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.

Figure 1

Relative abundance of mono- to hexanucleotide P-SSRs in different intragenic and intergenic regions of six bovids. ABCDEF represent 5′UTRs, coding regions, introns, 3′UTRs, TEs, and intergenic regions, respectively.

Figure 2

Distribution of different motfis of mono- to trinucleotide P-SSRs in different genomic regions of six bovid genomes. ABCDEF represent 5′UTRs, coding regions, introns, 3′UTRs, TEs, and intergenic regions, respectively.

Figure 3

GC-contents of different intragenic and intergenic regions in six bovid species.

Figure 4

GC-contents of mono- to hexanucleotide P-SSRs in different intragenic and intergenic regions of six bovid species. ABCDEF represent 5′UTRs, coding regions, introns, 3′UTRs, TEs, and intergenic regions, respectively.

Figure 5

Comparative analysis of repeat copy number (RCN) of mononucleotide P-SSRs in different genomic regions of six bovid genomes. ABCDEF represent 5′UTRs, coding regions, introns, 3′UTRs, TEs, and intergenic regions, respectively.

Figure 6

Comparative analysis of RCN of dinucleotide P-SSRs in different genomic regions of six bovid genomes. ABCDEF represent 5′UTRs, coding regions, introns, 3′UTRs, TEs, and intergenic regions, respectively.

Figure 7

Comparative analysis of RCN of trinucleotide P-SSRs in different genomic regions of six bovid genomes. ABCDEF represent 5′UTRs, coding regions, introns, 3′UTRs, TEs, and intergenic regions, respectively.

Figure 8

The CV analysis of RCN of SSRs in different genomic regions of six bovid genomes. ABCDEF represent 5′UTRs, coding regions, introns, 3′UTRs, TEs, and intergenic regions, respectively.