Whole-genome sequencing and analysis of the Malaysian cynomolgus macaque (Macaca fascicularis) genome

Atsunori Higashino, Ryuichi Sakate, Yosuke Kameoka, Ichiro Takahashi, Makoto Hirata, Reiko Tanuma, Toru Masui, Yasuhiro Yasutomi, Naoki Osada

Research output: Contribution to journalArticle

53 Citations (Scopus)

Abstract

Background: The genetic background of the cynomolgus macaque (Macaca fascicularis) is made complex by the high genetic diversity, population structure, and gene introgression from the closely related rhesus macaque (Macaca mulatta). Herein we report the whole-genome sequence of a Malaysian cynomolgus macaque male with more than 40-fold coverage, which was determined using a resequencing method based on the Indian rhesus macaque genome.Results: We identified approximately 9.7 million single nucleotide variants (SNVs) between the Malaysian cynomolgus and the Indian rhesus macaque genomes. Compared with humans, a smaller nonsynonymous/synonymous SNV ratio in the cynomolgus macaque suggests more effective removal of slightly deleterious mutations. Comparison of two cynomolgus (Malaysian and Vietnamese) and two rhesus (Indian and Chinese) macaque genomes, including previously published macaque genomes, suggests that Indochinese cynomolgus macaques have been more affected by gene introgression from rhesus macaques. We further identified 60 nonsynonymous SNVs that completely differentiated the cynomolgus and rhesus macaque genomes, and that could be important candidate variants for determining species-specific responses to drugs and pathogens. The demographic inference using the genome sequence data revealed that Malaysian cynomolgus macaques have experienced at least three population bottlenecks.Conclusions: This list of whole-genome SNVs will be useful for many future applications, such as an array-based genotyping system for macaque individuals. High-quality whole-genome sequencing of the cynomolgus macaque genome may aid studies on finding genetic differences that are responsible for phenotypic diversity in macaques and may help control genetic backgrounds among individuals.

Original languageEnglish
Article numberR58
JournalGenome Biology
Volume13
Issue number7
DOIs
Publication statusPublished - 2012 Jul 2
Externally publishedYes

Fingerprint

Macaca fascicularis
Macaca
genome
Genome
Macaca mulatta
Nucleotides
nucleotides
introgression
genetic background
analysis
population bottleneck
gene
genotyping
Population
Genes
population structure
mutation
drug
demographic statistics
genes

ASJC Scopus subject areas

  • Genetics
  • Cell Biology
  • Ecology, Evolution, Behavior and Systematics
  • Medicine(all)

Cite this

Higashino, A., Sakate, R., Kameoka, Y., Takahashi, I., Hirata, M., Tanuma, R., ... Osada, N. (2012). Whole-genome sequencing and analysis of the Malaysian cynomolgus macaque (Macaca fascicularis) genome. Genome Biology, 13(7), [R58]. https://doi.org/10.1186/gb-2012-13-7-r58

Whole-genome sequencing and analysis of the Malaysian cynomolgus macaque (Macaca fascicularis) genome. / Higashino, Atsunori; Sakate, Ryuichi; Kameoka, Yosuke; Takahashi, Ichiro; Hirata, Makoto; Tanuma, Reiko; Masui, Toru; Yasutomi, Yasuhiro; Osada, Naoki.

In: Genome Biology, Vol. 13, No. 7, R58, 02.07.2012.

Research output: Contribution to journalArticle

Higashino, A, Sakate, R, Kameoka, Y, Takahashi, I, Hirata, M, Tanuma, R, Masui, T, Yasutomi, Y & Osada, N 2012, 'Whole-genome sequencing and analysis of the Malaysian cynomolgus macaque (Macaca fascicularis) genome', Genome Biology, vol. 13, no. 7, R58. https://doi.org/10.1186/gb-2012-13-7-r58
Higashino, Atsunori ; Sakate, Ryuichi ; Kameoka, Yosuke ; Takahashi, Ichiro ; Hirata, Makoto ; Tanuma, Reiko ; Masui, Toru ; Yasutomi, Yasuhiro ; Osada, Naoki. / Whole-genome sequencing and analysis of the Malaysian cynomolgus macaque (Macaca fascicularis) genome. In: Genome Biology. 2012 ; Vol. 13, No. 7.
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