Genome-wide distribution and organization of microsatellites in six species of birds

• The genome-wide analyses of microsatellite distributions in six bird species were performed using in silico data mining approach.
• The genome-wide distribution and organization of SSRs in six bird species highlighted a non-random distribution of these repeats.
• The wealth of different motifs of genome-wide SSR markers identified in the present study.

Simple sequence repeats (SSRs), or microsatellites, are important genetic markers and play a significant role in genome organization. The genome-wide analyses of microsatellite distributions in six bird species (Gallus gallus, Meleagris gallopavo, Taeniopygia guttata, Geospiza fortis, Melopsittacus undulates, and Columba livia) were performed using in silico data mining approach. Under our search criteria, the total numbers of 1–6 bp perfect microsatellites detected ranged from 90,346 to 282,728 and covered from 0.13 to 0.49% in the complete genomes of the six bird species. The SSR abundance was not correlated with genome size, and mononucleotide repeats outnumbered other SSR categories in all of the six species examined. However, there is was a little difference in the most common repeat motifs for each length among the six different bird species considered, with obvious relation to the AT-richness of their genomes. The distribution of SSRs in the different genomic regions of three bird genomes (G. gallus, M. meleagris, and T. guttata) indicated that the intergenic regions exhibited the highest relative abundance compared to the intron and exon regions in all the six motif lengths. In the genome of G. gallus, the motif of (AGGA)n made up the most iterated microsatellite locus (spanning 108 repetitions) and 83.6% of these most abundant SSR motifs had a repeat number less than 12. What’s more, the number of microsatellites in different chromosomes was positively correlated with the size of the chromosomes in the genome of G. gallus.