The genome of the vervet (Chlorocebus aethiops sabaeus)

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• dc.contributor.author Warren, Wesley C.ca
• dc.contributor.author García Pérez, Raquel, 1989-ca
• dc.contributor.author Marquès i Bonet, Tomàs, 1975-ca
• dc.contributor.author Freimer, Nelson B.ca
• dc.date.accessioned 2016-02-23T13:42:20Z
• dc.date.available 2016-06-01T02:00:03Z
• dc.date.issued 2015
• dc.description.abstract We describe a genome reference of the African green monkey or vervet (Chlorocebus aethiops). This member of the Old World monkey (OWM) superfamily is uniquely valuable for genetic investigations of simian immunodeficiency virus (SIV), for which it is the most abundant natural host species, and of a wide range of health-related phenotypes assessed in Caribbean vervets (C. a. sabaeus), whose numbers have expanded dramatically since Europeans introduced small numbers of their ancestors from West Africa during the colonial era. We use the reference to characterize the genomic relationship between vervets and other primates, the intra-generic phylogeny of vervet subspecies, and genome-wide structural variations of a pedigreed C. a. sabaeus population. Through comparative analyses with human and rhesus macaque, we characterize at high resolution the unique chromosomal fission events that differentiate the vervets and their close relatives from most other catarrhine primates, in whom karyotype is highly conserved. We also provide a summary of transposable elements and contrast these with the rhesus macaque and human. Analysis of sequenced genomes representing each of the main vervet subspecies supports previously hypothesized relationships between these populations, which range across most of sub-Saharan Africa, while uncovering high levels of genetic diversity within each. Sequence-based analyses of major histocompatibility complex (MHC) polymorphisms reveal extremely low diversity in Caribbean C. a. sabaeus vervets, compared to vervets from putatively ancestral West African regions. In the C. a. sabaeus research population, we discover the first structural variations that are, in some cases, predicted to have a deleterious effect; future studies will determine the phenotypic impact of these variations.ca
• dc.description.sponsorship Funding to R.K.W. was provided by NIH-NHGRI grant 5U54HG00307907. Support for the Vervet Research Colony was provided by NIH grant RR019963/OD010965 to J.R.K. Funding to N.B.F. was provided by NIH grants R01RR016300 and R01OD010980. The French National Agency for Research on AIDS and Viral Hepatitis (ANRS) provided funding to M.C.M.-T. Funding to M.R. and R.S. was provided by the Ministero della Universita’ e della Ricerca. Funding to K.D. was provided by Genome Canada and Genome Quebec. B.A. and R.N. acknowledge upport from the Wellcome Trust (grant number WT095908) and the European Molecular Biology Laboratory.
• dc.format.mimetype application/pdfca
• dc.identifier.citation Warren WC, Jasinska AJ, García-Pérez R, Svardal H, Tomlinson C, Rocchi M et al. The genome of the vervet (Chlorocebus aethiops sabaeus). Genome Research. 2015; 25(12): 1921-1933. DOI 10.1101/gr.192922.115ca
• dc.identifier.doi http://dx.doi.org/10.1101/gr.192922.115
• dc.identifier.issn 1088-9051
• dc.identifier.uri http://hdl.handle.net/10230/25928
• dc.language.iso engca
• dc.publisher Cold Spring Harbor Laboratory Press (CSHL Press)ca
• dc.relation.ispartof Genome Research. 2015; 25(12): 1921-1933
• dc.rights © 2015 Warren et al. This article is distributed exclusively by Cold Spring Harbor Laboratory Press for the first six months after the full-issue publication date (see http://genome.cshlp.org/site/misc/terms.xhtml). After six months, it is available under a Creative Commons License (Attribution-NonCommercial 4.0 International), as described at http://creativecommons.org/licenses/by-nc/4.0/.ca
• dc.rights.accessRights info:eu-repo/semantics/openAccess
• dc.rights.uri http://creativecommons.org/licenses/by-nc/4.0/ca
• dc.subject.other Simisca
• dc.subject.other Genètica animalca
• dc.title The genome of the vervet (Chlorocebus aethiops sabaeus)ca
• dc.type info:eu-repo/semantics/articleca
• dc.type.version info:eu-repo/semantics/publishedVersionca