RhesusBase PopGateway: Genome-Wide Population Genetics Atlas in Rhesus Macaque

Zhong, Xiaoming; Peng, Jiguang; Shen, Qing Sunny; Chen, Jia Yu; Gao, Han; Luan, Xuke; Yan, Shouyu; Huang, X. T.; Zhang, Shi Jian; Xu, Lanfang; Zhang, Xiuqin; Tan, Bertrand Chin‐Ming; Li, Chuan Yun

doi:10.1093/molbev/msw025

Cited by 20 publications

(33 citation statements)

References 18 publications

(22 reference statements)

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“…Combined with our data, 9 of the 26 captive Chinese RMs reported by Zhong et al. [ 7 ] were found to cluster with M. m. littoralis , 16 with M. m. lasiotis , and 1 with M. m. mulatta (Fig. 4d ).…”

Section: Resultssupporting

confidence: 86%

“…(d) NJ tree including the 81 Chinese RMs derived from this study. The 26 captive Chinese RMs from Zhong et al [ 7 ] are indicated by blue dot.…”

Section: Resultsmentioning

confidence: 99%

“…As the most widely distributed nonhuman primate species, RMs occupy diverse ecological landscapes and habitats, making them an interesting model to address questions about how species evolve and adapt to local environmental variation, including characterizing the genomic architecture of adaptation to habitat, climate, and other biotic and abiotic factors. Yet, despite much work on primate comparative genomics, very few population genomic studies have been carried out on wild RMs [ 6 , 7 ]. Importantly, as RMs are widely used as a primate model in physiological, psychological, and cognitive studies [ 8 – 10 ], knowledge about their genomic architecture could improve and refine biomedical research [ 10 ] as the genomic composition of experimental animals can have a considerable influence on the outcome of experiments [ 11 , 12 ].…”

Section: Introductionmentioning

confidence: 99%

“…In addition, Zhong et al. [ 7 ] reported genomic variation in 26 Chinese captive RMs identifying ∼46 million (M) single-nucleotide polymorphisms (SNPs). Nevertheless, most of the RM genetic variation known to date is limited to captive populations that may contain composite genotypes due of admixture among animals of different and unclear origin [ 20 ].…”

Section: Introductionmentioning

confidence: 99%

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Population genomics of wild Chinese rhesus macaques reveals a dynamic demographic history and local adaptation, with implications for biomedical research

et al. 2018

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BackgroundThe rhesus macaque (RM, Macaca mulatta) is the most important nonhuman primate model in biomedical research. We present the first genomic survey of wild RMs, sequencing 81 geo-referenced individuals of five subspecies from 17 locations in China, a large fraction of the species’ natural distribution.ResultsPopulations were structured into five genetic lineages on the mainland and Hainan Island, recapitulating current subspecies designations. These subspecies are estimated to have diverged 125.8 to 51.3 thousand years ago, but feature recent gene flow. Consistent with the expectation of a larger body size in colder climates and smaller body size in warmer climates (Bergman's rule), the northernmost RM lineage (M. m. tcheliensis), possessing the largest body size of all Chinese RMs, and the southernmost lineage (M. m. brevicaudus), with the smallest body size of all Chinese RMs, feature positively selected genes responsible for skeletal development. Further, two candidate selected genes (Fbp1, Fbp2) found in M. m. tcheliensis are involved in gluconeogenesis, potentially maintaining stable blood glucose levels during starvation when food resources are scarce in winter. The tropical subspecies M. m. brevicaudus showed positively selected genes related to cardiovascular function and response to temperature stimuli, potentially involved in tropical adaptation. We found 118 single-nucleotide polymorphisms matching human disease-causing variants with 82 being subspecies specific.ConclusionsThese data provide a resource for selection of RMs in biomedical experiments. The demographic history of Chinese RMs and their history of local adaption offer new insights into their evolution and provide valuable baseline information for biomedical investigation.

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Section: Resultssupporting

confidence: 86%

“…(d) NJ tree including the 81 Chinese RMs derived from this study. The 26 captive Chinese RMs from Zhong et al [ 7 ] are indicated by blue dot.…”

Section: Resultsmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

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Population genomics of wild Chinese rhesus macaques reveals a dynamic demographic history and local adaptation, with implications for biomedical research

et al. 2018

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“…A couple of research labs including ourselves demonstrated that rhesus monkeys spontaneously developed obesity with aging, metabolic syndrome (MetS), and diabetes [ 18 , 19 ]. Furthermore, the whole genome of rhesus macaque is available and better annotated now [ 15 , 20 – 22 ]. However, naturally occurring NAFLD has not been evaluated and reported in rhesus macaques.…”

Section: Introductionmentioning

confidence: 99%

Characterization of spontaneously-developed non-alcoholic fatty liver disease in aged rhesus monkeys

Zheng

Liu

Shang

et al. 2018

Diabetol Metab Syndr

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BackgroundNon-alcoholic fatty liver disease (NAFLD) is a global epidemic afflicting 20–30% in the general population. The animal model of NAFLD available at the present are less clinically relevant. In this study. We aimed to establish a NAFLD model of rhesus monkeys and develop an ultrasonographic steatosis score (USS) system to grade hepatic steatosis in this model.MethodsWe performed hepatic ultrasonography and blood biochemical tests on 86 rhesus monkeys with and without metabolic syndrome (MetS), among which 45 animals were further assessed by histopathological analysis.ResultsThe liver histological features of rhesus monkeys NAFLD were resemble to those of NAFLD patients. There was a close correlation between the histological steatosis grade and the USS (Spearman’s coefficient, 0.705, p < 0.001). The USS sensitivity was 87.5% and the specificity was 94.6% when the cut-off was USS2. In addition, the prevalence of MetS was significantly higher in the USS2–3 group. Multiple risk factors of cardiometabolic disease, including obesity, insulin resistance and dyslipidemia were significantly correlated with the USS.ConclusionsNAFLD was developed spontaneously among aging in rhesus monkeys (with increased prevalence in the MetS monkeys), which provided an ideal model for NAFLD. The newly developed USS system can be used to evaluate fatty liver in the rhesus monkey. The model as well as the noninvasive assessment methodology will provide a powerful tool for mechanistic studies and preclinical test of novel therapies for NAFLD.

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Genomic resources for rhesus macaques (Macaca mulatta)

Rogers

2022

Mamm Genome

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Rhesus macaques ( Macaca mulatta ) are among the most extensively studied of nonhuman primates. This species has been the subject of many investigations concerning basic primate biology and behavior, including studies of social organization, developmental psychology, physiology, endocrinology, and neurodevelopment. Rhesus macaques are also critically important as a nonhuman primate model of human health and disease, including use in studies of infectious diseases, metabolic diseases, aging, and drug or alcohol abuse. Current research addressing fundamental biological and/or applied biomedical questions benefits from various genetic and genomic analyses. As a result, the genome of rhesus macaques has been the subject of more study than most nonhuman primates. This paper briefly discusses a number of information resources that can provide interested researchers with access to genetic and genomic data describing the content of the rhesus macaque genome, available information regarding genetic variation within the species, results from studies of gene expression, and other aspects of genomic analysis. Specific online databases are discussed, including the US National Center for Biotechnology Information, the University of California Santa Cruz genome browser, Ensembl genome browser, the Macaque Genotype and Phenotype database (mGAP), Rhesusbase, and others.

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RhesusBase PopGateway: Genome-Wide Population Genetics Atlas in Rhesus Macaque

Cited by 20 publications

References 18 publications

Population genomics of wild Chinese rhesus macaques reveals a dynamic demographic history and local adaptation, with implications for biomedical research

Population genomics of wild Chinese rhesus macaques reveals a dynamic demographic history and local adaptation, with implications for biomedical research

Characterization of spontaneously-developed non-alcoholic fatty liver disease in aged rhesus monkeys

Genomic resources for rhesus macaques (Macaca mulatta)

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