Genome-wide characterization of perfect microsatellites in yak (Bos grunniens)

Microsatellites or simple sequence repeats (SSRs) constitute a significant portion of genomes and play an important role in gene function and genome organization. The availability of a complete genome sequence for yak (Bos grunniens) has made it possible to carry out genome-wide analysis of microsatellites in this species. We analyzed the abundance and density of perfect SSRs in the yak genome. We found a total of 723,172 SSRs with 1-6 bp nucleotide motifs, indicating that about 0.47 % of the yak whole genome sequence (2.66 Gb) comprises perfect SSRs, the average length of which was 17.34 bp/Mb. The average frequency and density of perfect SSRs was 272.18 loci/Mb and 4719.25 bp/Mb, respectively. The proportion of the six classes of perfect SSRs was not evenly distributed in the yak genome. Mononucleotide repeats (44.04 %) with a total number of 318,435 and a average length of 14.71 bp appeared to be the most abundant SSRs class, while the percentages of dinucleotide, trinucleotide, pentanucleotide, tetranucleotide and hexanucleotide repeats was 24.11 %, 15.80 %, 9.50 %, 6.40 % and 0.15 %, respectively. Different repeat classes of SSRs varied in their repeat number with the highest being 1206. Our results suggest that 15 motifs comprised the predominant categories with a frequency above 1 loci/Mb: A, AC, AT, AG, AGC, AAC, AAT, ACC, ATTT, GTTT, AATG, CTTT, ATGG, AACTG and ATCTG.