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Versoza CJ, Weiss S, Johal R, La Rosa B, Jensen JD, Pfeifer SP. Novel Insights into the Landscape of Crossover and Noncrossover Events in Rhesus Macaques (Macaca mulatta). Genome Biol Evol 2024; 16:evad223. [PMID: 38051960 PMCID: PMC10773715 DOI: 10.1093/gbe/evad223] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2023] [Revised: 11/04/2023] [Accepted: 11/28/2023] [Indexed: 12/07/2023] Open
Abstract
Meiotic recombination landscapes differ greatly between distantly and closely related taxa, populations, individuals, sexes, and even within genomes; however, the factors driving this variation are yet to be well elucidated. Here, we directly estimate contemporary crossover rates and, for the first time, noncrossover rates in rhesus macaques (Macaca mulatta) from four three-generation pedigrees comprising 32 individuals. We further compare these results with historical, demography-aware, linkage disequilibrium-based recombination rate estimates. From paternal meioses in the pedigrees, 165 crossover events with a median resolution of 22.3 kb were observed, corresponding to a male autosomal map length of 2,357 cM-approximately 15% longer than an existing linkage map based on human microsatellite loci. In addition, 85 noncrossover events with a mean tract length of 155 bp were identified-similar to the tract lengths observed in the only other two primates in which noncrossovers have been studied to date, humans and baboons. Consistent with observations in other placental mammals with PRDM9-directed recombination, crossover (and to a lesser extent noncrossover) events in rhesus macaques clustered in intergenic regions and toward the chromosomal ends in males-a pattern in broad agreement with the historical, sex-averaged recombination rate estimates-and evidence of GC-biased gene conversion was observed at noncrossover sites.
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Affiliation(s)
- Cyril J Versoza
- School of Life Sciences, Arizona State University, Tempe, AZ, USA
- Center for Evolution and Medicine, Arizona State University, Tempe, AZ, USA
| | - Sarah Weiss
- School of Life Sciences, Arizona State University, Tempe, AZ, USA
| | - Ravneet Johal
- School of Life Sciences, Arizona State University, Tempe, AZ, USA
| | - Bruno La Rosa
- School of Life Sciences, Arizona State University, Tempe, AZ, USA
| | - Jeffrey D Jensen
- School of Life Sciences, Arizona State University, Tempe, AZ, USA
- Center for Evolution and Medicine, Arizona State University, Tempe, AZ, USA
| | - Susanne P Pfeifer
- School of Life Sciences, Arizona State University, Tempe, AZ, USA
- Center for Evolution and Medicine, Arizona State University, Tempe, AZ, USA
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2
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Biscola NP, Bartmeyer PM, Christe KL, Colman RJ, Havton LA. Detrusor underactivity is associated with metabolic syndrome in aged primates. Sci Rep 2023; 13:6716. [PMID: 37185781 PMCID: PMC10130177 DOI: 10.1038/s41598-023-33112-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2022] [Accepted: 04/07/2023] [Indexed: 05/17/2023] Open
Abstract
Lower urinary tract (LUT) dysfunction is prevalent in the elderly population, and clinical manifestations include urinary retention, incontinence, and recurrent urinary tract infections. Age-associated LUT dysfunction is responsible for significant morbidity, compromised quality of life, and rising healthcare costs in older adults, but its pathophysiology is not well understood. We aimed to investigate the effects of aging on LUT function by urodynamic studies and metabolic markers in non-human primates. Adult (n = 27) and aged (n = 20) female rhesus macaques were evaluated by urodynamic and metabolic studies. Cystometry showed detrusor underactivity (DU) with increased bladder capacity and compliance in aged subjects. Metabolic syndrome indicators were present in the aged subjects, including increased weight, triglycerides, lactate dehydrogenase (LDH), alanine aminotransferase (ALT), and high sensitivity C-reactive protein (hsCRP), whereas aspartate aminotransferase (AST) was unaffected and the AST/ALT ratio reduced. Principal component analysis and paired correlations showed a strong association between DU and metabolic syndrome markers in aged primates with DU but not in aged primates without DU. The findings were unaffected by prior pregnancies, parity, and menopause. Our findings provide insights into possible mechanisms for age-associated DU and may guide new strategies to prevent and treat LUT dysfunction in older adults.
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Affiliation(s)
- Natalia P Biscola
- Department of Neurology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Petra M Bartmeyer
- Department of Neurology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Kari L Christe
- California National Primate Research Center, University of California at Davis, Davis, CA, USA
| | - Ricki J Colman
- Wisconsin National Primate Research Center, University of Wisconsin-Madison, Madison, WI, USA
- Department of Cell and Regenerative Biology, University of Wisconsin-Madison, Madison, WI, USA
| | - Leif A Havton
- Departments of Neurology and Neuroscience, Icahn School of Medicine at Mount Sinai, 1468 Madison Avenue, New York, NY, 10029, USA.
- James J. Peters Veterans Affairs Medical Center, Bronx, NY, USA.
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3
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Kazahari N, Inoue E, Nakagawa N, Kawamoto Y, Uno T, Inoue-Murayama M. Genetic effects of demographic bottleneck and recovery in Kinkazan Island and mainland populations of Japanese macaques (Macaca fuscata). Primates 2023; 64:239-246. [PMID: 36806706 DOI: 10.1007/s10329-023-01050-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2022] [Accepted: 01/12/2023] [Indexed: 02/23/2023]
Abstract
Populations of Japanese macaques were significantly reduced in most areas from the 1900s to the 1960s and then recovered mainly in the northeastern part of Honshu. A drastic reduction in population size reduces genetic variability through a bottleneck effect. Demographic expansion after the reduction that accumulates new mutations can reduce the bottleneck effects or drive the recovery of genetic variability. We examined the genetic status of a small island population (Kinkazan Island) and a larger mainland population (southern Tohoku) of Japanese macaques that experienced recent demographic bottlenecks and recovery using eight microsatellite loci. The two populations were significantly genetically different from each other. The Kinkazan population exhibited lower genetic variability, remarkable evidence of bottleneck (i.e., significant heterozygosity excess and lower frequency of rare alleles), and a considerably smaller effective population size based on genetic data than based on the current census size. These results indicate that the genetic status has not completely recovered from the demographic bottleneck despite a full recovery in census size on Kinkazan Island. New mutations might rarely have accumulated because of the small carrying capacity of the island. Therefore, the genetic variability of the population would have been restrained by the severe bottleneck size, small carrying capacity, and long-term isolation. On the other hand, the bottleneck effect seems to be limited in the southern Tohoku population considering higher genetic variability, non-significant heterozygosity excess in many mutation conditions, and the highest frequency of rare alleles.
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Affiliation(s)
- N Kazahari
- Wildlife Research Center, Kyoto University, 2-24 Tanaka-Sekiden-cho, Sakyo, Kyoto, 606-8203, Japan.
- Field Science Center for Northern Biosphere, Hokkaido University, Sapporo, Japan.
| | - E Inoue
- Faculty of Science, Toho University, Chiba, Japan
| | - N Nakagawa
- Graduate School of Science, Kyoto University, Kyoto, Japan
| | - Y Kawamoto
- Primate Research Institute, Kyoto University, Inuyama, Japan
- Laboratory of Wildlife Medicine, School of Veterinary Medicine, Nippon Veterinary and Life Science University, Musashino, Japan
| | - T Uno
- Tohoku, Monkey and Mammal Management Center, Sendai, Japan
| | - M Inoue-Murayama
- Wildlife Research Center, Kyoto University, 2-24 Tanaka-Sekiden-cho, Sakyo, Kyoto, 606-8203, Japan
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4
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Wall JD, Robinson JA, Cox LA. High-Resolution Estimates of Crossover and Noncrossover Recombination from a Captive Baboon Colony. Genome Biol Evol 2022; 14:evac040. [PMID: 35325119 PMCID: PMC9048888 DOI: 10.1093/gbe/evac040] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/02/2022] [Indexed: 11/17/2022] Open
Abstract
Homologous recombination has been extensively studied in humans and a handful of model organisms. Much less is known about recombination in other species, including nonhuman primates. Here, we present a study of crossovers (COs) and noncrossover (NCO) recombination in olive baboons (Papio anubis) from two pedigrees containing a total of 20 paternal and 17 maternal meioses, and compare these results to linkage disequilibrium (LD) based recombination estimates from 36 unrelated olive baboons. We demonstrate how COs, combined with LD-based recombination estimates, can be used to identify genome assembly errors. We also quantify sex-specific differences in recombination rates, including elevated male CO and reduced female CO rates near telomeres. Finally, we add to the increasing body of evidence suggesting that while most NCO recombination tracts in mammals are short (e.g., <500 bp), there is a non-negligible fraction of longer (e.g., >1 kb) NCO tracts. For NCO tracts shorter than 10 kb, we fit a mixture of two (truncated) geometric distributions model to the NCO tract length distribution and estimate that >99% of all NCO tracts are very short (mean 24 bp), but the remaining tracts can be quite long (mean 4.3 kb). A single geometric distribution model for NCO tract lengths is incompatible with the data, suggesting that LD-based methods for estimating NCO recombination rates that make this assumption may need to be modified.
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Affiliation(s)
- Jeffrey D. Wall
- Institute for Human Genetics, University of California San Francisco, USA
| | | | - Laura A. Cox
- Center for Precision Medicine, Department of Internal Medicine, Wake Forest School of Medicine, Winston-Salem, USA
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5
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Genomic resources for rhesus macaques (Macaca mulatta). Mamm Genome 2022; 33:91-99. [PMID: 34999909 PMCID: PMC8742695 DOI: 10.1007/s00335-021-09922-z] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2021] [Accepted: 09/22/2021] [Indexed: 11/10/2022]
Abstract
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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6
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Chatterjee SK, Yadav S, Saraswathy KN, Mondal PR. Genetic polymorphism of dopamine receptor D4 (DRD4) gene in ten Indian rhesus macaques (Macaca mulatta mulatta). Meta Gene 2021. [DOI: 10.1016/j.mgene.2021.100891] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
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Kimura A, Yahashi S, Chatani F, Tanabe H. Identification of Chromosome 17 Trisomy in a Cynomolgus Monkey (Macaca fascicularis) by Multicolor FISH Techniques. Cytogenet Genome Res 2021; 161:243-248. [PMID: 34265761 DOI: 10.1159/000516337] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2021] [Accepted: 04/06/2021] [Indexed: 11/19/2022] Open
Abstract
A female cynomolgus monkey (Macaca fascicularis) with facial features characteristic of Down syndrome showed abnormal behavior, unwariness toward humans, and poor concentration. The number of metaphase chromosomes in blood lymphocytes was examined and found to be 43, which indicated one extra chromosome to the normal diploid number (2n = 42). We then used Q-banding and multicolor FISH techniques to identify the extra chromosome. The results revealed an additional chromosome 17, with no other chromosomal rearrangements, such as translocations. Since no mosaicism or heterozygous variant chromosomes were observed, full trisomy 17 was assessed in this female cynomolgus monkey. Chromosome 17 corresponds to human chromosome 13, and human trisomy 13, known as Patau syndrome, results in severe clinical signs and, often, a short life span; however, this individual has reached an age of 10 years with only mild clinical signs. Although genomic differences exist between human and macaques, this individual's case could help to reveal the pathological and genetic mechanisms of Patau syndrome.
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Affiliation(s)
- Aoi Kimura
- Drug Safety Research Laboratories, Shin Nippon Biomedical Laboratories, Ltd., Kagoshima, Japan
| | - Satowa Yahashi
- Drug Safety Research Laboratories, Shin Nippon Biomedical Laboratories, Ltd., Kagoshima, Japan
| | - Fumio Chatani
- Drug Safety Research Laboratories, Shin Nippon Biomedical Laboratories, Ltd., Kagoshima, Japan
| | - Hideyuki Tanabe
- Department of Evolutionary Studies of Biosystems, School of Advanced Sciences, The Graduate University for Advanced Studies, SOKENDAI, Hayama, Japan
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Abstract
Despite its important biological role, the evolution of recombination rates remains relatively poorly characterized. This owes, in part, to the lack of high-quality genomic resources to address this question across diverse species. Humans and our closest evolutionary relatives, anthropoid apes, have remained a major focus of large-scale sequencing efforts, and thus recombination rate variation has been comparatively well studied in this group-with earlier work revealing a conservation at the broad- but not the fine-scale. However, in order to better understand the nature of this variation, and the time scales on which substantial modifications occur, it is necessary to take a broader phylogenetic perspective. I here present the first fine-scale genetic map for vervet monkeys based on whole-genome population genetic data from ten individuals and perform a series of comparative analyses with the great apes. The results reveal a number of striking features. First, owing to strong positive correlations with diversity and weak negative correlations with divergence, analyses suggest a dominant role for purifying and background selection in shaping patterns of variation in this species. Second, results support a generally reduced broad-scale recombination rate compared with the great apes, as well as a narrower fraction of the genome in which the majority of recombination events are observed to occur. Taken together, this data set highlights the great necessity of future research to identify genomic features and quantify evolutionary processes that are driving these rate changes across primates.
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Affiliation(s)
- Susanne P Pfeifer
- Center for Evolution and Medicine, School of Life Sciences, Arizona State University, Tempe, AZ
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9
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Poirier C, Hamed SB, Garcia-Saldivar P, Kwok SC, Meguerditchian A, Merchant H, Rogers J, Wells S, Fox AS. Beyond MRI: on the scientific value of combining non-human primate neuroimaging with metadata. Neuroimage 2021; 228:117679. [PMID: 33359343 PMCID: PMC7903159 DOI: 10.1016/j.neuroimage.2020.117679] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2020] [Revised: 12/07/2020] [Accepted: 12/16/2020] [Indexed: 01/01/2023] Open
Abstract
Sharing and pooling large amounts of non-human primate neuroimaging data offer new exciting opportunities to understand the primate brain. The potential of big data in non-human primate neuroimaging could however be tremendously enhanced by combining such neuroimaging data with other types of information. Here we describe metadata that have been identified as particularly valuable by the non-human primate neuroimaging community, including behavioural, genetic, physiological and phylogenetic data.
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Affiliation(s)
- Colline Poirier
- Biosciences Institute & Centre for Behaviour and Evolution, Faculty of Medical Sciences, Newcastle 6, UK.
| | - Suliann Ben Hamed
- Institut des Sciences Cognitives Marc Jeannerod, UMR 5229, Université de Lyon - CNRS, France
| | - Pamela Garcia-Saldivar
- Instituto de Neurobiología, UNAM, Campus Juriquilla. Boulevard Juriquilla No. 3001 Querétaro, Qro. 76230 México
| | - Sze Chai Kwok
- Shanghai Key Laboratory of Brain Functional Genomics, Key Laboratory of Brain Functional Genomics Ministry of Education, Shanghai Key Laboratory of Magnetic Resonance, Affiliated Mental Health Center (ECNU), Shanghai Changning Mental Health Center, School of Psychology and Cognitive Science, East China Normal University, Shanghai, China; Division of Natural and Applied Sciences, Duke Kunshan University, Duke Institute for Brain Sciences, Kunshan, Jiangsu, China; NYU-ECNU Institute of Brain and Cognitive Science at NYU Shanghai, Shanghai, China
| | - Adrien Meguerditchian
- Laboratoire de Psychologie Cognitive, UMR7290, Université Aix-Marseille/CNRS, Institut Language, Communication and the Brain 13331 Marseille, France
| | - Hugo Merchant
- Instituto de Neurobiología, UNAM, Campus Juriquilla. Boulevard Juriquilla No. 3001 Querétaro, Qro. 76230 México
| | - Jeffrey Rogers
- Human Genome Sequencing Center and Dept. of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, USA 77030
| | - Sara Wells
- Centre for Macaques, MRC Harwell Institute, Porton Down, Salisbury, United Kingdom
| | - Andrew S Fox
- California National Primate Research Center, Department of Psychology, University of California, Davis, Davis, CA, 95616, USA
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10
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Petty LE, Phillippi-Falkenstein K, Kubisch HM, Raveendran M, Harris RA, Vallender EJ, Huff CD, Bohm RP, Rogers J, Below JE. Pedigree reconstruction and distant pairwise relatedness estimation from genome sequence data: A demonstration in a population of rhesus macaques (Macaca mulatta). Mol Ecol Resour 2021; 21:1333-1346. [PMID: 33386679 PMCID: PMC8247968 DOI: 10.1111/1755-0998.13317] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2019] [Revised: 11/13/2020] [Accepted: 12/07/2020] [Indexed: 12/30/2022]
Abstract
A primary challenge in the analysis of free‐ranging animal populations is the accurate estimation of relatedness among individuals. Many aspects of population analysis rely on knowledge of relatedness patterns, including socioecology, demography, heritability and gene mapping analyses, wildlife conservation and the management of breeding colonies. Methods for determining relatedness using genome‐wide data have improved our ability to determine kinship and reconstruct pedigrees in humans. However, methods for reconstructing complex pedigree structures and estimating distant relatedness (beyond third‐degree) have not been widely applied to other species. We sequenced the genomes of 150 male rhesus macaques from the Tulane National Primate Research Center colony to estimate pairwise relatedness, reconstruct closely related pedigrees, estimate more distant relationships and augment colony records. Methods for determining relatedness developed for human genetic data were applied and evaluated in the analysis of nonhuman primates, including identity‐by‐descent‐based methods for pedigree reconstruction and shared segment‐based inference of more distant relatedness. We compared the genotype‐based pedigrees and estimated relationships to available colony pedigree records and found high concordance (95.5% agreement) between expected and identified relationships for close relatives. In addition, we detected distant relationships not captured in colony records, including some as distant as twelfth‐degree. Furthermore, while deep sequence coverage is preferable, we show that this approach can also provide valuable information when only low‐coverage (5×) sequence data is available. Our findings demonstrate the value of these methods for determination of relatedness in various animal populations, with diverse applications to conservation biology, evolutionary and ecological research and biomedical studies.
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Affiliation(s)
- Lauren E Petty
- Vanderbilt Genetics Institute and Department of Genetic Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
| | | | - H Michael Kubisch
- Division of Veterinary Medicine, Tulane National Primate Research Center, Covington, LA, USA
| | - Muthuswamy Raveendran
- Human Genome Sequencing Center and Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - R Alan Harris
- Human Genome Sequencing Center and Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Eric J Vallender
- Division of Veterinary Medicine, Tulane National Primate Research Center, Covington, LA, USA.,Department of Psychiatry and Human Behavior, University of Mississippi Medical Center, Jackson, MS, USA
| | - Chad D Huff
- Department of Epidemiology, University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Rudolf P Bohm
- Division of Veterinary Medicine, Tulane National Primate Research Center, Covington, LA, USA
| | - Jeffrey Rogers
- Human Genome Sequencing Center and Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Jennifer E Below
- Vanderbilt Genetics Institute and Department of Genetic Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
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11
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Infant inhibited temperament in primates predicts adult behavior, is heritable, and is associated with anxiety-relevant genetic variation. Mol Psychiatry 2021; 26:6609-6618. [PMID: 34035480 PMCID: PMC8613309 DOI: 10.1038/s41380-021-01156-4] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/30/2020] [Revised: 04/23/2021] [Accepted: 05/04/2021] [Indexed: 02/04/2023]
Abstract
An anxious or inhibited temperament (IT) early in life is a major risk factor for the later development of stress-related psychopathology. Starting in infancy, nonhuman primates, like humans, begin to reveal their temperament when exposed to novel situations. Here, in Study 1 we demonstrate this infant IT predicts adult behavior. Specifically, in over 600 monkeys, we found that individuals scored as inhibited during infancy were more likely to refuse treats offered by potentially-threatening human experimenters as adults. In Study 2, using a sample of over 4000 monkeys from a large multi-generational family pedigree, we demonstrate that infant IT is partially heritable. The data revealed infant IT to reflect a co-inherited substrate that manifests across multiple latent variables. Finally, in Study 3 we performed whole-genome sequencing in 106 monkeys to identify IT-associated single-nucleotide variations (SNVs). Results demonstrated a genome-wide significant SNV near CTNNA2, suggesting a molecular target worthy of additional investigation. Moreover, we observed lower p values in genes implicated in human association studies of neuroticism and depression. Together, these data demonstrate the utility of our model of infant inhibited temperament in the rhesus monkey to facilitate discovery of genes that are relevant to the long-term inherited risk to develop anxiety and depressive disorders.
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12
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Xue C, Rustagi N, Liu X, Raveendran M, Harris RA, Venkata MG, Rogers J, Yu F. Reduced meiotic recombination in rhesus macaques and the origin of the human recombination landscape. PLoS One 2020; 15:e0236285. [PMID: 32841250 PMCID: PMC7447010 DOI: 10.1371/journal.pone.0236285] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2020] [Accepted: 07/01/2020] [Indexed: 11/18/2022] Open
Abstract
Characterizing meiotic recombination rates across the genomes of nonhuman primates is important for understanding the genetics of primate populations, performing genetic analyses of phenotypic variation and reconstructing the evolution of human recombination. Rhesus macaques (Macaca mulatta) are the most widely used nonhuman primates in biomedical research. We constructed a high-resolution genetic map of the rhesus genome based on whole genome sequence data from Indian-origin rhesus macaques. The genetic markers used were approximately 18 million SNPs, with marker density 6.93 per kb across the autosomes. We report that the genome-wide recombination rate in rhesus macaques is significantly lower than rates observed in apes or humans, while the distribution of recombination across the macaque genome is more uniform. These observations provide new comparative information regarding the evolution of recombination in primates.
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Affiliation(s)
- Cheng Xue
- Human Genome Sequencing Center and Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, United States of America
- * E-mail: (FY); (JR); (CX)
| | - Navin Rustagi
- Human Genome Sequencing Center and Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, United States of America
| | - Xiaoming Liu
- USF Genomics & College of Public Health, University of South Florida, Tampa, Florida, United States of America
| | - Muthuswamy Raveendran
- Human Genome Sequencing Center and Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, United States of America
| | - R. Alan Harris
- Human Genome Sequencing Center and Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, United States of America
| | | | - Jeffrey Rogers
- Human Genome Sequencing Center and Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, United States of America
- * E-mail: (FY); (JR); (CX)
| | - Fuli Yu
- Human Genome Sequencing Center and Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, United States of America
- * E-mail: (FY); (JR); (CX)
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13
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Wang RJ, Thomas GWC, Raveendran M, Harris RA, Doddapaneni H, Muzny DM, Capitanio JP, Radivojac P, Rogers J, Hahn MW. Paternal age in rhesus macaques is positively associated with germline mutation accumulation but not with measures of offspring sociability. Genome Res 2020; 30:826-834. [PMID: 32461224 PMCID: PMC7370888 DOI: 10.1101/gr.255174.119] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2019] [Accepted: 05/21/2020] [Indexed: 01/26/2023]
Abstract
Mutation is the ultimate source of all genetic novelty and the cause of heritable genetic disorders. Mutational burden has been linked to complex disease, including neurodevelopmental disorders such as schizophrenia and autism. The rate of mutation is a fundamental genomic parameter and direct estimates of this parameter have been enabled by accurate comparisons of whole-genome sequences between parents and offspring. Studies in humans have revealed that the paternal age at conception explains most of the variation in mutation rate: Each additional year of paternal age in humans leads to approximately 1.5 additional inherited mutations. Here, we present an estimate of the de novo mutation rate in the rhesus macaque (Macaca mulatta) using whole-genome sequence data from 32 individuals in four large pedigrees. We estimated an average mutation rate of 0.58 × 10−8 per base pair per generation (at an average parental age of 7.5 yr), much lower than found in direct estimates from great apes. As in humans, older macaque fathers transmit more mutations to their offspring, increasing the per generation mutation rate by 4.27 × 10−10 per base pair per year. We found that the rate of mutation accumulation after puberty is similar between macaques and humans, but that a smaller number of mutations accumulate before puberty in macaques. We additionally investigated the role of paternal age on offspring sociability, a proxy for normal neurodevelopment, by studying 203 male macaques in large social groups.
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Affiliation(s)
- Richard J Wang
- Department of Biology, Indiana University, Bloomington, Indiana 47405, USA
| | - Gregg W C Thomas
- Department of Biology, Indiana University, Bloomington, Indiana 47405, USA.,Department of Computer Science, Indiana University, Bloomington, Indiana 47405, USA
| | - Muthuswamy Raveendran
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas 77030, USA.,Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas 77030, USA
| | - R Alan Harris
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas 77030, USA.,Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas 77030, USA
| | - Harshavardhan Doddapaneni
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas 77030, USA.,Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas 77030, USA
| | - Donna M Muzny
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas 77030, USA.,Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas 77030, USA
| | - John P Capitanio
- California National Primate Research Center, University of California-Davis, Davis, California 95616, USA
| | - Predrag Radivojac
- Department of Computer Science, Indiana University, Bloomington, Indiana 47405, USA.,Khoury College of Computer Sciences, Northeastern University, Boston, Massachusetts 02115, USA
| | - Jeffrey Rogers
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas 77030, USA.,Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas 77030, USA
| | - Matthew W Hahn
- Department of Biology, Indiana University, Bloomington, Indiana 47405, USA.,Department of Computer Science, Indiana University, Bloomington, Indiana 47405, USA
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14
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Schall PZ, Ruebel ML, Midic U, VandeVoort CA, Latham KE. Temporal patterns of gene regulation and upstream regulators contributing to major developmental transitions during Rhesus macaque preimplantation development. Mol Hum Reprod 2020; 25:111-123. [PMID: 30698740 DOI: 10.1093/molehr/gaz001] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2018] [Revised: 12/11/2018] [Accepted: 01/24/2019] [Indexed: 02/07/2023] Open
Abstract
The preimplantation period of life in mammals encompasses a tremendous amount of restructuring and remodeling of the embryonic genome and reprogramming of gene expression. These vast changes support metabolic activation and cellular processes that drive early cleavage divisions and enable the creation of the earliest primitive cell lineages. A major question in mammalian embryology is how such vast, sweeping changes in gene expression are orchestrated, so that changes in gene expression are exactly appropriate to meet the developmental needs of the embryo over time. Using the rhesus macaque as an experimentally tractable model species closely related to the human, we combined high quality RNA-seq libraries, in-depth sequencing and advanced systems analysis to discover the underlying mechanisms that drive major changes in gene regulation during preimplantation development. We identified the major changes in mRNA population and the biological pathways and processes impacted by those changes. Most importantly, we identified 24 key upstream regulators that are themselves modulated during development and that are associated with the regulation of over 1000 downstream genes. Through their roles in extensive gene networks, these 24 upstream regulators are situated to either drive major changes in target gene expression or modify the cellular environment in which other genes function, thereby directing major developmental transitions in the preimplantation embryo. The data presented here highlight some of the specific molecular features that likely drive preimplantation development in a nonhuman primate species and provides an extensive database for novel hypothesis-driven studies.
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Affiliation(s)
- Peter Z Schall
- Department of Animal Science and Reproductive and Developmental Sciences Program, Michigan State University, East Lansing, MI, USA.,Comparative Medicine and Integrative Biology Program, Michigan State University, East Lansing, MI, USA
| | - Meghan L Ruebel
- Department of Animal Science and Reproductive and Developmental Sciences Program, Michigan State University, East Lansing, MI, USA
| | - Uros Midic
- Department of Animal Science and Reproductive and Developmental Sciences Program, Michigan State University, East Lansing, MI, USA
| | - Catherine A VandeVoort
- California National Primate Research Center and Department of Obstetrics and Gynecology, University of California, Davis, CA, USA
| | - Keith E Latham
- Department of Animal Science and Reproductive and Developmental Sciences Program, Michigan State University, East Lansing, MI, USA
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15
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Evolutionary Dynamics of the POTE Gene Family in Human and Nonhuman Primates. Genes (Basel) 2020; 11:genes11020213. [PMID: 32085667 PMCID: PMC7073761 DOI: 10.3390/genes11020213] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2019] [Revised: 02/06/2020] [Accepted: 02/13/2020] [Indexed: 12/20/2022] Open
Abstract
POTE (prostate, ovary, testis, and placenta expressed) genes belong to a primate-specific gene family expressed in prostate, ovary, and testis as well as in several cancers including breast, prostate, and lung cancers. Due to their tumor-specific expression, POTEs are potential oncogenes, therapeutic targets, and biomarkers for these malignancies. This gene family maps within human and primate segmental duplications with a copy number ranging from two to 14 in different species. Due to the high sequence identity among the gene copies, specific efforts are needed to assemble these loci in order to correctly define the organization and evolution of the gene family. Using single-molecule, real-time (SMRT) sequencing, in silico analyses, and molecular cytogenetics, we characterized the structure, copy number, and chromosomal distribution of the POTE genes, as well as their expression in normal and disease tissues, and provided a comparative analysis of the POTE organization and gene structure in primate genomes. We were able, for the first time, to de novo sequence and assemble a POTE tandem duplication in marmoset that is misassembled and collapsed in the reference genome, thus revealing the presence of a second POTE copy. Taken together, our findings provide comprehensive insights into the evolutionary dynamics of the primate-specific POTE gene family, involving gene duplications, deletions, and long interspersed nuclear element (LINE) transpositions to explain the actual repertoire of these genes in human and primate genomes.
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16
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He Y, Luo X, Zhou B, Hu T, Meng X, Audano PA, Kronenberg ZN, Eichler EE, Jin J, Guo Y, Yang Y, Qi X, Su B. Long-read assembly of the Chinese rhesus macaque genome and identification of ape-specific structural variants. Nat Commun 2019; 10:4233. [PMID: 31530812 PMCID: PMC6749001 DOI: 10.1038/s41467-019-12174-w] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2019] [Accepted: 08/27/2019] [Indexed: 12/20/2022] Open
Abstract
We present a high-quality de novo genome assembly (rheMacS) of the Chinese rhesus macaque (Macaca mulatta) using long-read sequencing and multiplatform scaffolding approaches. Compared to the current Indian rhesus macaque reference genome (rheMac8), rheMacS increases sequence contiguity 75-fold, closing 21,940 of the remaining assembly gaps (60.8 Mbp). We improve gene annotation by generating more than two million full-length transcripts from ten different tissues by long-read RNA sequencing. We sequence resolve 53,916 structural variants (96% novel) and identify 17,000 ape-specific structural variants (ASSVs) based on comparison to ape genomes. Many ASSVs map within ChIP-seq predicted enhancer regions where apes and macaque show diverged enhancer activity and gene expression. We further characterize a subset that may contribute to ape- or great-ape-specific phenotypic traits, including taillessness, brain volume expansion, improved manual dexterity, and large body size. The rheMacS genome assembly serves as an ideal reference for future biomedical and evolutionary studies. Comparative genomic analysis of human and primate relatives can reveal important biological and evolutionary insights. Here, the authors present a long-read assembly of the Chinese rhesus macaque genome and identify ape-specific structural variants.
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Affiliation(s)
- Yaoxi He
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650223, China.,Primate Research Center, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650223, China.,Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming, 650223, China.,Kunming College of Life Science, University of Chinese Academy of Sciences, Beijing, 100101, China
| | - Xin Luo
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650223, China.,Primate Research Center, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650223, China.,Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming, 650223, China.,Kunming College of Life Science, University of Chinese Academy of Sciences, Beijing, 100101, China
| | - Bin Zhou
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650223, China.,Primate Research Center, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650223, China.,Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming, 650223, China.,Kunming College of Life Science, University of Chinese Academy of Sciences, Beijing, 100101, China
| | - Ting Hu
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650223, China.,Primate Research Center, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650223, China.,Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming, 650223, China.,Kunming College of Life Science, University of Chinese Academy of Sciences, Beijing, 100101, China
| | - Xiaoyu Meng
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650223, China.,Primate Research Center, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650223, China.,Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming, 650223, China.,Kunming College of Life Science, University of Chinese Academy of Sciences, Beijing, 100101, China
| | - Peter A Audano
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA, 98195, USA
| | - Zev N Kronenberg
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA, 98195, USA
| | - Evan E Eichler
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA, 98195, USA.,Howard Hughes Medical Institute, University of Washington, Seattle, WA, 98195, USA
| | - Jie Jin
- Nextomics Biosciences, Wuhan, 430000, China
| | - Yongbo Guo
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650223, China.,Primate Research Center, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650223, China.,Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming, 650223, China.,Kunming College of Life Science, University of Chinese Academy of Sciences, Beijing, 100101, China
| | - Yanan Yang
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650223, China.,Primate Research Center, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650223, China
| | - Xuebin Qi
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650223, China.,Primate Research Center, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650223, China.,Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming, 650223, China
| | - Bing Su
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650223, China. .,Primate Research Center, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650223, China. .,Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming, 650223, China.
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17
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Xu Y, Hu Z, Li W, Zeng T, Zhang X, Li J, Zhang W, Yue B. Isolation and strategies of novel tetranucleotide microsatellites with polymorphisms from different chromosomes of the rhesus monkey (Macaca mulatta). Mol Biol Rep 2019; 46:3955-3966. [PMID: 31119442 DOI: 10.1007/s11033-019-04842-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2018] [Accepted: 04/26/2019] [Indexed: 11/26/2022]
Abstract
A total of 45 tetranucleotide chromosome-specific microsatellite markers with polymorphism were developed successfully based on three reference rhesus monkey genomes and on In-silico PCR prescreening. The polymorphic information content (PIC) values of 45 polymorphic microsatellite loci ranged from 0.487 to 0.879, with an average of 0.715, which were proven to be moderate to highly polymorphic. We detected 315 alleles on 45 microsatellite loci in 24 Rhesus monkeys. The number of alleles ranged from 3 to 15 and the mean number of alleles was 7 for each locus. Accordingly, the observed and expected heterozygosities obtained were between 0.417 and 1.0 and between 0.550 and 0.908, with an average value of 0.736 and 0.767, respectively. Genetic information demonstrated that 10 loci significantly deviated from Hardy-Weinberg equilibrium (P < 0.05). All 45 primers were not significant with regard to linkage disequilibrium (P > 0.001). Pearson correlation indicated that the PIC value exhibited a significant negative correlation with the loci number (r = - 0.741, P = 0.022), whereas the positive correlation with the number of the samples (r = 0.847, P = 0.070) was not significant. This may be attributed to the presence of random particularities within the loci. The T test of the sample groups indicated that the PIC difference was not significant when the number of samples was set at 10 and/or ≥ 15 (P = 0.7472 ~ 0.8564). These polymorphic and valuable microsatellite loci will facilitate further conservation genetics studies for rhesus monkeys and can be further applied to develop novel genetic markers for other species.
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Affiliation(s)
- Yongtao Xu
- Research Center for Wildlife Resources Conservation, College of Forestry, Jiangxi Agricultural University, Nanchang, 330045, People's Republic of China
- Key Laboratory of Bio-resources and Eco-environment (Ministry of Education), College of Life Sciences, Sichuan University, Chengdu, 610064, People's Republic of China
| | - Zongxiu Hu
- Yibin HengShu Animal Models Resourse Industry Technology Academy, Yibin, 644609, People's Republic of China
| | - Wujiao Li
- Key Laboratory of Bio-resources and Eco-environment (Ministry of Education), College of Life Sciences, Sichuan University, Chengdu, 610064, People's Republic of China
| | - Tao Zeng
- Yibin HengShu Animal Models Resourse Industry Technology Academy, Yibin, 644609, People's Republic of China
| | - Xiuyue Zhang
- Key Laboratory of Bio-resources and Eco-environment (Ministry of Education), College of Life Sciences, Sichuan University, Chengdu, 610064, People's Republic of China
| | - Jing Li
- Key Laboratory of Bio-resources and Eco-environment (Ministry of Education), College of Life Sciences, Sichuan University, Chengdu, 610064, People's Republic of China
| | - Weiwei Zhang
- Research Center for Wildlife Resources Conservation, College of Forestry, Jiangxi Agricultural University, Nanchang, 330045, People's Republic of China
| | - Bisong Yue
- Key Laboratory of Bio-resources and Eco-environment (Ministry of Education), College of Life Sciences, Sichuan University, Chengdu, 610064, People's Republic of China.
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18
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Wang J, Zhang L, Xiao R, Li Y, Liao S, Zhang Z, Yang W, Liang B. Plasma lipidomic signatures of spontaneous obese rhesus monkeys. Lipids Health Dis 2019; 18:8. [PMID: 30621707 PMCID: PMC6323686 DOI: 10.1186/s12944-018-0952-9] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2018] [Accepted: 12/18/2018] [Indexed: 12/12/2022] Open
Abstract
Background Obesity plays crucial roles in the pathogenesis of metabolic diseases such as hyperlipidemia, nonalcoholic fatty liver disease (NAFLD), and type 2 diabetes (T2D). The underlying mechanisms linking obesity to metabolic diseases are still less understandable. Methods Previously, we screened a group of spontaneously obese rhesus monkeys. Here, we performed a plasma lipidomic analysis of normal and obese monkeys using gas chromatography/mass spectroscopy (GC/MS) and ultra-high performance liquid chromatography/mass spectroscopy (UPLC/MS). Results In total, 143 lipid species were identified, quantified, and classified into free fatty acids (FFA), phosphatidylcholine (PC), phosphatidylethanolamine (PE), phosphatidylinositol (PI), phosphatidylserine (PS), phosphatidylglycerol (PG), lysophosphatidylcholine (LPC), lysophosphatidic acid (LPA), and sphingomyelin (SM). Data analysis showed that the obese monkeys had increased levels of fatty acids palmitoleic acid (C16:1) and arachidonic acid (C20:4), FFA especially palmitic acid (C16:0), as well as certain PC species and SM species. Surprisingly, the plasma level of LPA-C16:0 was approximately four-fold greater in the obese monkeys. Conversely, the levels of most PE species were obviously reduced in the obese monkeys. Conclusion Collectively, our work suggests that lipids such as FFA C16:0 and 16:0-LPA may be potential candidates for the diagnosis and study of obesity-related diseases.
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Affiliation(s)
- Junlong Wang
- Key Laboratory of Animal Models and Human Disease Mechanisms of the Chinese Academy of Sciences and Yunnan province, Chinese Academy of Sciences, Kunming Institute of Zoology, Kunming, 650223, China.,Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming, 650223, China.,College of Pharmaceutical Sciences, Soochow University, Suzhou, 215123, China
| | - Linqiang Zhang
- Key Laboratory of Animal Models and Human Disease Mechanisms of the Chinese Academy of Sciences and Yunnan province, Chinese Academy of Sciences, Kunming Institute of Zoology, Kunming, 650223, China.,Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming, 650223, China
| | - Ruyue Xiao
- Key Laboratory of Animal Models and Human Disease Mechanisms of the Chinese Academy of Sciences and Yunnan province, Chinese Academy of Sciences, Kunming Institute of Zoology, Kunming, 650223, China.,Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming, 650223, China
| | - Yunhai Li
- Key Laboratory of Animal Models and Human Disease Mechanisms of the Chinese Academy of Sciences and Yunnan province, Chinese Academy of Sciences, Kunming Institute of Zoology, Kunming, 650223, China.,Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming, 650223, China
| | - Shasha Liao
- School of Life Sciences, Anhui University, Hefei, 230601, Anhui, China
| | - Zhiguo Zhang
- Key Laboratory of Animal Models and Human Disease Mechanisms of the Chinese Academy of Sciences and Yunnan province, Chinese Academy of Sciences, Kunming Institute of Zoology, Kunming, 650223, China.,Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming, 650223, China
| | - Wenhui Yang
- Key Laboratory of Cardiovascular Disease of Yunnan Province, Department of Geriatrics, Yan'an Affiliated Hospital of Kunming Medical University, Kunming, China
| | - Bin Liang
- Key Laboratory of Animal Models and Human Disease Mechanisms of the Chinese Academy of Sciences and Yunnan province, Chinese Academy of Sciences, Kunming Institute of Zoology, Kunming, 650223, China. .,Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming, 650223, China.
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19
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Wang J, Xu S, Gao J, Zhang L, Zhang Z, Yang W, Li Y, Liao S, Zhou H, Liu P, Liang B. SILAC-based quantitative proteomic analysis of the livers of spontaneous obese and diabetic rhesus monkeys. Am J Physiol Endocrinol Metab 2018; 315:E294-E306. [PMID: 29664677 DOI: 10.1152/ajpendo.00016.2018] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Type 2 diabetes mellitus (T2DM) is a severe metabolic disorder that affects more than 10% of the population worldwide. Obesity is a major cause of insulin resistance and contributes to the development of T2DM. Liver is an essential metabolic organ that plays crucial roles in the pathogenesis of obesity and diabetes. However, the underlying mechanisms of liver in the transition of obesity to diabetes are not fully understood. The nonhuman primate rhesus monkey is an appropriate animal for research of human diseases. Here, we first screened and selected three individuals of spontaneously diabetic rhesus monkeys. Interestingly, the diabetic monkeys were obese with a high body mass index at the beginning, but gradually lost their body weight during one year of observation. Furthermore, we performed stable isotope labeling with amino acids in cell culture-based quantitative proteomics to identify proteins and signaling pathways with altered expression in the liver of obese and diabetic monkeys. In total, 3,509 proteins were identified and quantified, of which 185 proteins displayed an altered expression level. Gene ontology analysis revealed that the expression of proteins involved in fatty acids β-oxidation and galactose metabolism was increased in obese monkeys; while proteins involved in oxidative phosphorylation and branched chain amino acid (BCAA) degradation were upregulated in diabetic monkeys. In addition, we observed mild apoptosis in the liver of diabetic monkeys, suggesting liver injury at the late onset of diabetes. Taken together, our liver proteomics may reveal a distinct metabolic transition from fatty acids β-oxidation in obese monkey to BCAA degradation in diabetic monkeys.
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Affiliation(s)
- Junlong Wang
- College of Pharmaceutical Sciences, Soochow University , Suzhou , China
- Key Laboratory of Animal Models and Human Disease Mechanisms of the Chinese Academy of Sciences and Yunnan Province, Kunming Institute of Zoology, Chinese Academy of Sciences , Kunming , China
- Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences , Kunming , China
| | - Shimeng Xu
- National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences , Beijing , China
| | - Jing Gao
- Department of Analytical Chemistry and CAS Key Laboratory of Receptor Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences , Shanghai , China
| | - Linqiang Zhang
- Key Laboratory of Animal Models and Human Disease Mechanisms of the Chinese Academy of Sciences and Yunnan Province, Kunming Institute of Zoology, Chinese Academy of Sciences , Kunming , China
- Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences , Kunming , China
| | - Zhiguo Zhang
- Key Laboratory of Animal Models and Human Disease Mechanisms of the Chinese Academy of Sciences and Yunnan Province, Kunming Institute of Zoology, Chinese Academy of Sciences , Kunming , China
- Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences , Kunming , China
| | - Wenhui Yang
- Key Laboratory of Cardiovascular Disease of Yunnan Province, Department of Geriatrics, Yan'an Affiliated Hospital of Kunming Medical University , Kunming , China
| | - Yunhai Li
- Key Laboratory of Animal Models and Human Disease Mechanisms of the Chinese Academy of Sciences and Yunnan Province, Kunming Institute of Zoology, Chinese Academy of Sciences , Kunming , China
- Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences , Kunming , China
| | - Shasha Liao
- Key Laboratory of Animal Models and Human Disease Mechanisms of the Chinese Academy of Sciences and Yunnan Province, Kunming Institute of Zoology, Chinese Academy of Sciences , Kunming , China
- Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences , Kunming , China
| | - Hu Zhou
- Department of Analytical Chemistry and CAS Key Laboratory of Receptor Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences , Shanghai , China
| | - Pingsheng Liu
- National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences , Beijing , China
| | - Bin Liang
- College of Pharmaceutical Sciences, Soochow University , Suzhou , China
- Key Laboratory of Animal Models and Human Disease Mechanisms of the Chinese Academy of Sciences and Yunnan Province, Kunming Institute of Zoology, Chinese Academy of Sciences , Kunming , China
- Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences , Kunming , China
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20
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Gad PN, Kokikian N, Christe KL, Edgerton VR, Havton LA. Noninvasive neurophysiological mapping of the lower urinary tract in adult and aging rhesus macaques. J Neurophysiol 2018; 119:1521-1527. [PMID: 29361664 DOI: 10.1152/jn.00840.2017] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023] Open
Abstract
The lower urinary tract (LUT) may be activated by spinal cord stimulation, but the physiological mapping characteristics of LUT activation with noninvasive transcutaneous spinal cord stimulation (TSCS) are not known. The effects of aging on the contractile properties of the detrusor are also not well understood. Therefore, TSCS was applied over the T10/T11 to L6/L7 spinous processes in adult ( n = 6) and aged ( n = 9) female rhesus macaques. A combination of urodynamic studies and electromyography recordings of the external urethral sphincter (EUS), external anal sphincter (EAS), and pelvic floor muscles was performed. Distinct functional maps were demonstrated for TSCS-evoked detrusor and urethral pressures and for the activation of the EUS, EAS, and pelvic floor muscles. The magnitude of responses for each peripheral target organ was dependent on TSCS location and strength. The strongest detrusor contraction was observed with TSCS at the L1/L2 site in adults and the L3/L4 site in aged subjects. TSCS-evoked bladder pressure at the L1/L2 site was significantly higher for the adults compared with the aged subjects ( P < 0.05). Cumulative normalized TSCS-evoked pressures, calculated for five consecutive sites between the T11/T12 and L3/L4 levels, were significantly lower for aged compared with adult subjects ( P < 0.05). The aged animals also showed a caudal shift for the TSCS site that generated the strongest detrusor contraction. We conclude that natural aging in rhesus macaques is associated with decreased detrusor contractility, a finding of significant translational research relevance as detrusor underactivity is a common occurrence with aging in humans. NEW & NOTEWORTHY Transcutaneous spinal cord stimulation (TSCS) was used to map lower urinary tract function in adult and aged rhesus macaques. Aging was associated with decreased peak pressure responses to TSCS, reduced cumulative normalized evoked bladder pressure responses, and a caudal shift for the site generating the strongest TSCS-induced detrusor contraction. We demonstrate the utility of TSCS as a new diagnostic tool for detrusor contractility assessments and conclude that aging is associated with decreased detrusor contractility in primates.
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Affiliation(s)
- Parag N Gad
- Department of Integrative Biology and Physiology, University of California , Los Angeles, California
| | - Nelly Kokikian
- Department of Integrative Biology and Physiology, University of California , Los Angeles, California
| | - Kari L Christe
- California National Primate Research Center, University of California , Davis, California
| | - V Reggie Edgerton
- Department of Integrative Biology and Physiology, University of California , Los Angeles, California.,Department of Neurobiology, David Geffen School of Medicine at University of California , Los Angeles, California.,Department of Neurosurgery, David Geffen School of Medicine at University of California , Los Angeles, California.,Brain Research Institute, University of California , Los Angeles, California.,Institut Guttmann, Hospital de Neurorehabilitació, Universitat Autònoma de Barcelona, Badalona, Spain.,Centre for Neuroscience and Regenerative Medicine, University of Technology , Sydney , Australia
| | - Leif A Havton
- Department of Neurobiology, David Geffen School of Medicine at University of California , Los Angeles, California.,Department of Neurology, David Geffen School of Medicine at University of California , Los Angeles, California
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21
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Xue C, Raveendran M, Harris RA, Fawcett GL, Liu X, White S, Dahdouli M, Rio Deiros D, Below JE, Salerno W, Cox L, Fan G, Ferguson B, Horvath J, Johnson Z, Kanthaswamy S, Kubisch HM, Liu D, Platt M, Smith DG, Sun B, Vallender EJ, Wang F, Wiseman RW, Chen R, Muzny DM, Gibbs RA, Yu F, Rogers J. The population genomics of rhesus macaques (Macaca mulatta) based on whole-genome sequences. Genome Res 2016; 26:1651-1662. [PMID: 27934697 PMCID: PMC5131817 DOI: 10.1101/gr.204255.116] [Citation(s) in RCA: 73] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2016] [Accepted: 10/12/2016] [Indexed: 12/30/2022]
Abstract
Rhesus macaques (Macaca mulatta) are the most widely used nonhuman primate in biomedical research, have the largest natural geographic distribution of any nonhuman primate, and have been the focus of much evolutionary and behavioral investigation. Consequently, rhesus macaques are one of the most thoroughly studied nonhuman primate species. However, little is known about genome-wide genetic variation in this species. A detailed understanding of extant genomic variation among rhesus macaques has implications for the use of this species as a model for studies of human health and disease, as well as for evolutionary population genomics. Whole-genome sequencing analysis of 133 rhesus macaques revealed more than 43.7 million single-nucleotide variants, including thousands predicted to alter protein sequences, transcript splicing, and transcription factor binding sites. Rhesus macaques exhibit 2.5-fold higher overall nucleotide diversity and slightly elevated putative functional variation compared with humans. This functional variation in macaques provides opportunities for analyses of coding and noncoding variation, and its cellular consequences. Despite modestly higher levels of nonsynonymous variation in the macaques, the estimated distribution of fitness effects and the ratio of nonsynonymous to synonymous variants suggest that purifying selection has had stronger effects in rhesus macaques than in humans. Demographic reconstructions indicate this species has experienced a consistently large but fluctuating population size. Overall, the results presented here provide new insights into the population genomics of nonhuman primates and expand genomic information directly relevant to primate models of human disease.
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Affiliation(s)
- Cheng Xue
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas 77030, USA
| | - Muthuswamy Raveendran
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas 77030, USA
| | - R Alan Harris
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas 77030, USA.,Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas 77030, USA
| | - Gloria L Fawcett
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas 77030, USA
| | - Xiaoming Liu
- University of Texas Health Science Center, Houston, Texas 77030, USA
| | - Simon White
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas 77030, USA
| | - Mahmoud Dahdouli
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas 77030, USA
| | - David Rio Deiros
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas 77030, USA
| | - Jennifer E Below
- University of Texas Health Science Center, Houston, Texas 77030, USA
| | - William Salerno
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas 77030, USA
| | - Laura Cox
- Southwest National Primate Research Center, San Antonio, Texas 78227, USA
| | - Guoping Fan
- Department of Human Genetics, University of California, Los Angeles, California 90095, USA
| | - Betsy Ferguson
- Oregon National Primate Research Center, Beaverton, Oregon 97006, USA
| | - Julie Horvath
- North Carolina Museum of Natural Sciences, Raleigh, North Carolina 27601, USA.,Biological and Biomedical Sciences, North Carolina Central University, Durham, North Carolina 27707, USA.,Department of Evolutionary Anthropology, Duke University, Durham, North Carolina 27708, USA
| | - Zach Johnson
- Yerkes National Primate Research Center, Atlanta, Georgia 30322, USA
| | - Sree Kanthaswamy
- California National Primate Research Center, Davis, California 95616, USA.,School of Mathematical and Natural Sciences, Arizona State University, Phoenix, Arizona 85004, USA
| | - H Michael Kubisch
- Tulane National Primate Research Center, Covington, Louisiana 70433, USA
| | - Dahai Liu
- Center for Stem Cell and Translational Medicine, Anhui University, Anhui, China 230601
| | - Michael Platt
- Department of Neurobiology, Duke University, Durham, North Carolina 27708, USA.,Department of Neuroscience, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
| | - David G Smith
- California National Primate Research Center, Davis, California 95616, USA
| | - Binghua Sun
- Center for Stem Cell and Translational Medicine, Anhui University, Anhui, China 230601
| | - Eric J Vallender
- Tulane National Primate Research Center, Covington, Louisiana 70433, USA.,New England National Primate Research Center, Southborough, Massachusetts 01772, USA
| | - Feng Wang
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas 77030, USA
| | - Roger W Wiseman
- Wisconsin National Primate Research Center, Madison, Wisconsin 53711, USA
| | - Rui Chen
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas 77030, USA.,Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas 77030, USA
| | - Donna M Muzny
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas 77030, USA
| | - Richard A Gibbs
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas 77030, USA.,Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas 77030, USA
| | - Fuli Yu
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas 77030, USA.,Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas 77030, USA
| | - Jeffrey Rogers
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas 77030, USA.,Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas 77030, USA
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Xu Y, Hu Z, Wang C, Zhang X, Li J, Yue B. Characterization of perfect microsatellite based on genome-wide and chromosome level in Rhesus monkey (Macaca mulatta). Gene 2016; 592:269-75. [PMID: 27395431 DOI: 10.1016/j.gene.2016.07.016] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2016] [Revised: 06/21/2016] [Accepted: 07/05/2016] [Indexed: 10/21/2022]
Abstract
Microsatellite studies based on chromosomes level would contribute to the biometric correlation analysis of chromosome and microsatellite applications on the specific chromosome. In this study, the total microsatellite length of 1,141,024 loci was 21.8Mb, which covered about 0.74% of the male Rhesus monkey genome. Perfect mononucleotide SSRs were the most abundant, followed by the pattern: perfect di->tetra->tri->penta->hexanucleotide SSRs. The main range of repeat times focused on 12-32 times (mono-), 7-23 times (di-), 5-10 times (tri-), 4-14 times (tetra-), 4-9 times (penta-), 4-8 times (hexa-), respectively. The largest SSRs number was found in chromosome 1 with 94,347 loci, followed by chromosome 3, 2, 7 and 5, and the smallest number was in chromosome 18. The predominant repeat types in male Rhesus monkey genome and chromosome Y were basically A, AC, AG, AAT, AAC, AAAT, AAAC, AAAG, AAACA and AAACAA. SSRs number of all chromosomes was closely positively correlated with chromosome sequence size (r=0.969, p<0.01), and significantly negatively correlated with abundance (r=-0.24, 0.01<p<0.05). The lengths of all chromosomes were significantly negatively correlated with microsatellite density (r=-0.456, 0.01<p<0.05), and relative abundance and density of SSRs in all chromosomes were significantly negatively correlated with SSR GC content (r=-0.939/-0.928, p<0.01). The SSRs GC content on chromosome X (accounting for 16.71%) was found to be the highest in female Rhesus monkey, which might contributed to the DNA methylation of CpG islands for sex chromosome X inactivation and expression regulation. These results and exported tetranucleotide repeat sequences in each chromosome for primer design would facilitate the exploration of microsatellites structural function, composition mode and molecular markers development in Rhesus monkey genome.
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Affiliation(s)
- Yongtao Xu
- Key Laboratory of Bio-resources and Eco-environment (Ministry of Education), College of Life Sciences, Sichuan University, Chengdu 610064, PR China; Sichuan Key Laboratory of Conservation Biology on Endangered Wildlife, College of Life Sciences, Sichuan University, Chengdu 610064, PR China
| | - Zongxiu Hu
- Yibin HengShu Animal Models Resourse Industry Technology Academy, Yibin 644609, PR China
| | - Chen Wang
- Key Laboratory of Bio-resources and Eco-environment (Ministry of Education), College of Life Sciences, Sichuan University, Chengdu 610064, PR China
| | - Xiuyue Zhang
- Key Laboratory of Bio-resources and Eco-environment (Ministry of Education), College of Life Sciences, Sichuan University, Chengdu 610064, PR China; Sichuan Key Laboratory of Conservation Biology on Endangered Wildlife, College of Life Sciences, Sichuan University, Chengdu 610064, PR China
| | - Jing Li
- Key Laboratory of Bio-resources and Eco-environment (Ministry of Education), College of Life Sciences, Sichuan University, Chengdu 610064, PR China; Sichuan Key Laboratory of Conservation Biology on Endangered Wildlife, College of Life Sciences, Sichuan University, Chengdu 610064, PR China
| | - Bisong Yue
- Key Laboratory of Bio-resources and Eco-environment (Ministry of Education), College of Life Sciences, Sichuan University, Chengdu 610064, PR China; Sichuan Key Laboratory of Conservation Biology on Endangered Wildlife, College of Life Sciences, Sichuan University, Chengdu 610064, PR China.
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Abstract
The rhesus macaque (Macaca mulatta) is one of the most extensively used nonhuman primate models for human diseases. This article presents a literature review focusing on major organ systems and age-associated conditions in humans and primates, combined with information from the Wisconsin National Primate Research Center Electronic Health Record database to highlight and contrast age-associated lesions in geriatric rhesus macaques with younger cohorts. Rhesus macaques are excellent models for age-associated conditions, including diabetes, osteoarthritis, endometriosis, visual accommodation, hypertension, osteoporosis, and amyloidosis. Adenocarcinoma of the large intestine (ileocecocolic junction, cecum, and colon) is the most common spontaneous neoplasm in the rhesus macaque. A combination of cross-sectional and longitudinal studies is required to truly define mechanisms of maturation, aging, and the pathology of age-associated conditions in macaques and thus humans. The rhesus macaque is and will continue to be an appropriate and valuable model for investigation of the mechanisms and treatment of age-associated diseases.
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Affiliation(s)
- H A Simmons
- Wisconsin National Primate Research Center, University of Wisconsin-Madison, Madison, WI, USA
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24
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Ng J, Fass JN, Durbin-Johnson B, Smith DG, Kanthaswamy S. Identifying rhesus macaque gene orthologs using heterospecific human CNV probes. GENOMICS DATA 2015; 6:202-7. [PMID: 26697375 PMCID: PMC4664757 DOI: 10.1016/j.gdata.2015.09.016] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/24/2015] [Accepted: 09/12/2015] [Indexed: 12/14/2022]
Abstract
We used the Affymetrix(®) Genome-Wide Human SNP Array 6.0 to identify heterospecific markers and compare copy number and structural genomic variation between humans and rhesus macaques. Over 200,000 human copy number variation (CNV) probes were mapped to a Chinese and an Indian rhesus macaque sample. Observed genomic rearrangements and synteny were in agreement with the results of a previously published genomic comparison between humans and rhesus macaques. Comparisons between each of the two rhesus macaques and humans yielded 206 regions with copy numbers that differed by at least two fold in the Indian rhesus macaque and human, 32 in the Chinese rhesus macaque and human, and 147 in both rhesus macaques. The detailed genomic map and preliminary CNV data are useful for better understanding genetic variation in rhesus macaques, identifying derived changes in human CNVs that may have evolved by selection, and determining the suitability of rhesus macaques as human models for particular biomedical studies.
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Affiliation(s)
- Jillian Ng
- Molecular Anthropology Laboratory, Department of Anthropology, University of California, Davis, CA, USA
| | - Joseph N. Fass
- Genome Center Bioinformatics Core, University of California, Davis, CA, USA
| | | | - David Glenn Smith
- Molecular Anthropology Laboratory, Department of Anthropology, University of California, Davis, CA, USA
- California National Primate Research Center, University of California, Davis, CA, USA
| | - Sree Kanthaswamy
- California National Primate Research Center, University of California, Davis, CA, USA
- School of Mathematics and Natural Sciences, Arizona State University (ASU) at the West Campus, Glendale, AZ, USA
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25
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Smith GR, Bauer L, Crane MM, Johnson ZP. Immunogenetic characterization of a captive colony of sooty mangabeys (Cercocebus atys) used for SIV research. J Med Primatol 2015; 44:76-88. [PMID: 25645218 DOI: 10.1111/jmp.12161] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/15/2014] [Indexed: 11/27/2022]
Abstract
BACKGROUND African non-human primates are SIV natural hosts and do not develop disease following infection. Understanding disease avoidance mechanisms in these species is important for HIV vaccine development. The largest captive population of sooty mangabeys, a SIV natural host species, resides at the Yerkes National Primate Research Center. METHODS Thirteen primer sets that amplify polymorphic microsatellite loci within the MHC region were used to genotype 144 animals. Immunogenetic Management Software (IMS) was used to identify MHC haplotypes and organize data. RESULTS Seventy-three haplotypes were identified. Limited haplotype diversity was observed in this population with 88.2% of included animals carrying one of 18 haplotypes. Differences in haplotype frequency were observed between SIV (+) and SIV (-) populations. CONCLUSIONS We have developed a novel tool for others to use in the analysis of the role of the MHC in a natural host non-human primate model species used for SIV research.
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Affiliation(s)
- Geary R Smith
- Division of Animal Resources, Yerkes National Primate Research Center, Emory University, Atlanta, GA, USA
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26
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Zimin AV, Cornish AS, Maudhoo MD, Gibbs RM, Zhang X, Pandey S, Meehan DT, Wipfler K, Bosinger SE, Johnson ZP, Tharp GK, Marçais G, Roberts M, Ferguson B, Fox HS, Treangen T, Salzberg SL, Yorke JA, Norgren RB. A new rhesus macaque assembly and annotation for next-generation sequencing analyses. Biol Direct 2014; 9:20. [PMID: 25319552 PMCID: PMC4214606 DOI: 10.1186/1745-6150-9-20] [Citation(s) in RCA: 136] [Impact Index Per Article: 13.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2014] [Accepted: 10/03/2014] [Indexed: 12/13/2022] Open
Abstract
Background The rhesus macaque (Macaca mulatta) is a key species for advancing biomedical research. Like all draft mammalian genomes, the draft rhesus assembly (rheMac2) has gaps, sequencing errors and misassemblies that have prevented automated annotation pipelines from functioning correctly. Another rhesus macaque assembly, CR_1.0, is also available but is substantially more fragmented than rheMac2 with smaller contigs and scaffolds. Annotations for these two assemblies are limited in completeness and accuracy. High quality assembly and annotation files are required for a wide range of studies including expression, genetic and evolutionary analyses. Results We report a new de novo assembly of the rhesus macaque genome (MacaM) that incorporates both the original Sanger sequences used to assemble rheMac2 and new Illumina sequences from the same animal. MacaM has a weighted average (N50) contig size of 64 kilobases, more than twice the size of the rheMac2 assembly and almost five times the size of the CR_1.0 assembly. The MacaM chromosome assembly incorporates information from previously unutilized mapping data and preliminary annotation of scaffolds. Independent assessment of the assemblies using Ion Torrent read alignments indicates that MacaM is more complete and accurate than rheMac2 and CR_1.0. We assembled messenger RNA sequences from several rhesus tissues into transcripts which allowed us to identify a total of 11,712 complete proteins representing 9,524 distinct genes. Using a combination of our assembled rhesus macaque transcripts and human transcripts, we annotated 18,757 transcripts and 16,050 genes with complete coding sequences in the MacaM assembly. Further, we demonstrate that the new annotations provide greatly improved accuracy as compared to the current annotations of rheMac2. Finally, we show that the MacaM genome provides an accurate resource for alignment of reads produced by RNA sequence expression studies. Conclusions The MacaM assembly and annotation files provide a substantially more complete and accurate representation of the rhesus macaque genome than rheMac2 or CR_1.0 and will serve as an important resource for investigators conducting next-generation sequencing studies with nonhuman primates. Reviewers This article was reviewed by Dr. Lutz Walter, Dr. Soojin Yi and Dr. Kateryna Makova.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | - Robert B Norgren
- Department of Genetics, Cell Biology and Anatomy, University of Nebraska Medical Center, Omaha, Nebraska 68198, USA.
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Mascher M, Stein N. Genetic anchoring of whole-genome shotgun assemblies. Front Genet 2014; 5:208. [PMID: 25071835 PMCID: PMC4083584 DOI: 10.3389/fgene.2014.00208] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2014] [Accepted: 06/19/2014] [Indexed: 12/30/2022] Open
Abstract
The recent advances in sequencing throughput and genome assembly algorithms have established whole-genome shotgun (WGS) assemblies as the cornerstone of the genomic infrastructure for many species. WGS assemblies can be constructed with comparative ease and give a comprehensive representation of the gene space even of large and complex genomes. One major obstacle in utilizing WGS assemblies for important research applications such as gene isolation or comparative genomics has been the lack of chromosomal positioning and contextualization of short sequence contigs. Assigning chromosomal locations to sequence contigs required the construction and integration of genome-wide physical maps and dense genetic linkage maps as well as synteny to model species. Recently, methods to rapidly construct ultra-dense linkage maps encompassing millions of genetic markers from WGS sequencing data of segregating populations have made possible the direct assignment of genetic positions to short sequence contigs. Here, we review recent developments in the integration of WGS assemblies and sequence-based linkage maps, discuss challenges for further improvement of the methodology and outline possible applications building on genetically anchored WGS assemblies.
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Affiliation(s)
- Martin Mascher
- Leibniz Institute of Plant Genetics and Crop Plant Research, Stadt Seeland Germany
| | - Nils Stein
- Leibniz Institute of Plant Genetics and Crop Plant Research, Stadt Seeland Germany
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29
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Dubuc C, Ruiz-Lambides A, Widdig A. Variance in male lifetime reproductive success and estimation of the degree of polygyny in a primate. Behav Ecol 2014; 25:878-889. [PMID: 25024637 PMCID: PMC4095946 DOI: 10.1093/beheco/aru052] [Citation(s) in RCA: 46] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2013] [Revised: 02/18/2014] [Accepted: 02/20/2014] [Indexed: 11/12/2022] Open
Abstract
The degree of polygyny is predicted to influence the strength of direct male-male competition, leading to a high variance in male lifetime reproductive success and to reproduction limited to the prime period of adulthood. Here, we explore the variance in male lifetime reproductive success and reproductive time in an anthropoid primate forming multimale-multifemale groups. Males of this species form dominance hierarchies, which are expected to skew reproduction toward few high-ranking males. At the same time, however, females mate with multiple males (polygynandry), which should limit the degree of polygyny. Using 20 years of genetic and demographic data, we calculated lifetime reproductive success for the free-ranging rhesus macaque (Macaca mulatta) population of Cayo Santiago for subjects that died naturally or reached senescence. Our results show that 1) male lifetime reproductive success was significantly skewed (range: 0-47 offspring; males reproducing below average: 62.8%; nonbreeders: 17.4%), 2) variance in male lifetime reproductive success was 5 times larger than in females, and 3) male lifetime reproductive success was more influenced by variation in fecundity (60%) than longevity (25%), suggesting that some direct male-male competition takes place. However, the opportunity for selection (i.e., standardized variance in male lifetime reproductive success) is low compared with that in other large mammal species characterized by a high degree of polygyny. Moreover, male reproductive life extended much beyond the prime period, showing that physical strength was not required to acquire mates. We conclude that rhesus macaques exhibit a moderate degree of polygyny and, therefore, low levels of direct male-male competition for fertile females, despite the fact that males form linear dominance hierarchies.
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Affiliation(s)
- Constance Dubuc
- Junior Research Group of Primate Kin Selection, Department of Primatology, Max-Planck Institute for Evolutionary Anthropology , Deutscher Platz 6, 04103 Leipzig , Germany , ; Center for the Study of Human Origins, Department of Anthropology, New York University , 25 Waverly Place, New York, NY 10003 , USA
| | - Angelina Ruiz-Lambides
- Junior Research Group of Primate Kin Selection, Department of Primatology, Max-Planck Institute for Evolutionary Anthropology , Deutscher Platz 6, 04103 Leipzig , Germany , ; Cayo Santiago, Caribbean Primate Research Center, University of Puerto Rico , PO Box 306, Punta Santiago, PR 00741 , USA , and
| | - Anja Widdig
- Junior Research Group of Primate Kin Selection, Department of Primatology, Max-Planck Institute for Evolutionary Anthropology , Deutscher Platz 6, 04103 Leipzig , Germany , ; Research Group of Behavioural Ecology, Institute of Biology, Faculty of Bioscience, Pharmacy and Psychology, University of Leipzig , Talstrasse 33, 04103 Leipzig , Germany
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Fan Z, Zhao G, Li P, Osada N, Xing J, Yi Y, Du L, Silva P, Wang H, Sakate R, Zhang X, Xu H, Yue B, Li J. Whole-genome sequencing of tibetan macaque (Macaca Thibetana) provides new insight into the macaque evolutionary history. Mol Biol Evol 2014; 31:1475-89. [PMID: 24648498 PMCID: PMC4032132 DOI: 10.1093/molbev/msu104] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
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.
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Affiliation(s)
- Zhenxin Fan
- Key Laboratory of Bioresources and Ecoenvironment (Ministry of Education), College of Life Sciences, Sichuan University, Chengdu, People's Republic of China
| | - Guang Zhao
- Sichuan Key Laboratory of Conservation Biology on Endangered Wildlife, College of Life Sciences, Sichuan University, Chengdu, People's Republic of China
| | - Peng Li
- Key Laboratory of Bioresources and Ecoenvironment (Ministry of Education), College of Life Sciences, Sichuan University, Chengdu, People's Republic of China
| | - Naoki Osada
- Division of Evolutionary Genetics, Department of Population Genetics, National Institute of Genetics, Mishima, Shizuoka, Japan
| | - Jinchuan Xing
- Department of Genetics, Rutgers, the State University of New Jersey
| | - Yong Yi
- Experimental Animal Institute of Sichuan Academy of Medical Sciences & Sichuan Provincial People's Hospital, Chengdu, People's Republic of China
| | - Lianming Du
- Key Laboratory of Bioresources and Ecoenvironment (Ministry of Education), College of Life Sciences, Sichuan University, Chengdu, People's Republic of China
| | - Pedro Silva
- Research Center in Biodiversity and Genetic Resources, University of Porto (CIBIO-UP), Campus Agrário de Vairão, Vila do Conde, Portugal
| | - Hongxing Wang
- Experimental Animal Institute of Sichuan Academy of Medical Sciences & Sichuan Provincial People's Hospital, Chengdu, People's Republic of China
| | - Ryuichi Sakate
- Laboratory of Rare Disease Biospecimen, Department of Disease Bioresources Research, National Institute of Biomedical Innovation, Ibaraki, Osaka, Japan
| | - Xiuyue Zhang
- Key Laboratory of Bioresources and Ecoenvironment (Ministry of Education), College of Life Sciences, Sichuan University, Chengdu, People's Republic of China
| | - Huailiang Xu
- College of Animal Science and Technology, Sichuan Agricultural University, Ya'an, People's Republic of China
| | - Bisong Yue
- Sichuan Key Laboratory of Conservation Biology on Endangered Wildlife, College of Life Sciences, Sichuan University, Chengdu, People's Republic of China
| | - Jing Li
- Key Laboratory of Bioresources and Ecoenvironment (Ministry of Education), College of Life Sciences, Sichuan University, Chengdu, People's Republic of China
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Pfefferle D, Ruiz-Lambides AV, Widdig A. Female rhesus macaques discriminate unfamiliar paternal sisters in playback experiments: support for acoustic phenotype matching. Proc Biol Sci 2014; 281:20131628. [PMID: 24225452 PMCID: PMC3843825 DOI: 10.1098/rspb.2013.1628] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2013] [Accepted: 10/17/2013] [Indexed: 11/12/2022] Open
Abstract
Widespread evidence exists that when relatives live together, kinship plays a central role in shaping the evolution of social behaviour. Previous studies showed that female rhesus macaques (Macaca mulatta) recognize familiar maternal kin using vocal cues. Recognizing paternal kin might, however, be more difficult as rhesus females mate promiscuously during the possible conception period, most probably concealing paternity. Behavioural observations indicate that semi free-ranging female rhesus macaques prefer to associate with their paternal half-sisters in comparison to unrelated females within the same group, particularly when born within the same age cohort. However, the cues and mechanism/s used in paternal kin discrimination remain under debate. Here, we investigated whether female rhesus macaques use the acoustic modality to discriminate between paternal half-sisters and non-kin, and tested familiarity and phenotype matching as the underlying mechanisms. We found that test females responded more often to calls of paternal half-sisters compared with calls of unrelated females, and that this discrimination ability was independent of the level of familiarity between callers and test females, which provides, to our knowledge, the first evidence for acoustic phenotype matching. Our study strengthens the evidence that female rhesus macaques can recognize their paternal kin, and that vocalizations are used as a cue.
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Affiliation(s)
- Dana Pfefferle
- Junior Research Group of Primate Kin Selection, Department of Primatology, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
- Behavioural Ecology Research Group, Institute of Biology, University of Leipzig, Germany
| | - Angelina V. Ruiz-Lambides
- Behavioural Ecology Research Group, Institute of Biology, University of Leipzig, Germany
- Caribbean Primate Research Center-Cayo Santiago, University of Puerto Rico, Punta Santiago, USA
| | - Anja Widdig
- Junior Research Group of Primate Kin Selection, Department of Primatology, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
- Behavioural Ecology Research Group, Institute of Biology, University of Leipzig, Germany
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32
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Cross-species amplification of human microsatellite markers in pig-tailed and stump-tailed macaques. J Genet 2013. [DOI: 10.1007/s12041-011-0029-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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Osada N, Nakagome S, Mano S, Kameoka Y, Takahashi I, Terao K. Finding the factors of reduced genetic diversity on X chromosomes of Macaca fascicularis: male-driven evolution, demography, and natural selection. Genetics 2013; 195:1027-35. [PMID: 24026095 PMCID: PMC3813834 DOI: 10.1534/genetics.113.156703] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2013] [Accepted: 08/28/2013] [Indexed: 11/18/2022] Open
Abstract
The ratio of genetic diversity on X chromosomes relative to autosomes in organisms with XX/XY sex chromosomes could provide fundamental insight into the process of genome evolution. Here we report this ratio for 24 cynomolgus monkeys (Macaca fascicularis) originating in Indonesia, Malaysia, and the Philippines. The average X/A diversity ratios in these samples was 0.34 and 0.20 in the Indonesian-Malaysian and Philippine populations, respectively, considerably lower than the null expectation of 0.75. A Philippine population supposed to derive from an ancestral population by founding events showed a significantly lower ratio than the parental population, suggesting a demographic effect for the reduction. Taking sex-specific mutation rate bias and demographic effect into account, expected X/A diversity ratios generated by computer simulations roughly agreed with the observed data in the intergenic regions. In contrast, silent sites in genic regions on X chromosomes showed strong reduction in genetic diversity and the observed X/A diversity ratio in the genic regions cannot be explained by mutation rate bias and demography, indicating that natural selection also reduces the level of polymorphism near genes. Whole-genome analysis of a female cynomolgus monkey also supported the notion of stronger reduction of genetic diversity near genes on the X chromosome.
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Affiliation(s)
- Naoki Osada
- Department of Population Genetics, National Institute of Genetics, Mishima, Shizuoka 4118540, Japan
- Department of Genetics, The Graduate University of Advanced Studies (SOKENDAI), Mishima, Shizuoka 4118540, Japan
| | - Shigeki Nakagome
- The Institute of Statistical Mathematics, Tachikawa, Tokyo 1908562, Japan
| | - Shuhei Mano
- The Institute of Statistical Mathematics, Tachikawa, Tokyo 1908562, Japan
| | - Yosuke Kameoka
- Department of Disease Bioresources Research, National Institute of Biomedical Innovation, Osaka 5670085 Japan
| | - Ichiro Takahashi
- Department of Disease Bioresources Research, National Institute of Biomedical Innovation, Osaka 5670085 Japan
| | - Keiji Terao
- Tsukuba Primate Research Center, National Institute of Biomedical Innovation, Tsukuba 3050843, Japan
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Xu YR, Li JH, Zhu Y, Sun BH. Development of a microsatellite set for paternity assignment of captive rhesus macaques (Macaca mulatta) from Anhui Province, China. RUSS J GENET+ 2013. [DOI: 10.1134/s1022795413070144] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
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35
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Beyond one billion time series: indexing and mining very large time series collections with $$i$$ SAX2+. Knowl Inf Syst 2013. [DOI: 10.1007/s10115-012-0606-6] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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Abstract
The study of nonhuman primates (NHP) is key to understanding human evolution, in addition to being an important model for biomedical research. NHPs are especially important for translational medicine. There are now exciting opportunities to greatly increase the utility of these models by incorporating Next Generation (NextGen) sequencing into study design. Unfortunately, the draft status of nonhuman genomes greatly constrains what can currently be accomplished with available technology. Although all genomes contain errors, draft assemblies and annotations contain so many mistakes that they make currently available nonhuman primate genomes misleading to investigators conducting evolutionary studies; and these genomes are of insufficient quality to serve as references for NextGen studies. Fortunately, NextGen sequencing can be used in the production of greatly improved genomes. Existing Sanger sequences can be supplemented with NextGen whole genome, and exomic genomic sequences to create new, more complete and correct assemblies. Additional physical mapping, and an incorporation of information about gene structure, can be used to improve assignment of scaffolds to chromosomes. In addition, mRNA-sequence data can be used to economically acquire transcriptome information, which can be used for annotation. Some highly polymorphic and complex regions, for example MHC class I and immunoglobulin loci, will require extra effort to properly assemble and annotate. However, for the vast majority of genes, a modest investment in money, and a somewhat greater investment in time, can greatly improve assemblies and annotations sufficient to produce true, reference grade nonhuman primate genomes. Such resources can reasonably be expected to transform nonhuman primate research.
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Affiliation(s)
- Robert B. Norgren
- Address correspondence and reprint requests to Dr. Robert B. Norgren, Department of Genetics, Cell Biology and Anatomy, University of Nebraska Medical Center, 985805 Nebraska Medical Center, Omaha, NE 68198 or email
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Kanthaswamy S, Ng J, Ross CT, Trask JS, Smith DG, Buffalo VS, Fass JN, Lin D. Identifying human-rhesus macaque gene orthologs using heterospecific SNP probes. Genomics 2012; 101:30-7. [PMID: 22982528 DOI: 10.1016/j.ygeno.2012.09.001] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2012] [Revised: 07/27/2012] [Accepted: 09/04/2012] [Indexed: 02/07/2023]
Abstract
We genotyped a Chinese and an Indian-origin rhesus macaque using the Affymetrix Genome-Wide Human SNP Array 6.0 and cataloged 85,473 uniquely mapping heterospecific SNPs. These SNPs were assigned to rhesus chromosomes according to their probe sequence alignments as displayed in the human and rhesus reference sequences. The conserved gene order (synteny) revealed by heterospecific SNP maps is in concordance with that of the published human and rhesus macaque genomes. Using these SNPs' original human rs numbers, we identified 12,328 genes annotated in humans that are associated with these SNPs, 3674 of which were found in at least one of the two rhesus macaques studied. Due to their density, the heterospecific SNPs allow fine-grained comparisons, including approximate boundaries of intra- and extra-chromosomal rearrangements involving gene orthologs, which can be used to distinguish rhesus macaque chromosomes from human chromosomes.
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Affiliation(s)
- Sree Kanthaswamy
- Molecular Anthropology Lab., Dept. of Anthropology, UC Davis, CA, USA.
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38
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Kean LS, Singh K, Blazar BR, Larsen CP. Nonhuman primate transplant models finally evolve: detailed immunogenetic analysis creates new models and strengthens the old. Am J Transplant 2012; 12:812-9. [PMID: 22177005 PMCID: PMC3482466 DOI: 10.1111/j.1600-6143.2011.03873.x] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Nonhuman primate (NHP) models play a critical role in the translation of novel therapies for transplantation to the clinic. However, although MHC disparity significantly affects the outcome of transplantation, until recently, experiments using NHP models were performed without the ability to rigorously control the degree of MHC disparity in transplant cohorts. In this review, we discuss several key technical breakthroughs in the field, which have finally enabled detailed immunogenetic data to be incorporated into NHP transplantation studies. These advances have created a new gold-standard for NHP transplantation research, which incorporates detailed information regarding the degree of relatedness and the degree of MHC haplotype disparity between transplant pairs and the precise MHC alleles that both donors and recipients express. The adoption of this new standard promises to increase the rigor of NHP transplantation studies and to ensure that these experiments are optimally translatable to patient care.
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Affiliation(s)
- L S Kean
- Aflac Cancer Center and Blood Disorders Service, Children's Healthcare of Atlanta and Department of Pediatrics, Emory University School of Medicine, Atlanta, GA, USA.
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39
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Tachibana M, Sparman M, Ramsey C, Ma H, Lee HS, Penedo MCT, Mitalipov S. Generation of chimeric rhesus monkeys. Cell 2012; 148:285-95. [PMID: 22225614 DOI: 10.1016/j.cell.2011.12.007] [Citation(s) in RCA: 126] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2011] [Revised: 10/25/2011] [Accepted: 12/05/2011] [Indexed: 01/12/2023]
Abstract
Totipotent cells in early embryos are progenitors of all stem cells and are capable of developing into a whole organism, including extraembryonic tissues such as placenta. Pluripotent cells in the inner cell mass (ICM) are the descendants of totipotent cells and can differentiate into any cell type of a body except extraembryonic tissues. The ability to contribute to chimeric animals upon reintroduction into host embryos is the key feature of murine totipotent and pluripotent cells. Here, we demonstrate that rhesus monkey embryonic stem cells (ESCs) and isolated ICMs fail to incorporate into host embryos and develop into chimeras. However, chimeric offspring were produced following aggregation of totipotent cells of the four-cell embryos. These results provide insights into the species-specific nature of primate embryos and suggest that a chimera assay using pluripotent cells may not be feasible.
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Affiliation(s)
- Masahito Tachibana
- Oregon National Primate Research Center, Oregon Health & Science University, 505 N.W. 185(th) Avenue, Beaverton, OR 97006, USA
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40
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Trask JS, Garnica WT, Kanthaswamy S, Malhi RS, Smith DG. 4040 SNPs for genomic analysis in the rhesus macaque (Macaca mulatta). Genomics 2011; 98:352-8. [PMID: 21907785 PMCID: PMC3207016 DOI: 10.1016/j.ygeno.2011.08.004] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2011] [Revised: 08/11/2011] [Accepted: 08/17/2011] [Indexed: 11/17/2022]
Abstract
Although the rhesus macaque (Macaca mulatta) is commonly used for biomedical research and becoming a preferred model for translational medicine, quantification of genome-wide variation has been slow to follow the publication of the genome in 2007. Here we report the properties of 4040 single nucleotide polymorphisms discovered and validated in Chinese and Indian rhesus macaques from captive breeding colonies in the United States. Frequency-matched measures of linkage disequilibrium were much greater in the Indian sample. Although the majority of polymorphisms were shared between the two populations, rare alleles were over twice as common in the Chinese sample. Indian rhesus had higher rates of heterozygosity, as well as previously undetected substructure, potentially due to admixture from Burma in wild populations and demographic events post-captivity.
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Affiliation(s)
- J Satkoski Trask
- Department of Anthropology, University of California, Davis, USA.
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41
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Yasukochi Y, Satta Y. Evolution of the CYP2D gene cluster in humans and four non-human primates. Genes Genet Syst 2011; 86:109-16. [PMID: 21670550 DOI: 10.1266/ggs.86.109] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
The human cytochrome P450 2D6 (CYP2D6) is a primary enzyme involved in the metabolism of about 25% of commonly used therapeutic drugs. CYP2D6 belongs to the CYP2D subfamily, a gene cluster located on chromosome 22, which comprises the CYP2D6 gene and pseudogenes CYP2D7P and CYP2D8P. Although the chemical and physiological properties of CYP2D6 have been extensively studied, there has been no study to date on molecular evolution of the CYP2D subfamily in the human genome. Such knowledge could greatly contribute to the understanding of drug metabolism in humans because it makes us to know when and how the current metabolic system has been constructed. The knowledge moreover can be useful to find differences in exogenous substrates in a particular metabolism between human and other animals such as experimental animals. Here, we conducted a preliminary study to investigate the evolution and gene organization of the CYP2D subfamily, focused on humans and four non-human primates (chimpanzees, orangutans, rhesus monkeys, and common marmosets). Our results indicate that CYP2D7P has been duplicated from CYP2D6 before the divergence between humans and great apes, whereas CYP2D6 and CYP2D8P have been already present in the stem lineages of New World monkeys and Catarrhini. Furthermore, the origin of the CYP2D subfamily in the human genome can be traced back to before the divergence between amniotes and amphibians. Our analyses also show that reported chimeric sequences of the CYP2D6 and CYP2D7 genes in the chimpanzee genome appear to be exchanged in its genome database.
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Affiliation(s)
- Yoshiki Yasukochi
- Department of Evolutionary Studies of Biosystems, the Graduate University for Advanced Studies, Shonan Village, Hayama, Kanagawa 240-0193, Japan.
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Evaluating the reliability of microsatellite genotyping from low-quality DNA templates with a polynomial distribution model. CHINESE SCIENCE BULLETIN-CHINESE 2011. [DOI: 10.1007/s11434-011-4634-5] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
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McGraw LA, Davis JK, Young LJ, Thomas JW. A genetic linkage map and comparative mapping of the prairie vole (Microtus ochrogaster) genome. BMC Genet 2011; 12:60. [PMID: 21736755 PMCID: PMC3143096 DOI: 10.1186/1471-2156-12-60] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2011] [Accepted: 07/07/2011] [Indexed: 02/02/2023] Open
Abstract
BACKGROUND The prairie vole (Microtus ochrogaster) is an emerging rodent model for investigating the genetics, evolution and molecular mechanisms of social behavior. Though a karyotype for the prairie vole has been reported and low-resolution comparative cytogenetic analyses have been done in this species, other basic genetic resources for this species, such as a genetic linkage map, are lacking. RESULTS Here we report the construction of a genome-wide linkage map of the prairie vole. The linkage map consists of 406 markers that are spaced on average every 7 Mb and span an estimated ~90% of the genome. The sex average length of the linkage map is 1707 cM, which, like other Muroid rodent linkage maps, is on the lower end of the length distribution of linkage maps reported to date for placental mammals. Linkage groups were assigned to 19 out of the 26 prairie vole autosomes as well as the X chromosome. Comparative analyses of the prairie vole linkage map based on the location of 387 Type I markers identified 61 large blocks of synteny with the mouse genome. In addition, the results of the comparative analyses revealed a potential elevated rate of inversions in the prairie vole lineage compared to the laboratory mouse and rat. CONCLUSIONS A genetic linkage map of the prairie vole has been constructed and represents the fourth genome-wide high-resolution linkage map reported for Muroid rodents and the first for a member of the Arvicolinae sub-family. This resource will advance studies designed to dissect the genetic basis of a variety of social behaviors and other traits in the prairie vole as well as our understanding of genome evolution in the genus Microtus.
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Affiliation(s)
- Lisa A McGraw
- Department of Human Genetics, Emory University School of Medicine, Atlanta, GA, USA
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Garcia-Cruz R, Pacheco S, Brieño MA, Steinberg ER, Mudry MD, Ruiz-Herrera A, Garcia-Caldés M. A comparative study of the recombination pattern in three species of Platyrrhini monkeys (primates). Chromosoma 2011; 120:521-30. [PMID: 21735165 DOI: 10.1007/s00412-011-0329-6] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2011] [Revised: 05/30/2011] [Accepted: 06/23/2011] [Indexed: 01/26/2023]
Abstract
Homologous chromosomes exchange genetic information through recombination during meiotic synapsis, a process that increases genetic diversity and is fundamental to sexual reproduction. Meiotic studies in mammalian species are scarce and mainly focused on human and mouse. Here, the meiotic recombination events were determined in three species of Platyrrhini monkeys (Cebus libidinosus, Cebus nigritus and Alouatta caraya) by analysing the distribution of MLH1 foci at the stage of pachytene. Moreover, the combination of immunofluorescence and fluorescent in situ hybridisation has enabled us to construct recombination maps of primate chromosomes that are homologous to human chromosomes 13 and 21. Our results show that (a) the overall number of MLH1 foci varies among all three species, (b) the presence of heterochromatin blocks does not have a major influence on the distribution of MLH1 foci and (c) the distribution of crossovers in the homologous chromosomes to human chromosomes 13 and 21 are conserved between species of the same genus (C. libidinosus and C. nigritus) but are significantly different between Cebus and Alouatta. This heterogeneity in recombination behaviour among Ceboidea species may reflect differences in genetic diversity and genome composition.
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Affiliation(s)
- Raquel Garcia-Cruz
- Departament de Biologia Cellular, Fisiologia i Immunologia, Universitat Autònoma de Barcelona, UAB Campus, Bellaterra, Spain
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45
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Fang X, Zhang Y, Zhang R, Yang L, Li M, Ye K, Guo X, Wang J, Su B. Genome sequence and global sequence variation map with 5.5 million SNPs in Chinese rhesus macaque. Genome Biol 2011; 12:R63. [PMID: 21733155 PMCID: PMC3218825 DOI: 10.1186/gb-2011-12-7-r63] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2010] [Revised: 05/01/2011] [Accepted: 07/06/2011] [Indexed: 11/25/2022] Open
Abstract
Background Rhesus macaque (Macaca mulatta) is the most widely used nonhuman primate animal in biomedical research. A global map of genetic variations in rhesus macaque is valuable for both evolutionary and functional studies. Results Using next-generation sequencing technology, we sequenced a Chinese rhesus macaque genome with 11.56-fold coverage. In total, 96% of the reference Indian macaque genome was covered by at least one read, and we identified 2.56 million homozygous and 2.94 million heterozygous SNPs. We also detected a total of 125,150 structural variations, of which 123,610 were deletions with a median length of 184 bp (ranging from 25 bp to 10 kb); 63% of these deletions were located in intergenic regions and 35% in intronic regions. We further annotated 5,187 and 962 nonsynonymous SNPs to the macaque orthologs of human disease and drug-target genes, respectively. Finally, we set up a genome-wide genetic variation database with the use of Gbrowse. Conclusions Genome sequencing and construction of a global sequence variation map in Chinese rhesus macaque with the concomitant database provide applicable resources for evolutionary and biomedical research.
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Affiliation(s)
- Xiaodong Fang
- Beijing Genomics Institute-Shenzhen, Chinese Academy of Sciences, Shenzhen 518083, China
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46
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Bradley BJ, Lawler RR. Linking genotypes, phenotypes, and fitness in wild primate populations. Evol Anthropol 2011; 20:104-19. [DOI: 10.1002/evan.20306] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
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47
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Guo G, Zhou Z, Wang Y, Zhao K, Zhu L, Lust G, Hunter L, Friedenberg S, Li J, Zhang Y, Harris S, Jones P, Sandler J, Krotscheck U, Todhunter R, Zhang Z. Canine hip dysplasia is predictable by genotyping. Osteoarthritis Cartilage 2011; 19:420-9. [PMID: 21215318 PMCID: PMC3065507 DOI: 10.1016/j.joca.2010.12.011] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/27/2010] [Revised: 12/14/2010] [Accepted: 12/21/2010] [Indexed: 02/02/2023]
Abstract
OBJECTIVE To establish a predictive method using whole genome genotyping for early intervention in canine hip dysplasia (CHD) risk management, for the prevention of the progression of secondary osteoarthritis (OA), and for selective breeding. DESIGN Two sets of dogs (six breeds) were genotyped with dense SNPs covering the entire canine genome. The first set contained 359 dogs upon which a predictive formula for genomic breeding value (GBV) was derived by using their estimated breeding value (EBV) of the Norberg angle (a measure of CHD) and their genotypes. To investigate how well the formula would work for an individual dog with genotype only (without using EBV), a cross validation was performed by masking the EBV of one dog at a time. The genomic data and the EBV of the remaining dogs were used to predict the GBV for the single dog that was left out. The second set of dogs included 38 new Labrador retriever dogs, which had no pedigree relationship to the dogs in the first set. RESULTS The cross validation showed a strong correlation (R>0.7) between the EBV and the GBV. The independent validation showed a moderate correlation (R=0.5) between GBV for the Norberg angle and the observed Norberg angle (no EBV was available for the new 38 dogs). Sensitivity, specificity, positive and negative predictive values of the genomic data were all above 70%. CONCLUSIONS Prediction of CHD from genomic data is feasible, and can be applied for risk management of CHD and early selection for genetic improvement to reduce the prevalence of CHD in breeding programs. The prediction can be implemented before maturity, at which age current radiographic screening programs are traditionally applied, and as soon as DNA is available.
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Affiliation(s)
- Gang Guo
- Department of Animal Science, China Agricultural University, Beijing, China
| | - Zhengkui Zhou
- College of Animal Science and Technology, Northwest A&F University, Yangling, China
,Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, China
,Department of Clinical Sciences, College of Veterinary Medicine, Cornell University, Ithaca, New York, United States of America
| | - Yachun Wang
- Department of Animal Science, China Agricultural University, Beijing, China
| | - Keyan Zhao
- Department of Computational Biology and Statistics, Cornell University, Ithaca, New York, United States of America
| | - Lan Zhu
- Department of Statistics, Oklahoma State University, Stillwater, Oklahoma, United States of America
| | - George Lust
- Baker Institute for Animal Health, Cornell University, Ithaca, New York, United States of America
| | - Linda Hunter
- Department of Clinical Sciences, College of Veterinary Medicine, Cornell University, Ithaca, New York, United States of America
| | - Steven Friedenberg
- Department of Clinical Sciences, College of Veterinary Medicine, Cornell University, Ithaca, New York, United States of America
| | - Junya Li
- Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Yuan Zhang
- Department of Animal Science, China Agricultural University, Beijing, China
| | - Stephen Harris
- The WALTHAM Centre for Pet Nutrition, Waltham on the Wolds, Leicestershire, UK
| | - Paul Jones
- The WALTHAM Centre for Pet Nutrition, Waltham on the Wolds, Leicestershire, UK
| | - Jody Sandler
- Guiding Eyes for the Blind, Yorktown Hts, New York, United States of America
| | - Ursula Krotscheck
- Department of Clinical Sciences, College of Veterinary Medicine, Cornell University, Ithaca, New York, United States of America
| | - Rory Todhunter
- Department of Clinical Sciences, College of Veterinary Medicine, Cornell University, Ithaca, New York, United States of America
| | - Zhiwu Zhang
- Institute for Genomic Diversity, Cornell University, Ithaca, New York, United States of America
,Address for correspondence: Zhiwu Zhang, Institute for Genomic Diversity, Biotechnology, Cornell University, Ithaca NY 14853, Phone: 607 255 3270, Fax: 607 255 6465,
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48
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Trask JAS, Malhi RS, Kanthaswamy S, Johnson J, Garnica WT, Malladi VS, Smith DG. The effect of SNP discovery method and sample size on estimation of population genetic data for Chinese and Indian rhesus macaques (Macaca mulatta). Primates 2011; 52:129-38. [PMID: 21207104 DOI: 10.1007/s10329-010-0232-4] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2010] [Accepted: 11/25/2010] [Indexed: 11/28/2022]
Abstract
This study was designed to address issues regarding sample size and marker location that have arisen from the discovery of SNPs in the genomes of poorly characterized primate species and the application of these markers to the study of primate population genetics. We predict the effect of discovery sample size on the probability of discovering both rare and common SNPs and then compare this prediction with the proportion of common and rare SNPs discovered when different numbers of individuals are sequenced. Second, we examine the effect of genomic region on estimates of common population genetic data, comparing markers from both coding and non-coding regions of the rhesus macaque genome and the population genetic data calculated from these markers, to measure the degree and direction of bias introduced by SNPs located in coding versus non-coding regions of the genome. We found that both discovery sample size and genomic region surveyed affect SNP marker attributes and population genetic estimates, even when these are calculated from an expanded data set containing more individuals than the original discovery data set. Although none of the SNP detection methods or genomic regions tested in this study was completely uninformative, these results show that each has a different kind of genetic variation that is suitable for different purposes, and each introduces specific types of bias. Given that each SNP marker has an individual evolutionary history, we calculated that the most complete and unbiased representation of the genetic diversity present in the individual can be obtained by incorporating at least 10 individuals into the discovery sample set, to ensure the discovery of both common and rare polymorphisms.
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Affiliation(s)
- Jessica A Satkoski Trask
- Department of Anthropology, University of California, Davis, 330 Young Hall, One Shields Avenue, Davis, CA 95616, USA.
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Zhou Z, Sheng X, Zhang Z, Zhao K, Zhu L, Guo G, Friedenberg SG, Hunter LS, Vandenberg-Foels WS, Hornbuckle WE, Krotscheck U, Corey E, Moise NS, Dykes NL, Li J, Xu S, Du L, Wang Y, Sandler J, Acland GM, Lust G, Todhunter RJ. Differential genetic regulation of canine hip dysplasia and osteoarthritis. PLoS One 2010; 5:e13219. [PMID: 20949002 PMCID: PMC2952589 DOI: 10.1371/journal.pone.0013219] [Citation(s) in RCA: 49] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2010] [Accepted: 09/12/2010] [Indexed: 12/17/2022] Open
Abstract
BACKGROUND Canine hip dysplasia (HD) is a common polygenic trait characterized by hip malformation that results in osteoarthritis (OA). The condition in dogs is very similar to developmental dysplasia of the human hip which also leads to OA. METHODOLOGY/PRINCIPAL FINDINGS A total of 721 dogs, including both an association and linkage population, were genotyped. The association population included 8 pure breeds (Labrador retriever, Greyhounds, German Shepherd, Newfoundland, Golden retriever, Rottweiler, Border Collie and Bernese Mountain Dog). The linkage population included Labrador retrievers, Greyhounds, and their crosses. Of these, 366 dogs were genotyped at ∼22,000 single nucleotide polymorphism (SNP) loci and a targeted screen across 8 chromosomes with ∼3,300 SNPs was performed on 551 dogs (196 dogs were common to both sets). A mixed linear model approach was used to perform an association study on this combined association and linkage population. The study identified 4 susceptibility SNPs associated with HD and 2 SNPs associated with hip OA. CONCLUSION/SIGNIFICANCE The identified SNPs included those near known genes (PTPRD, PARD3B, and COL15A1) reported to be associated with, or expressed in, OA in humans. This suggested that the canine model could provide a unique opportunity to identify genes underlying natural HD and hip OA, which are common and debilitating conditions in both dogs and humans.
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Affiliation(s)
- Zhengkui Zhou
- College of Animal Science and Technology, Northwest A&F University, Yangling, China
- Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, China
- Department of Clinical Sciences, College of Veterinary Medicine, Cornell University, Ithaca, New York, United States of America
| | - Xihui Sheng
- Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, China
- Department of Clinical Sciences, College of Veterinary Medicine, Cornell University, Ithaca, New York, United States of America
- Department of Animal Science and Technology, Beijing University of Agriculture, Beijing, China
| | - Zhiwu Zhang
- Institute for Genomic Diversity, Cornell University, Ithaca, New York, United States of America
| | - Keyan Zhao
- Department of Computational Biology and Statistics, Cornell University, Ithaca, New York, United States of America
| | - Lan Zhu
- Department of Statistics, Oklahoma State University, Stillwater, Oklahoma, United States of America
| | - Gang Guo
- Department of Animal Science, China Agricultural University, Beijing, China
| | - Steve G. Friedenberg
- Department of Clinical Sciences, College of Veterinary Medicine, Cornell University, Ithaca, New York, United States of America
| | - Linda S. Hunter
- Department of Clinical Sciences, College of Veterinary Medicine, Cornell University, Ithaca, New York, United States of America
| | - Wendy S. Vandenberg-Foels
- Department of Clinical Sciences, College of Veterinary Medicine, Cornell University, Ithaca, New York, United States of America
| | - William E. Hornbuckle
- Department of Clinical Sciences, College of Veterinary Medicine, Cornell University, Ithaca, New York, United States of America
| | - Ursula Krotscheck
- Department of Clinical Sciences, College of Veterinary Medicine, Cornell University, Ithaca, New York, United States of America
| | - Elizabeth Corey
- Department of Clinical Sciences, College of Veterinary Medicine, Cornell University, Ithaca, New York, United States of America
| | - Nancy S. Moise
- Department of Clinical Sciences, College of Veterinary Medicine, Cornell University, Ithaca, New York, United States of America
| | - Nathan L. Dykes
- Department of Clinical Sciences, College of Veterinary Medicine, Cornell University, Ithaca, New York, United States of America
| | - Junya Li
- Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Shangzhong Xu
- Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Lixin Du
- Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Yachun Wang
- Department of Animal Science, China Agricultural University, Beijing, China
| | - Jody Sandler
- Guiding Eyes for the Blind, Yorktown Heights, New York, United States of America
| | - Gregory M. Acland
- Baker Institute for Animal Health, Cornell University, Ithaca, New York, United States of America
| | - George Lust
- Baker Institute for Animal Health, Cornell University, Ithaca, New York, United States of America
| | - Rory J. Todhunter
- Department of Clinical Sciences, College of Veterinary Medicine, Cornell University, Ithaca, New York, United States of America
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50
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Tung J, Alberts SC, Wray GA. Evolutionary genetics in wild primates: combining genetic approaches with field studies of natural populations. Trends Genet 2010; 26:353-62. [PMID: 20580115 PMCID: PMC2933653 DOI: 10.1016/j.tig.2010.05.005] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2010] [Revised: 05/17/2010] [Accepted: 05/22/2010] [Indexed: 11/19/2022]
Abstract
Ecological and evolutionary studies of wild primates hold important keys to understanding both the shared characteristics of primate biology and the genetic and phenotypic differences that make specific lineages, including our own, unique. Although complementary genetic research on nonhuman primates has long been of interest, recent technological and methodological advances now enable functional and population genetic studies in an unprecedented manner. In the past several years, novel genetic data sets have revealed new information about the demographic history of primate populations and the genetics of adaptively important traits. In combination with the rich history of behavioral, ecological, and physiological work on natural primate populations, genetic approaches promise to provide a compelling picture of primate evolution in the past and in the present day.
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Affiliation(s)
- Jenny Tung
- Department of Biology, Duke University, P.O. Box 90338, Durham NC 27708, USA.
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