Microsatellite Diversity and Complexity in Eighteen Staphylococcus Phage Genomes

Abstract

: The present study focused on Staphylococcus phage genomes, which have been classified to 3 categories on the basis of their size. Overall, 18 classes of II Staphylococcus phage genomes with genome size around 40 kbp were investigated to elucidate the presence, distribution, and complexity of SSRs therein. The full length genome sequences from NCBI were analyzed using the IMEx software. A total of 3656 simple sequence repeats (SSRs) and 213 compound SSRs (cSSR) were present in the studied genomes. The incident frequency of SSR and cSSR per genome ranged from 183 to 308 and 8 to 19, respectively. The SSRs distribution across genomes was non-linear and so was its conversion to cSSR (the range of cSSR percentage was from 4.15 to 9.13) implicating a non-uniform incidence and clustering in genomes. The AT rich content of genomes was reflected in the prevalence of repeats with A, AT/TA, and AAG/GAA being the highest represented mono-, di-, and tri-nucleotide repeat motifs, respectively. An increase in dMAX was accompanied by greater cSSRs in the genomes yet the increase was neither uniform across genomes nor linear. The SSRs and cSSRs are predominantly localized on the coding region. The non-coding region accounts for ~ 19% in SSR and ~ 30% in cSSR while a hypothetical protein accounted for ~30% in SSRs as well as cSSR. The relative frequencies and distribution of different classes of simple and compound microsatellites within and across genomes are suggestive of these sequences being involved in genome evolution and adaptation.