Comparative analysis on precise distribution-patterns of microsatellites in HIV-1 with differential statistical method

Abstract

Microsatellite is a short tandem-repeated sequence found in most of the genomes. The former microsatellite analysis usually identified their positions and applied relatively rough statistics, herein, the genomic differential statistical method was raised to show precise distribution-patterns of microsatellites along the whole analyzed sequences in different extents, which processed differential on the genome and calculated the microsatellites per differential-unit. The genomic sequences of 75 Human Immunodeficiency Virus Type 1 (HIV-1) isolates, which came from three subtypes, were selected as the representatives to firstly practice the new method. The results showed that the regionally different distributions of the microsatellites in HIV-1 genome, and totally, relatively fewer microsatellites occurred in the middle of these analyzed genomic sequences. In detail, More mononucleotide microsatellites appeared in the forepart of HIV-1 genomes (5′ side), while dinucleotide microsatellites tended to be rich in the latter-half of genomes (3′ side), and most of trinucleotide microsatellites accumulated in the rear of the genomes (3′ side). Tetranucleotide to hexanucleotide microsatellites were closely absent. And there were different microsatellite distributions in 3 subtypes in some regions. The regionally different distributions of microsatellites in HIV-1 genome suggested that microsatellite distributions might have faced with powerful pressures and regional selections, which might be related with the evolution of HIV-1 genomes. The differential statistical method could help to precisely clarify microsatellite distribution-patterns to associate with series of selection and genomic evolution.