An In-Silico Analysis of Microsatellites Among Viruses with Double Stranded RNA Genomes in Four Genera of Partitiviridae

摘要

Microsatellites are universally present in eukaryotic, prokaryotic and viral genomes. In this study, 36 complete genomes of Partitiviridae containing Alpha-, Beta-, Delta-and Gammapartiti virus were downloaded from NCBI and the microsatellites in these genomes were extracted with IMEx software. Two parameters were chosen to analyze the incidence of microsatellites. Results showed that a higher frequency of microsatellites occurred in Alpha-and Betapartitivirus, while the occurrence of Gammapartitivirus was lowest in same parameters. Trinucleotide repeats were richest for all types of microsatellites with 5, 3, 2, 2, 2 and 2 parameters, and they were comparatively suitable than 6, 3, 3, 3, 3 and 3, parameters, in understanding the distribution of all types of repeats. The relationship between same microsatellite (SM) and classification of viruses, including the host of the virus, were also discussed in this paper. It was revealed that more SMs existed in the same species of viruses and their similarity index (SI) was high when the host of the virus was same isolate /cultivar by pair-wise comparison. These observations may help in understanding the distribution of microsatellites and evolution of viruses in the four genera in Partitiviridae.