Dataset Information

Complete mitochondrial genome of a Toque Macaque (Macaca sinica).

ABSTRACT: The Toque macaque (Macaca sinica) is the only macaque species on Sri Lanka and endemic to the island. The newly generated mitochondrial genome (Genbank accession number MG870385), obtained from a captive individual, has a length of 16,525?bp and exhibits the typical structure of mammalian mitochondrial genomes. Phylogenetically, the Toque macaque is nested within the Macaca sinica species group and represents a sister lineage to a M. assamensis/M. thibetana clade. The new data help to further illuminate and better understand the complex phylogeny of macaques.

SUBMITTER: Roos C

PROVIDER: S-EPMC7799606 | biostudies-literature | 2018 Feb

REPOSITORIES: biostudies-literature

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Publications

Complete mitochondrial genome of a Toque Macaque (Macaca sinica).

Roos Christian C

Mitochondrial DNA. Part B, Resources 20180210 1

The Toque macaque (Macaca sinica) is the only macaque species on Sri Lanka and endemic to the island. The newly generated mitochondrial genome (Genbank accession number MG870385), obtained from a captive individual, has a length of 16,525 bp and exhibits the typical structure of mammalian mitochondrial genomes. Phylogenetically, the Toque macaque is nested within the Macaca sinica species group and represents a sister lineage to a M. assamensis/M. thibetana clade. The new da ...[more]

PMID: 33474111

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Project description:Macaques are the most widely distributed nonhuman primates and used as animal models in biomedical research. The availability of full-genome sequences from them would be essential to both biomedical and primate evolutionary studies. Previous studies have reported whole-genome sequences from rhesus macaque (Macaca mulatta) and cynomolgus macaque (M. fascicularis, CE), both of which belong to the fascicularis group. Here, we present a 37-fold coverage genome sequence of the Tibetan macaque (M. thibetana; TM). TM is an endemic species to China belonging to the sinica group. On the basis of mapping to the rhesus macaque genome, we identified approximately 11.9 million single-nucleotide variants), of which 3.9 million were TM specific, as assessed by comparison two Chinese rhesus macaques (CR) and two CE genomes. Some genes carried TM-specific homozygous nonsynonymous variants (TSHNVs), which were scored as deleterious in human by both PolyPhen-2 and SIFT (Sorting Tolerant From Intolerant) and were enriched in the eye disease genes. In total, 273 immune response and disease-related genes carried at least one TSHNV. The heterozygosity rates of two CRs (0.002617 and 0.002612) and two CEs (0.003004 and 0.003179) were approximately three times higher than that of TM (0.000898). Polymerase chain reaction resequencing of 18 TM individuals showed that 29 TSHNVs exhibited high allele frequencies, thus confirming their low heterozygosity. Genome-wide genetic divergence analysis demonstrated that TM was more closely related to CR than to CE. We further detected unusual low divergence regions between TM and CR. In addition, after applying statistical criteria to detect putative introgression regions (PIRs) in the TM genome, up to 239,620 kb PIRs (8.84% of the genome) were identified. Given that TM and CR have overlapping geographical distributions, had the same refuge during the Middle Pleistocene, and show similar mating behaviors, it is highly likely that there was an ancient introgression event between them. Moreover, demographic inferences revealed that TM exhibited a similar demographic history as other macaques until 0.5 Ma, but then it maintained a lower effective population size until present time. Our study has provided new insight into the macaque evolutionary history, confirming hybridization events between macaque species groups based on genome-wide data.

Dataset Information

Complete mitochondrial genome of a Toque Macaque (Macaca sinica).

Publications

Complete mitochondrial genome of a Toque Macaque (<i>Macaca sinica</i>).

Similar Datasets

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