Abstract
The Tibetan macaque, which is endemic to China, is currently listed as a Near Endangered primate species by the International Union for Conservation of Nature (IUCN)(2017). Short tandem repeats (STRs) refer to repetitive elements of genome sequence that range in length from 1–6 bp. They are found in many organisms and are widely applied in population genetic studies. To clarify the distribution characteristics of genome-wide STRs and understand their variation among Tibetan macaques, we conducted a genome-wide survey of STRs with next-generation sequencing of five macaque samples. A total of 1 077 790 perfect STRs were mined from our assembly, with an N50 of 4 966 bp. Mono-nucleotide repeats were the most abundant, followed by tetra- and di-nucleotide repeats. Analysis of GC content and repeats showed consistent results with other macaques. Furthermore, using STR analysis software (lobSTR), we found that the proportion of base pair deletions in the STRs was greater than that of insertions in the five Tibetan macaque individuals (P<0.05, t-test). We also found a greater number of homozygous STRs than heterozygous STRs (P<0.05, t-test), with the Emei and Jianyang Tibetan macaques showing more heterozygous loci than Huangshan Tibetan macaques. The proportion of insertions and mean variation of alleles in the Emei and Jianyang individuals were slightly higher than those in the Huangshan individuals, thus revealing differences in STR allele size between the two populations. The polymorphic STR loci identified based on the reference genome showed good amplification efficiency and could be used to study population genetics in Tibetan macaques. The neighbor-joining tree classified the five macaques into two different branches according to their geographical origin, indicating high genetic differentiation between the Huangshan and Sichuan populations. We elucidated the distribution characteristics of STRs in the Tibetan macaque genome and provided an effective method for screening polymorphic STRs. Our results also lay a foundation for future genetic variation studies of macaques.
Highlights
Short tandem repeats (STRs), known as microsatellites, are highly variable repetitive elements with nucleotide motifsScience Press of 1–6 bp and are ubiquitous in most eukaryotic organisms (Oliveira et al, 2006)
We discovered that the predominant STR loci contained more A or T bases, except for dinucleotide repeats in which the AC motif was the most abundant, which has been observed in humans (Subramanian et al, 2003)
Owing to the limited number of samples, our results provide an initial understanding of the genetic variation of STRs in Tibetan macaques, and future studies are needed to investigate population genetic variations using more samples from distinct populations
Summary
Short tandem repeats (STRs), known as microsatellites, are highly variable repetitive elements with nucleotide motifsScience Press of 1–6 bp and are ubiquitous in most eukaryotic organisms (Oliveira et al, 2006). Short tandem repeats (STRs), known as microsatellites, are highly variable repetitive elements with nucleotide motifs. Microsatellite mutations are generally derived from replication slippage, leading to the insertion or deletion of one or several repeat motifs (Levinson & Gutman, 1987; Schlötterer, 2000; Schlötterer & Tautz, 1992). STRs are frequently applied to genetic mapping, forensic identification, and phylogenetic studies as molecular markers due to their high abundance, neutrality, high variability, and codominance (Schlötterer, 1998). STRs have been used as molecular markers for the study of genetic diversity and population genetic structure (Qin et al, 2016; Sunnucks, 2000). We determined genome-wide STR variation in Tibetan macaque populations based on high-throughput sequencing
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