Abstract
Microsatellites or simple sequence repeats (SSRs) have become the most popular source of genetic markers, which are ubiquitously distributed in many eukaryotic and prokaryotic genomes. This is the first study examining and comparing SSRs in completely sequenced genomes of the Bovidae. We analyzed and compared the number of SSRs, relative abundance, relative density, guanine-cytosine (GC) content and proportion of SSRs in six taxonomically different bovid species: Bos taurus, Bubalus bubalis, Bos mutus, Ovis aries, Capra hircus, and Pantholops hodgsonii. Our analysis revealed that, based on our search criteria, the total number of perfect SSRs found ranged from 663,079 to 806,907 and covered from 0.44% to 0.48% of the bovid genomes. Relative abundance and density of SSRs in these Bovinae genomes were non-significantly correlated with genome size (Pearson, r < 0.420, p > 0.05). Perfect mononucleotide SSRs were the most abundant, followed by the pattern: perfect di- > tri- > penta- > tetra- > hexanucleotide SSRs. Generally, the number of SSRs, relative abundance, and relative density of SSRs decreased as the motif repeat length increased in each species of Bovidae. The most GC-content was in trinucleotide SSRs and the least was in the mononucleotide SSRs in the six bovid genomes. The GC-contents of tri- and pentanucleotide SSRs showed a great deal of similarity among different chromosomes of B. taurus, O. aries, and C. hircus. SSR number of all chromosomes in the B. taurus, O.aries, and C. hircus is closely positively correlated with chromosome sequence size (Pearson, r > 0.980, p < 0.01) and significantly negatively correlated with GC-content (Pearson, r < -0.638, p < 0.01). Relative abundance and density of SSRs in all chromosomes of the three species were significantly negatively correlated with GC-content (Pearson, r < -0.333, P < 0.05) but not significantly correlated with chromosome sequence size (Pearson, r < -0.185, P > 0.05). Relative abundances of the same nucleotide SSR type showed great similarity among different chromosomes of B. taurus, O. aries, and C. hircus.
Highlights
Microsatellites, known as simple sequence repeats (SSRs), are tandem repetitions of 1–6 base pair nucleotide motifs of DNA sequences [1]
Results here indicated that the number, relative abundance, and density of the same repeat type of perfect SSRs showed great similarity in the six bovid species
The results showed that the most GC-content is in the trinucleotide, ranging from 57.32% (C. hircus) to 59.89% (B. taurus), and the least is in the mononucleotide, ranging from 1.97% to 7.94% in these genomes
Summary
Microsatellites, known as simple sequence repeats (SSRs), are tandem repetitions of 1–6 base pair (bp) nucleotide motifs of DNA sequences [1]. SSRs have been developed into one of the most popular sources of genetic markers owing to their high reproducibility, multi-allelic nature, co-dominant mode of inheritance, abundance, and wide genome coverage [2], which have been widely employed in population genetics, phylogenetics, genetic mapping, linkage, and kinship relationships [3]. The conventional methods of generating SSR markers from genomic libraries are challenging, costly, labor consuming and time consuming [14], which are being replaced rapidly by in silico mining of SSR sequences from DNA-sequence databases [15,16]. The availability of enormous genome sequences for a wide range of organisms, together with new methodological developments of in silico mining of SSRs, has accelerated research aimed at understanding the origin and functions of SSRs and at searching for new applications, and will certainly promote the study of genomic distribution of SSRs in the eukaryotic and prokaryotic genomes. Scientific and reasonable microsatellite mining helps in addressing biological questions and facilitates better exploitation of microsatellites for various applications
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