis like genome size or GC content which has an influence on the number, simple and compound microsatellite of relative abundance and relative densities. Conclusion: We conclude that largest DNA virus of invertebrates show a higher percentage of microsatellites and repeat motif than the vertebrate poxviruses. The genome size and GC content is an important factor in affecting the occurrence of repeat motif as well microsatellites, in vertebrate and invertebrate poxviruses. The analysis on the phylogenetic relationships and microsatellites in vertebrates and invertebrates, as well the pattern of their evolution, may help to understand (the understanding) of poxviruses in the course of natural evolution.