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


Autoři: Marina Brasó-Vives aff001;  Inna S. Povolotskaya aff004;  Diego A. Hartasánchez aff001;  Xavier Farré aff001;  Marcos Fernandez-Callejo aff005;  Muthuswamy Raveendran aff006;  R. Alan Harris aff006;  Douglas L. Rosene aff008;  Belen Lorente-Galdos aff009;  Arcadi Navarro aff001;  Tomas Marques-Bonet aff001;  Jeffrey Rogers aff006;  David Juan aff001;  Inna S. Povolotskaya aff003;  Marcos Fernandez-Callejo aff004;  Muthuswamy Raveendran aff005;  R. Alan Harris aff005;  Douglas L. Rosene aff007;  Belen Lorente-Galdos aff008;  Jeffrey Rogers aff005
Působiště autorů: Institut de Biologia Evolutiva (CSIC-Universitat Pompeu Fabra), Parc de Recerca Biomèdica de Barcelona, Barcelona, Catalonia, Spain aff001;  Departament de Ciències Experimentals i de la Salut, Universitat Pompeu Fabra, Barcelona, Catalonia, Spain aff002;  Laboratoire de Biométrie et Biologie Évolutive UMR 5558, Université de Lyon, Université Lyon 1, CNRS, Villeurbanne, France aff002;  Laboratoire de Biométrie et Biologie Évolutive UMR 5558, Université de Lyon, Université Lyon 1, CNRS, Villeurbanne, France aff003;  Veltischev Research and Clinical Institute for Pediatrics of the Pirogov Russian National Research Medical University, Moscow, Russia aff003;  Veltischev Research and Clinical Institute for Pediatrics of the Pirogov Russian National Research Medical University, Moscow, Russia aff004;  National Centre for Genomic Analysis-Centre for Genomic Regulation, Barcelona Institute of Science and Technology, Barcelona, Catalonia, Spain aff004;  National Centre for Genomic Analysis-Centre for Genomic Regulation, Barcelona Institute of Science and Technology, Barcelona, Catalonia, Spain aff005;  Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas, United States of America aff005;  Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas, United States of America aff006;  Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, United States of America aff006;  Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, United States of America aff007;  Department of Anatomy and Neurobiology, Boston University School of Medicine, Boston, Massachusetts, United States of America aff007;  Department of Anatomy and Neurobiology, Boston University School of Medicine, Boston, Massachusetts, United States of America aff008;  Department of Neuroscience, Yale School of Medicine, New Haven, Connecticut, United States of America aff008;  Department of Neuroscience, Yale School of Medicine, New Haven, Connecticut, United States of America aff009;  National Institute for Bioinformatics (INB), Barcelona, Catalonia, Spain aff009;  National Institute for Bioinformatics (INB), Barcelona, Catalonia, Spain aff010;  Institució Catalana de Recerca i Estudis Avançats, Barcelona, Catalonia, Spain aff010;  Institució Catalana de Recerca i Estudis Avançats, Barcelona, Catalonia, Spain aff011;  Institut Català de Paleontologia Miquel Crusafont, Universitat Autònoma de Barcelona, Cerdanyola del Vallès, Catalonia, Spain aff011;  Institut Català de Paleontologia Miquel Crusafont, Universitat Autònoma de Barcelona, Cerdanyola del Vallès, Catalonia, Spain aff012
Vyšlo v časopise: Copy number variants and fixed duplications among 198 rhesus macaques (Macaca mulatta). PLoS Genet 16(5): e32767. doi:10.1371/journal.pgen.1008742
Kategorie: Research Article
doi: 10.1371/journal.pgen.1008742

Souhrn

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.

Klíčová slova:

Comparative genomics – Copy number variation – Genome-wide association studies – Human genomics – Macaque – Mammalian genomics – Primates – Rhesus monkeys


Zdroje

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