Analysis of Microsatellite Distribution Characteristics in\nthe Entire Genome of Macaca fascicularis

Abstract

Microsatellites(short tandem repeats(STRs))are potent molecular markers that are widely distributed in the genomes of eucaryotic and procaryotic organisms.Crab-eating macaque is an important animal model of non-human primates in biomedical studies.We investigated the distribution of STRs across the entire genome of crab-eating macaque to contribute to the selection and exploration of more STR markers.We searched for STRs by using bioinformatics software.A total of 1284929 STRs were obtained with a sequence of 26044651 bp length,accounting for 0.890% of the entire genome.The frequency and density of STRs in the entire genome were 451.3 loci/Mb and 9118.7 bp/Mb,respectively.The dominant repeat type motifs were mononucleotide(56.7%),followed by tetranucleotide(16.7%),dinucleotide(16.7%),trinucleotide(6.0%),pentanucleotide(3.4%),and hexanucleotide(0.6%).The largest STR count was found in chromosome 1,followed by chromosome 3.The smallest STR count was observed in chromosome 18.The frequency and density of STRs in all chromosomes were significantly positively correlated with guanine-cytosine(GC)content of the chromosome(P<0.01)and significantly negatively correlated with GC content of the STRs(P<0.01).The top five STR repeat type motifs occurred most frequently as A,AC,AAAT,AG and AT.The dominant STRs of mononucleotide,dinucleotide,trinucleotide,tetranucleotide,pentanucleotide and hexanucleotide were A,AC,AAT,AAAT,AAACA and AAACAA,respectively.