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

TitleCopy number variants and fixed duplications among 198 rhesus macaques (Macaca mulatta).
Publication TypeJournal Article
Year of Publication2020
AuthorsBrasó-Vives, M, Povolotskaya, IS, Hartasánchez, DA, Farré, X, Fernandez-Callejo, M, Raveendran, M, R Harris, A, Rosene, DL, Lorente-Galdos, B, Navarro, A, Marques-Bonet, T, Rogers, J, Juan, D
JournalPLoS Genet
Date Published2020 05
KeywordsAnimals, Chromosome Mapping, DNA Copy Number Variations, Female, Gene Duplication, Genetics, Population, Genome, High-Throughput Nucleotide Sequencing, Humans, Macaca mulatta, Male, Open Reading Frames, Phylogeny, Sequence Analysis, DNA, Species Specificity

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.

Alternate JournalPLoS Genet
PubMed ID32392208
PubMed Central IDPMC7241854
Grant ListR24 OD011173 / OD / NIH HHS / United States
UM1 HG008898 / HG / NHGRI NIH HHS / United States
/ HH / Howard Hughes Medical Institute / United States
R24 OD010962 / OD / NIH HHS / United States