Systems biology of the genomes’ microsatellite signature of Orthopoxvirus including the Monkeypox virus

Abstract

This study is an attempt to extract and analyse the microsatellites or simple sequence repeats (SSRs) from the genomes of eight species of the genus Orthopoxvirus. The average size of genomes included in the study was 205 kb while the GC% was 33% for all but one. A total of 10,584 SSRs and 854 cSSRs were observed. POX2 with the largest genome of 224.499 kb had maximum of 1493 SSRs and 121 cSSRs (compound SSR) while POX7 with the smallest genome of 185.578 kb had minimum incident SSRs and cSSRs at 1181 and 96, respectively. There was significant correlation between genome size and SSR incidence. Di-nucleotide repeats were the most prevalent (57.47%) followed by mono- at 33% and tri- at 8.6%. Mono-nucleotide SSRs were predominantly T (51%) and A (48.4%). A majority of 80.32% SSRs were in the coding region. The three most similar genomes as per heat map POX1, POX7 and POX5 (93% similarity) are adjacent to one another in the phylogenetic tree. Ankyrin/Ankyrin like protein and Kelch protein which are associated with host determination and divergence have the highest SSR density in almost all studied viruses. Thus, SSRs are involved in genome evolution and host determination of viruses.