In- silico exploration of thirty alphavirus genomes for analysis of the simple sequence repeats

Abstract

The compilation of simple sequence repeats (SSRs) in viruses and its analysis with reference to incidence, distribution and variation would be instrumental in understanding the functional and evolutionary aspects of repeat sequences. Present study encompasses the analysis of SSRs across 30 species of alphaviruses. The full length genome sequences, assessed from NCBI were used for extraction and analysis of repeat sequences using IMEx software. The repeats of different motif sizes (mono- to penta-nucleotide) observed therein exhibited variable incidence across the species. Expectedly, mononucleotide A/T was the most prevalent followed by dinucleotide AG/GA and trinucleotide AAG/GAA in these genomes. The conversion of SSRs to imperfect microsatellite or compound microsatellite (cSSR) is low. cSSR, primarily constituted by variant motifs accounted for up to 12.5% of the SSRs. Interestingly, seven species lacked cSSR in their genomes. However, the SSR and cSSR are predominantly localized to the coding region ORFs for non structural protein and structural proteins. The relative frequencies of different classes of simple and compound microsatellites within and across genomes have been highlighted.

Keywords: Compound microsatellite; IMEx, Imperfect Microsatellite Extraction; Imperfect Microsatellite Extraction (IMEx); RA, Relative abundance; RD, Relative density; Relative abundance; Relative density; SSR, Simple sequence repeat; Simple sequence repeats (SSR); cSSR, Compound simple sequence repeat.

Fig. 1

Analysis of SSRs and cSSRs (a) Incidence (b) Relative abundance: SSRs/cSSRs present per Kb of genome (c) Relative density: Total length covered by SSR/cSSR per Kb of genome.

Fig. 2

Analysis of cSSR-% (Number of cSSR/Total number of SSR*100) across different alphavirus genomes.

Fig. 3

Frequency of cSSR-% (Percentage of individual microsatellites being part of a compound microsatellite) in relation to varying dMAX (10 to 50) across six randomly selected alphavirus species.

Fig. 4

Correlation analysis of (a) SSRs and (b) cSSR with genome size and GC content across alphavirus genomes.

Fig. 5

Differential composition of (a) Mono-nucleotide repeats (b) Di-nucleotide repeat motifs (c) Tri-nucleotide repeat motifs.

Fig. 6

Comparative distribution of (a) SSRs and (b) cSSR across coding and non-coding regions of alphavirus genomes.

Fig. 7

Differential contribution of mono-, di- and tri-nucleotide SSR motifs across Structural proteins ORF, Non-structural proteins ORF and Non-coding regions of alphavirus genomes.