Genome-wide mining and comparative analysis of microsatellites in five domestic birds

Abstract

Microsatellites are widely present in the gene sequences of most species and are closely associated with genome structure, function and certain diseases. To identify microsatellites in five domesticated bird species, we searched and compared Amazona aestiva, Aaes; Myiopsitta monachus, Mmon; Acridotheres tristis, Atri; Anas platyrhynchos, Apla; Gallus gallus. Perfect microsatellites (P-SSR) with nucleotide lengths between 1 and 6 in the Ggal gene sequence were identified. A total of 101,395, 171,161, 226,953, 458,231 and 272,487 P-SSRs were identified. the most common perfect SSRs were single nucleotide SSRs. the next most common SSRs for Aaes, Mmon and Apla were tetranucleotides (11.30%, 15.22% and 15.62%) the least while for Atri and Ggal they were pentanucleotides (23.67% and 19.57%) and the least were dinucleotide SSRs (5.75%) and trinucleotide SSRs (5.89%), respectively. In the GC content statistics for all SSRs, the total GC content accounted for 1.95% (Aaes), 3.19% (Mmon) 29.71% (Atri), 16.73% (Apla) and 27.39% (Ggal) of the total length of SSRs, respectively. The GC content of almost all types of SSRs was higher than that of the whole genome, except for single nucleotide SSRs, and the lowest GC content was found in single nucleotide SSRs. and, the single nucleotide GC content of Ggal (11.89%) was 45 times higher than that of Aaes (0.26%). The comparison of several aspects of the distribution frequency of SSRs, GC content and repeat sequences of nucleotides showed that the microsatellite distribution characteristics in the five species differed significantly between species. The above results and data reveal differences among the five bird species at the genomic level and genetic diversity of species in domesticated birds. Our data will contribute to comparative genome mapping, understanding the distribution and genomic structure of SSRs among these animal models, and laying the foundation for further development and identification of more domesticated bird-specific SSRs.