Copy number variants and fixed duplications among 198 rhesus macaques (Macaca mulatta)

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• dc.contributor.author Brasó-Vives, Marina, 1990-
• dc.contributor.author Povolotskaya, Inna, 1986-
• dc.contributor.author Hartasánchez Frenk, Diego Andrés, 1982-
• dc.contributor.author Farré, Xavier
• dc.contributor.author Fernández Callejo, Marcos
• dc.contributor.author Raveendran, Muthuswamy
• dc.contributor.author Harris, R. Alan
• dc.contributor.author Rosene, Douglas L.
• dc.contributor.author Lorente Galdós, Maria Belén
• dc.contributor.author Navarro i Cuartiellas, Arcadi, 1969-
• dc.contributor.author Marquès i Bonet, Tomàs, 1975-
• dc.contributor.author Rogers, Jeffrey
• dc.contributor.author Juan Sopeña, David Alejandro, 1975-
• dc.date.accessioned 2020-06-04T06:23:32Z
• dc.date.available 2020-06-04T06:23:32Z
• dc.date.issued 2020
• dc.description.abstract The rhesus macaque is an abundant species of Old World monkeys and a valuable model organism for biomedical research due to its close phylogenetic relationship to humans. Copy number variation is one of the main sources of genomic diversity within and between species and a widely recognized cause of inter-individual differences in disease risk. However, copy number differences among rhesus macaques and between the human and macaque genomes, as well as the relevance of this diversity to research involving this nonhuman primate, remain understudied. Here we present a high-resolution map of sequence copy number for the rhesus macaque genome constructed from a dataset of 198 individuals. Our results show that about one-eighth of the rhesus macaque reference genome is composed of recently duplicated regions, either copy number variable regions or fixed duplications. Comparison with human genomic copy number maps based on previously published data shows that, despite overall similarities in the genome-wide distribution of these regions, there are specific differences at the chromosome level. Some of these create differences in the copy number profile between human disease genes and their rhesus macaque orthologs. Our results highlight the importance of addressing the number of copies of target genes in the design of experiments and cautions against human-centered assumptions in research conducted with model organisms. Overall, we present a genome-wide copy number map from a large sample of rhesus macaque individuals representing an important novel contribution concerning the evolution of copy number in primate genomes.
• dc.description.sponsorship This work was supported in part by NIH grants R24-OD011173 to J.R., UM1-HG008898 to R.A.H., AGAUR (FI – DGR 2015) to M.B.-V., BFU2017-86471-P (MINECO/FEDER, UE), Howard Hughes International Early Career, Obra Social "La Caixa" and Secretaria d’Universitats i Recerca and CERCA Programme del Departament d’Economia i Coneixement de la Generalitat de Catalunya (GRC 2017 SGR 880) to T.M.B. D.J. is supported by Juan de la Cierva fellowship (FJCI-2016-29558) from MICINN. In addition, we wish to acknowledge NIH grant R24-OD010962 to J. Capitanio which supported the development of the Biobehavioral Assessment resource and associated DNA samples from California NPRC rhesus macaques. We also acknowledge NIH grant support to specific National Primate Research Centers: California NPRC (OD011107) and Oregon NPRC (OD011092 and OD021324). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.
• dc.format.mimetype application/pdf
• dc.identifier.citation Brasó-Vives M, Povolotskaya IS, Hartasánchez DA, Farré X, Fernandez-Callejo M, Raveendran M, Harris RA, Rosene DL, Lorente-Galdos B, Navarro A, Marques-Bonet T, Rogers J, Juan D. Copy number variants and fixed duplications among 198 rhesus macaques (Macaca mulatta). PLoS Genet. 2020; 16(5):e1008742. DOI: 10.1371/journal.pgen.1008742
• dc.identifier.doi http://dx.doi.org/10.1371/journal.pgen.1008742
• dc.identifier.issn 1553-7390
• dc.identifier.uri http://hdl.handle.net/10230/44896
• dc.language.iso eng
• dc.publisher Public Library of Science (PLoS)
• dc.relation.ispartof PLoS Genet. 2020; 16(5):e1008742
• dc.relation.projectID info:eu-repo/grantAgreement/ES/2PE/BFU2017-86471-P
• dc.rights © 2020 Brasó-Vives et al. This is an open access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.
• dc.rights.accessRights info:eu-repo/semantics/openAccess
• dc.rights.uri http://creativecommons.org/licenses/by/4.0/
• dc.subject.keyword Macaque
• dc.subject.keyword Rhesus monkeys
• dc.subject.keyword Mammalian genomics
• dc.subject.keyword Copy number variation
• dc.subject.keyword Genome-wide association studies
• dc.subject.keyword Human genomics
• dc.subject.keyword Comparative genomics
• dc.subject.keyword Primates
• dc.title Copy number variants and fixed duplications among 198 rhesus macaques (Macaca mulatta)
• dc.type info:eu-repo/semantics/article
• dc.type.version info:eu-repo/semantics/publishedVersion