Genome sequencing and comparison of two nonhuman primate animal models, the cynomolgus and Chinese rhesus macaques

Guangmei Yan; Guojie Zhang; Xiaodong Fang; Yanfeng Zhang; Cai Li; Fei Ling; David N Cooper; Qiye Li; Yan Li; Alain J. van Gool; Hongli Du; Jiesi Chen; Ronghua Chen; Pei Zhang; Zhiyong Huang; John R Thompson; Yuhuan Meng; Yinqi Bai; Jufang Wang; Min Zhuo; Tao Wang; Ying Huang; Liqiong Wei; Jianwen Li; Zhiwen Wang; Haofu Hu; Pengcheng Yang; Liang Le; Peter D Stenson; Bo Li; Xiaoming Liu; Edward V Ball; Na An; Quanfei Huang; Yong Zhang; Wei Fan; Xiuqing Zhang; Yingrui Li; Wen Wang; Michael G Katze; Bing Su; Rasmus Nielsen; Huanming Yang; Jun Wang; Xiaoning Wang; Jian Wang

doi:10.1038/nbt.1992

Genome sequencing and comparison of two nonhuman primate animal models, the cynomolgus and Chinese rhesus macaques

Guangmei Yan, Guojie Zhang, Xiaodong Fang, Yanfeng Zhang, Cai Li, Fei Ling, David N Cooper, Qiye Li, Yan Li, Alain J. van Gool, Hongli Du, Jiesi Chen, Ronghua Chen, Pei Zhang, Zhiyong Huang, John R Thompson, Yuhuan Meng, Yinqi Bai, Jufang Wang, Min ZhuoTao Wang, Ying Huang, Liqiong Wei, Jianwen Li, Zhiwen Wang, Haofu Hu, Pengcheng Yang, Liang Le, Peter D Stenson, Bo Li, Xiaoming Liu, Edward V Ball, Na An, Quanfei Huang, Yong Zhang, Wei Fan, Xiuqing Zhang, Yingrui Li, Wen Wang, Michael G Katze, Bing Su, Rasmus Nielsen, Huanming Yang, Jun Wang, Xiaoning Wang, Jian Wang

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Abstract

The nonhuman primates most commonly used in medical research are from the genus Macaca. To better understand the genetic differences between these animal models, we present high-quality draft genome sequences from two macaque species, the cynomolgus/crab-eating macaque and the Chinese rhesus macaque. Comparison with the previously sequenced Indian rhesus macaque reveals that all three macaques maintain abundant genetic heterogeneity, including millions of single-nucleotide substitutions and many insertions, deletions and gross chromosomal rearrangements. By assessing genetic regions with reduced variability, we identify genes in each macaque species that may have experienced positive selection. Genetic divergence patterns suggest that the cynomolgus macaque genome has been shaped by introgression after hybridization with the Chinese rhesus macaque. Macaque genes display a high degree of sequence similarity with human disease gene orthologs and drug targets. However, we identify several putatively dysfunctional genetic differences between the three macaque species, which may explain functional differences between them previously observed in clinical studies.

Originalsprog	Engelsk
Tidsskrift	Nature Biotechnology
Vol/bind	29
Udgave nummer	11
Sider (fra-til)	1019-1023
Antal sider	5
ISSN	1087-0156
DOI	https://doi.org/10.1038/nbt.1992
Status	Udgivet - nov. 2011

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Yan, G., Zhang, G., Fang, X., Zhang, Y., Li, C., Ling, F., Cooper, D. N., Li, Q., Li, Y., van Gool, A. J., Du, H., Chen, J., Chen, R., Zhang, P., Huang, Z., Thompson, J. R., Meng, Y., Bai, Y., Wang, J., ... Wang, J. (2011). Genome sequencing and comparison of two nonhuman primate animal models, the cynomolgus and Chinese rhesus macaques. Nature Biotechnology, 29(11), 1019-1023. https://doi.org/10.1038/nbt.1992

Yan, G, Zhang, G, Fang, X, Zhang, Y, Li, C, Ling, F, Cooper, DN, Li, Q, Li, Y, van Gool, AJ, Du, H, Chen, J, Chen, R, Zhang, P, Huang, Z, Thompson, JR, Meng, Y, Bai, Y, Wang, J, Zhuo, M, Wang, T, Huang, Y, Wei, L, Li, J, Wang, Z, Hu, H, Yang, P, Le, L, Stenson, PD, Li, B, Liu, X, Ball, EV, An, N, Huang, Q, Zhang, Y, Fan, W, Zhang, X, Li, Y, Wang, W, Katze, MG, Su, B, Nielsen, R, Yang, H, Wang, J, Wang, X & Wang, J 2011, 'Genome sequencing and comparison of two nonhuman primate animal models, the cynomolgus and Chinese rhesus macaques', Nature Biotechnology, bind 29, nr. 11, s. 1019-1023. https://doi.org/10.1038/nbt.1992

@article{305965d1fc684a6d90062d196fdd2e23,

title = "Genome sequencing and comparison of two nonhuman primate animal models, the cynomolgus and Chinese rhesus macaques",

abstract = "The nonhuman primates most commonly used in medical research are from the genus Macaca. To better understand the genetic differences between these animal models, we present high-quality draft genome sequences from two macaque species, the cynomolgus/crab-eating macaque and the Chinese rhesus macaque. Comparison with the previously sequenced Indian rhesus macaque reveals that all three macaques maintain abundant genetic heterogeneity, including millions of single-nucleotide substitutions and many insertions, deletions and gross chromosomal rearrangements. By assessing genetic regions with reduced variability, we identify genes in each macaque species that may have experienced positive selection. Genetic divergence patterns suggest that the cynomolgus macaque genome has been shaped by introgression after hybridization with the Chinese rhesus macaque. Macaque genes display a high degree of sequence similarity with human disease gene orthologs and drug targets. However, we identify several putatively dysfunctional genetic differences between the three macaque species, which may explain functional differences between them previously observed in clinical studies.",

keywords = "Animals, Base Sequence, Chromosome Aberrations, Evolution, Molecular, Genome, Humans, Macaca fascicularis, Macaca mulatta, Models, Animal, Molecular Sequence Data, Polymorphism, Genetic, Sequence Analysis, DNA, Species Specificity",

author = "Guangmei Yan and Guojie Zhang and Xiaodong Fang and Yanfeng Zhang and Cai Li and Fei Ling and Cooper, {David N} and Qiye Li and Yan Li and {van Gool}, {Alain J.} and Hongli Du and Jiesi Chen and Ronghua Chen and Pei Zhang and Zhiyong Huang and Thompson, {John R} and Yuhuan Meng and Yinqi Bai and Jufang Wang and Min Zhuo and Tao Wang and Ying Huang and Liqiong Wei and Jianwen Li and Zhiwen Wang and Haofu Hu and Pengcheng Yang and Liang Le and Stenson, {Peter D} and Bo Li and Xiaoming Liu and Ball, {Edward V} and Na An and Quanfei Huang and Yong Zhang and Wei Fan and Xiuqing Zhang and Yingrui Li and Wen Wang and Katze, {Michael G} and Bing Su and Rasmus Nielsen and Huanming Yang and Jun Wang and Xiaoning Wang and Jian Wang",

year = "2011",

month = nov,

doi = "10.1038/nbt.1992",

language = "English",

volume = "29",

pages = "1019--1023",

journal = "Nature Biotechnology",

issn = "1087-0156",

publisher = "nature publishing group",

number = "11",

}

TY - JOUR

T1 - Genome sequencing and comparison of two nonhuman primate animal models, the cynomolgus and Chinese rhesus macaques

AU - Yan, Guangmei

AU - Zhang, Guojie

AU - Fang, Xiaodong

AU - Zhang, Yanfeng

AU - Li, Cai

AU - Ling, Fei

AU - Cooper, David N

AU - Li, Qiye

AU - Li, Yan

AU - van Gool, Alain J.

AU - Du, Hongli

AU - Chen, Jiesi

AU - Chen, Ronghua

AU - Zhang, Pei

AU - Huang, Zhiyong

AU - Thompson, John R

AU - Meng, Yuhuan

AU - Bai, Yinqi

AU - Wang, Jufang

AU - Zhuo, Min

AU - Wang, Tao

AU - Huang, Ying

AU - Wei, Liqiong

AU - Li, Jianwen

AU - Wang, Zhiwen

AU - Hu, Haofu

AU - Yang, Pengcheng

AU - Le, Liang

AU - Stenson, Peter D

AU - Li, Bo

AU - Liu, Xiaoming

AU - Ball, Edward V

AU - An, Na

AU - Huang, Quanfei

AU - Zhang, Yong

AU - Fan, Wei

AU - Zhang, Xiuqing

AU - Li, Yingrui

AU - Wang, Wen

AU - Katze, Michael G

AU - Su, Bing

AU - Nielsen, Rasmus

AU - Yang, Huanming

AU - Wang, Jun

AU - Wang, Xiaoning

AU - Wang, Jian

PY - 2011/11

Y1 - 2011/11

N2 - The nonhuman primates most commonly used in medical research are from the genus Macaca. To better understand the genetic differences between these animal models, we present high-quality draft genome sequences from two macaque species, the cynomolgus/crab-eating macaque and the Chinese rhesus macaque. Comparison with the previously sequenced Indian rhesus macaque reveals that all three macaques maintain abundant genetic heterogeneity, including millions of single-nucleotide substitutions and many insertions, deletions and gross chromosomal rearrangements. By assessing genetic regions with reduced variability, we identify genes in each macaque species that may have experienced positive selection. Genetic divergence patterns suggest that the cynomolgus macaque genome has been shaped by introgression after hybridization with the Chinese rhesus macaque. Macaque genes display a high degree of sequence similarity with human disease gene orthologs and drug targets. However, we identify several putatively dysfunctional genetic differences between the three macaque species, which may explain functional differences between them previously observed in clinical studies.

AB - The nonhuman primates most commonly used in medical research are from the genus Macaca. To better understand the genetic differences between these animal models, we present high-quality draft genome sequences from two macaque species, the cynomolgus/crab-eating macaque and the Chinese rhesus macaque. Comparison with the previously sequenced Indian rhesus macaque reveals that all three macaques maintain abundant genetic heterogeneity, including millions of single-nucleotide substitutions and many insertions, deletions and gross chromosomal rearrangements. By assessing genetic regions with reduced variability, we identify genes in each macaque species that may have experienced positive selection. Genetic divergence patterns suggest that the cynomolgus macaque genome has been shaped by introgression after hybridization with the Chinese rhesus macaque. Macaque genes display a high degree of sequence similarity with human disease gene orthologs and drug targets. However, we identify several putatively dysfunctional genetic differences between the three macaque species, which may explain functional differences between them previously observed in clinical studies.

KW - Animals

KW - Base Sequence

KW - Chromosome Aberrations

KW - Evolution, Molecular

KW - Genome

KW - Humans

KW - Macaca fascicularis

KW - Macaca mulatta

KW - Models, Animal

KW - Molecular Sequence Data

KW - Polymorphism, Genetic

KW - Sequence Analysis, DNA

KW - Species Specificity

U2 - 10.1038/nbt.1992

DO - 10.1038/nbt.1992

M3 - Letter

C2 - 22002653

SN - 1087-0156

VL - 29

SP - 1019

EP - 1023

JO - Nature Biotechnology

JF - Nature Biotechnology

IS - 11

ER -

Genome sequencing and comparison of two nonhuman primate animal models, the cynomolgus and Chinese rhesus macaques

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