Genome-Wide Survey and Analysis of Microsatellite Sequences in Bovid Species

Wen-Hua Qi; Xue-Mei Jiang; Lian-Ming Du; Guo-Sheng Xiao; Ting-Zhang Hu; Bi-Song Yue; Qiu-Mei Quan

doi:10.1371/journal.pone.0133667

Genome-Wide Survey and Analysis of Microsatellite Sequences in Bovid Species

PLoS One. 2015 Jul 21;10(7):e0133667. doi: 10.1371/journal.pone.0133667. eCollection 2015.

Authors

Wen-Hua Qi¹, Xue-Mei Jiang², Lian-Ming Du³, Guo-Sheng Xiao¹, Ting-Zhang Hu¹, Bi-Song Yue³, Qiu-Mei Quan⁴

Affiliations

¹ College of Life Science and Engineering, Chongqing Three Gorges University, Chongqing, 404100, China.
² College of Environmental and Chemistry Engineering, Chongqing Three Gorges University, Chongqing, 404100, China.
³ Key Laboratory of Bio-resources and Eco-environment (Ministry of Education), College of Life Sciences, Sichuan University, Chengdu, 610064, China.
⁴ School of Life Sciences, China West Normal University, Nanchong, 637009, China.

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.

Publication types

Research Support, Non-U.S. Gov't

MeSH terms

Animals
Base Composition
Cattle / classification
Cattle / genetics*
Genome*
Genome-Wide Association Study
Microsatellite Repeats*
Polymorphism, Genetic

Grants and funding

This work was supported by the Scientific and Technological Research Program of Chongqing Municipal Education Commission (No. KJ1401004) and Wanzhou District (No. 201403068), Talent Introduction Project (No. 12RC03) and Youth Project (No. 13QN12) of Chongqing Three Gorges University.