High GC content of simple sequence repeats in Herpes simplex virus type 1 genome

The presence, locations and composition of simple sequence repeats (SSRs) in Herpes simplex virus type 1 (HSV-1) genome were extracted and analyzed by using the software Imperfect Microsatellite Extractor (IMEx). There were 663 mon-, 502 di-, 184 tri-, 20 tetra-, 4 penta- and 4 hexanucleotide SSRs that were observed in different distribution between coding and noncoding regions in the HSV-1 genome. G/C, GC/CG, and (GGC)n were predominant in mononucleotide, dinucletide, trinucleotide repeats respectively. Indeed, the results showed that GC content in simple sequence repeats was notably higher than that in entire HSV-1 genome. Our data might be helpful for studying the pathogenesis, genome structure and evolution of HSV-1.

► We analyzed the distribution of SSRs in coding, noncoding regions of HSV-1 genome. ► G/C, GC/CG, (GGC)n were excessive in mono-, di-, trinucleotide repeats respectively. ► In all SSRs the GC content was higher than that in entire genome. ► High GC content SSRs might be related to genome structure and pathogenesis of HSV-1.