Copy number variation analysis in the great apes reveals species-specific patterns of structural variation

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• dc.contributor.author Gazave, Elodieca
• dc.contributor.author Darre, Fleurca
• dc.contributor.author Morcillo Suárez, Carlos, 1969-ca
• dc.contributor.author Petit, Nataliaca
• dc.contributor.author Carreño Torres, Angelca
• dc.contributor.author Marigorta, Urko M.ca
• dc.contributor.author Ryder, Oliver A.ca
• dc.contributor.author Blancher, Antoineca
• dc.contributor.author Rocchi, Marianoca
• dc.contributor.author Bosch Fusté, Elenaca
• dc.contributor.author Baker, Carlca
• dc.contributor.author Marquès i Bonet, Tomàs, 1975-ca
• dc.contributor.author Eichler, Evan E.ca
• dc.contributor.author Navarro i Cuartiellas, Arcadi, 1969-ca
• dc.date.accessioned 2015-12-18T15:04:07Z
• dc.date.available 2015-12-18T15:04:07Z
• dc.date.issued 2011
• dc.description.abstract Copy number variants (CNVs) are increasingly acknowledged as an important source of evolutionary novelties in the human lineage. However, our understanding of their significance is still hindered by the lack of primate CNV data. We performed intraspecific comparative genomic hybridizations to identify loci harboring copy number variants in each of the four great apes: bonobos, chimpanzees, gorillas, and orangutans. For the first time, we could analyze differences in CNV location and frequency in these four species, and compare them with human CNVs and primate segmental duplication (SD) maps. In addition, for bonobo and gorilla, patterns of CNV and nucleotide diversity were studied in the same individuals. We show that CNVs have been subject to different selective pressures in different lineages. Evidence for purifying selection is stronger in gorilla CNVs overlapping genes, while positive selection appears to have driven the fixation of structural variants in the orangutan lineage. In contrast, chimpanzees and bonobos present high levels of common structural polymorphism, which is indicative of relaxed purifying selection together with the higher mutation rates induced by the known burst of segmental duplication in the ancestor of the African apes. Indeed, the impact of the duplication burst is noticeable by the fact that bonobo and chimpanzee share more CNVs with gorilla than expected. Finally, we identified a number of interesting genomic regions that present high-frequency CNVs in all great apes, while containing only very rare or even pathogenic structural variants in humans.ca
• dc.description.sponsorship Financial support was provided by a Beatriu de Pinos postdoctoral Grant to E.G., the Spanish Ministry of Science and Innovation (Grant BFU2009-13409-C02-02 to A.N.), and the Spanish National Institute for Bioinformatics (INB, www.inab.org). E.E.E. is an investigator of the Howard Hughes Medical Institute. M.R. is grateful to CEGBA (Centro di Eccellenza Geni in campo Biosanitario e Agroalimentare) and MIUR (Ministero Italiano della Un iversita’ e della Ricerca; Cluster CO3, Prog. L.488/92)
• dc.format.mimetype application/pdfca
• dc.identifier.citation Gazave E, Darré F, Morcillo-Suarez C, Petit-Marty N, Carreño A, Marigorta UM et al. Copy number variation analysis in the great apes reveals species-specific patterns of structural variation. Genome research. 2011;21(10):1626-39. DOI: 10.1101/gr.117242.110ca
• dc.identifier.doi http://dx.doi.org/10.1101/gr.117242.110
• dc.identifier.issn 1088-9051
• dc.identifier.uri http://hdl.handle.net/10230/25475
• dc.language.iso engca
• dc.publisher Cold Spring Harbor Laboratory Press (CSHL Press)ca
• dc.relation.ispartof Genome research. 2011;21(10):1626-39
• dc.relation.projectID info:eu-repo/grantAgreement/ES/3PN/BFU2009-13409-C02-02
• dc.rights © 2012 Gazave et al. This is an Open Access article distributed under the terms of a Creative Commons Attribution Licenseca
• dc.rights.accessRights info:eu-repo/semantics/openAccessca
• dc.subject.other Cromosomesca
• dc.subject.other ADNca
• dc.subject.other Polimorfisme genèticca
• dc.title Copy number variation analysis in the great apes reveals species-specific patterns of structural variationca
• dc.type info:eu-repo/semantics/articleca
• dc.type.version info:eu-repo/semantics/publishedVersionca