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

AuthorsBrasó-Vives, Marina ; Povolotskaya, Inna S.; Hartasánchez Frenk, Diego ; Farré, Xavier; Fernández-Callejo, Marcos
Issue Date11-May-2020
PublisherPublic Library of Science
CitationPLoS Genetics 16(5): e1008742 (2020)
Abstract[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.
[Author summary] One commonly used model organism in biomedical research is a species of Old World monkey, the rhesus macaque (Macaca mulatta). When translating biomedical research findings from rhesus macaques to humans, knowledge about the genetic differences between these two species is fundamental. In this study, we focus on copy number variation, which happens as a consequence of large duplication and deletion events in the genome, and which often has been overlooked. Copy number variation is a type of genetic variation which consists of one individual having more copies of a particular genomic region than another individual. We have performed an extensive evaluation of the copy number variants and fixed duplications among the genomes of 198 rhesus macaques and have generated a copy number map of high resolution for this species. We find that the overall pattern of within-species variation is similar to that in humans. However, when comparing specific duplicated regions between rhesus macaques and humans, we do find differences that could potentially have functional consequences. We have identified genes associated with human disease that have different copy number profiles between these two species, and therefore, we suggest avoiding human-centered assumptions in biomedical research conducted with model organisms.
Publisher version (URL)https://doi.org/10.1371/journal.pgen.1008742
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