Elucidating the Microsatellite Signature of the Tri-Partite Genomes of the Viral Family Peribunyaviridae.

Abstract

Peribunyaviridae family belonging to the order Bunyavirales possesses four Genera: Herbevirus (3 species), Orthobunyavirus (125 classified and 14 unclassified species), Pacuvirus (5 species), Shangavirus (1), and three unclassified members. Each of the genomes had three segments: Large (L), Medium (M), and Small (S). Simple sequence repeats (SSR), or microsatellites, as a signature have been used to illustrate the evolutionary relation between viruses. The present study attempts to extract and analyze the incidence, composition and distribution of microsatellites in the 151 genomes of Peribunyaviridae with reference to possible implications in evolution and host determination. Several databases, online tools, and software such as ICTV, NCBI, MISA, MAFFT, and MEGA were utilized in the analysis. The average size of the studied genomes (kbp) ranged from ~ 6.909 (L), ~ 4.43 (M), and ~ 0.98(S) segments. Correspondingly, the average GC% for segments were 33.66% (L), 34.47% (M), and 40.10% (S). A total of 8517 SSRs and 713 cSSRs (compound simple sequence repeats) were extracted in the study. The three segments comprise 1651, 907, and 228 mono-repeat motifs, respectively. Total di-repeat segment-wise incidences observed were L (2855), M (1895), and S (278). Further, > 90% of the SSRs were in the CDS region. Phylogenetic analysis indicated differential evolution of the three genome segments. Also, the species that had the mono-SSRs localized exclusively to the A/T region had predominantly mosquitoes as hosts, suggesting a plausible role in host determination. The absence of any pattern in these microsatellites' incidence within and across the genomes suggests their unique role in genome function and evolution.