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PMID: 32392208 Published · epublish English Comparative Study Journal Article Research Support, N.I.H., Extramural Research Support, Non-U.S. Gov't

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

PLoS genetics ·Vol. 16 ·No. 5 ·2020-00-00 ·Pages e1008742

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

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.

MeSH Terms
Animals Chromosome Mapping/veterinary DNA Copy Number Variations/physiology Female Gene Duplication/physiology Genetics, Population Genome High-Throughput Nucleotide Sequencing/veterinary Humans Macaca mulatta/classification,genetics Male Open Reading Frames/genetics Phylogeny Sequence Analysis, DNA/veterinary Species Specificity
Authors & Affiliations
13 authors, click to expand affiliations / ORCID
Brasó-Vives Marina ORCID
Institut de Biologia Evolutiva (CSIC-Universitat Pompeu Fabra), Parc de Recerca Biomèdica de Barcelona, Barcelona, Catalonia, Spain. | Laboratoire de Biométrie et Biologie Évolutive UMR 5558, Université de Lyon, Université Lyon 1, CNRS, Villeurbanne, France.
Povolotskaya Inna S ORCID
Veltischev Research and Clinical Institute for Pediatrics of the Pirogov Russian National Research Medical University, Moscow, Russia.
Hartasánchez Diego A ORCID
Institut de Biologia Evolutiva (CSIC-Universitat Pompeu Fabra), Parc de Recerca Biomèdica de Barcelona, Barcelona, Catalonia, Spain.
Farré Xavier ORCID
Institut de Biologia Evolutiva (CSIC-Universitat Pompeu Fabra), Parc de Recerca Biomèdica de Barcelona, Barcelona, Catalonia, Spain.
Fernandez-Callejo Marcos ORCID
National Centre for Genomic Analysis-Centre for Genomic Regulation, Barcelona Institute of Science and Technology, Barcelona, Catalonia, Spain.
Raveendran Muthuswamy
Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas, United States of America. | Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, United States of America.
Harris R Alan ORCID
Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas, United States of America. | Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, United States of America.
Rosene Douglas L
Department of Anatomy and Neurobiology, Boston University School of Medicine, Boston, Massachusetts, United States of America.
Lorente-Galdos Belen ORCID
Department of Neuroscience, Yale School of Medicine, New Haven, Connecticut, United States of America.
Navarro Arcadi
Institut de Biologia Evolutiva (CSIC-Universitat Pompeu Fabra), Parc de Recerca Biomèdica de Barcelona, Barcelona, Catalonia, Spain. | National Institute for Bioinformatics (INB), Barcelona, Catalonia, Spain. | Institució Catalana de Recerca i Estudis Avançats, Barcelona, Catalonia, Spain.
Marques-Bonet Tomas ORCID
Institut de Biologia Evolutiva (CSIC-Universitat Pompeu Fabra), Parc de Recerca Biomèdica de Barcelona, Barcelona, Catalonia, Spain. | National Centre for Genomic Analysis-Centre for Genomic Regulation, Barcelona Institute of Science and Technology, Barcelona, Catalonia, Spain. | Institució Catalana de Recerca i Estudis Avançats, Barcelona, Catalonia, Spain. | Institut Català de Paleontologia Miquel Crusafont, Universitat Autònoma de Barcelona, Cerdanyola del Vallès, Catalonia, Spain.
Rogers Jeffrey ORCID
Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas, United States of America. | Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, United States of America.
Juan David ORCID
Institut de Biologia Evolutiva (CSIC-Universitat Pompeu Fabra), Parc de Recerca Biomèdica de Barcelona, Barcelona, Catalonia, Spain.
Conflict of Interest

The authors have declared that no competing interests exist.

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Article Info
Journal
PLoS genetics
Abbr.
PLoS Genet
ISSN
1553-7404
DOI
10.1371/journal.pgen.1008742
Published
2020-00-00
Epub
2020-00-11
Pages
e1008742
Language
English
Region
United States
NLM ID
101239074
PMCID
PMC7241854
Subset
IM
Grants
NIH HHS · R24 OD011173 · United States
NHGRI NIH HHS · UM1 HG008898 · United States
Howard Hughes Medical Institute · United States
NIH HHS · R24 OD010962 · United States
External Links
PubMed source DOI: 10.1371/journal.pgen.1008742 PMC Full Text View journal details
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