Distribution patterns and variation analysis of simple sequence repeats in different genomic regions of bovid genomes

Abstract

As the first examination of distribution, guanine-cytosine (GC) pattern, and variation analysis of microsatellites (SSRs) in different genomic regions of six bovid species, SSRs displayed nonrandomly distribution in different regions. SSR abundances are much higher in the introns, transposable elements (TEs), and intergenic regions compared to the 3′-untranslated regions (3′UTRs), 5′UTRs and coding regions. Trinucleotide perfect SSRs (P-SSRs) were the most frequent in the coding regions, whereas, mononucleotide P-SSRs were the most in the introns, 3′UTRs, TEs, and intergenic regions. Trifold P-SSRs had more GC-contents in the 5′UTRs and coding regions than that in the introns, 3′UTRs, TEs, and intergenic regions, whereas mononucleotide P-SSRs had the least GC-contents in all genomic regions. The repeat copy numbers (RCN) of the same mono- to hexanucleotide P-SSRs showed significantly different distributions in different regions (P < 0.01). Except for the coding regions, mononucleotide P-SSRs had the most RCNs, followed by the pattern: di- > tri- > tetra- > penta- > hexanucleotide P-SSRs in the same regions. The analysis of coefficient of variability (CV) of SSRs showed that the CV variations of RCN of the same mono- to hexanucleotide SSRs were relative higher in the intronic and intergenic regions, followed by the CV variation of RCN in the TEs, and the relative lower was in the 5′UTRs, 3′UTRs, and coding regions. Wide SSR analysis of different genomic regions has helped to reveal biological significances of their distributions.

Genome-wide characterization and analysis of microsatellite sequences in camelid species

“…Mononucleotide SSRs were the most abundant in exons, intronic, and intergenic regions, with the exception of V. pacos, in which trinucleotide and dinucleotide SSRs were identified to be most frequent types in exons and intergenic regions, respectively. This was consistent with observations from other eukaryotic genomes (Sharma et al 2007;Qi et al 2016;Qi et al 2018). Pentanucleotide SSRs were the least common type in CDSs, whereas hexanucleotide SSRs were the least common type in exons and intronic and intergenic regions, except in C. dromedarius and V. pacos, where pentanucleotide SSRs were the least common type in exons.…”

“…In CDSs, trinucleotide SSRs were the most frequent type, consistent with results observed in primates (Qi et al 2016) and bovids (Qi et al 2018). Such predominance of triplets over other SSR repeat types in coding regions may be explained by purifying selection, which serves to eliminate non-trimeric SSRs in coding regions as they may cause frameshift mutations (Metzgar et al 2000).…”

“…However, camelid species have very large genomes (> 2 Gb). For this reason, the criteria utilized in this study to search for perfect SSRs were as follows: motif size of 1 to 6 nucleotides long using (-m option) and (-M option), and minimum repeat numbers restricted to 12 repeats for mononucleotides, seven repeats for dinucleotides, five repeats for trinucleotides, and four repeats for tetra-, penta-, and hexanucleotides, which were consistent with previous studies (Qi et al 2015;Liu et al 2017;Qi et al 2018). All other settings were set as default.…”

Complete Chloroplast Genomes of Chlorophytum comosum and Chlorophytum gallabatense: Genome Structures, Comparative and Phylogenetic Analysis

“…This result supports another study where the A/T repeats were abundant [60]. Genetic diversity is reflected in the regions with high mutation rates [61]. The identified loci, in this study, could be good molecular markers, useful in the study of population genetics of C. comosum and C. gallabatense and phylogenetic study in the future.…”

Genome-wide characterization of simple sequence repeats in Palmae genomes

“…A number of criteria were adopted to identify perfect SSRs. Specifically, repeat sizes of 1 to 6 nucleotides long were searched, and minimum repeat numbers were restricted to 12 repeats for mononucleotides, 7 repeats for dinucleotides, 5 repeats for trinucleotides, and 4 repeats for tetra-, penta-and hexanucleotides, consistent with previous studies (Liu et al 2017;Qi et al 2018). The remaining parameters were set as default.…”