title: The genome of the vervet (Chlorocebus aethiops sabaeus).
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.
authors.affiliation: The Genome Institute, Washington University School of Medicine, St. Louis, Missouri 63108, USA;
authors.forename: Wesley C
authors.initials: WC
authors.lastname: Warren
authors.affiliation: Center for Neurobehavioral Genetics, Semel Institute for Neuroscience and Human Behavior, University of California Los Angeles, Los Angeles, California 90095, USA; Institute of Bioorganic Chemistry, Polish Academy of Sciences, 61-704 Poznan, Poland;
authors.forename: Anna J
authors.initials: AJ
authors.lastname: Jasinska
authors.affiliation: ICREA at Institut de Biologia Evolutiva, (UPF-CSIC) and Centro Nacional de Analisis Genomico (CNAG), PRBB/PCB, 08003 Barcelona, Spain;
authors.forename: Raquel
authors.initials: R
authors.lastname: García-Pérez
authors.affiliation: Gregor Mendel Institute, Austrian Academy of Sciences, Vienna Biocenter (VBC), 1030 Vienna, Austria;
authors.forename: Hannes
authors.initials: H
authors.lastname: Svardal
authors.affiliation: The Genome Institute, Washington University School of Medicine, St. Louis, Missouri 63108, USA;
authors.forename: Chad
authors.initials: C
authors.lastname: Tomlinson
authors.affiliation: Department of Biology, University of Bari, Bari 70126, Italy;
authors.forename: Mariano
authors.initials: M
authors.lastname: Rocchi
authors.affiliation: Department of Biology, University of Bari, Bari 70126, Italy;
authors.forename: Nicoletta
authors.initials: N
authors.lastname: Archidiacono
authors.affiliation: Department of Biology, University of Bari, Bari 70126, Italy;
authors.forename: Oronzo
authors.initials: O
authors.lastname: Capozzi
authors.affiliation: The Genome Institute, Washington University School of Medicine, St. Louis, Missouri 63108, USA;
authors.forename: Patrick
authors.initials: P
authors.lastname: Minx
authors.affiliation: The Genome Institute, Washington University School of Medicine, St. Louis, Missouri 63108, USA;
authors.forename: Michael J
authors.initials: MJ
authors.lastname: Montague
authors.affiliation: The Genome Institute, Washington University School of Medicine, St. Louis, Missouri 63108, USA;
authors.forename: Kim
authors.initials: K
authors.lastname: Kyung
authors.affiliation: The Genome Institute, Washington University School of Medicine, St. Louis, Missouri 63108, USA;
authors.forename: LaDeana W
authors.initials: LW
authors.lastname: Hillier
authors.affiliation: The Genome Institute, Washington University School of Medicine, St. Louis, Missouri 63108, USA;
authors.forename: Milinn
authors.initials: M
authors.lastname: Kremitzki
authors.affiliation: The Genome Institute, Washington University School of Medicine, St. Louis, Missouri 63108, USA;
authors.forename: Tina
authors.initials: T
authors.lastname: Graves
authors.affiliation: The Genome Institute, Washington University School of Medicine, St. Louis, Missouri 63108, USA;
authors.forename: Colby
authors.initials: C
authors.lastname: Chiang
authors.affiliation: Whitehead Institute, Cambridge, Massachusetts 02142, USA;
authors.forename: Jennifer
authors.initials: J
authors.lastname: Hughes
authors.affiliation: Center for Neurobehavioral Genetics, Semel Institute for Neuroscience and Human Behavior, University of California Los Angeles, Los Angeles, California 90095, USA;
authors.forename: Nam
authors.initials: N
authors.lastname: Tran
authors.affiliation: Center for Neurobehavioral Genetics, Semel Institute for Neuroscience and Human Behavior, University of California Los Angeles, Los Angeles, California 90095, USA;
authors.forename: Yu
authors.initials: Y
authors.lastname: Huang
authors.affiliation: Center for Neurobehavioral Genetics, Semel Institute for Neuroscience and Human Behavior, University of California Los Angeles, Los Angeles, California 90095, USA;
authors.forename: Vasily
authors.initials: V
authors.lastname: Ramensky
authors.affiliation: Center for Neurobehavioral Genetics, Semel Institute for Neuroscience and Human Behavior, University of California Los Angeles, Los Angeles, California 90095, USA;
authors.forename: Oi-Wa
authors.initials: OW
authors.lastname: Choi
authors.affiliation: Center for Neurobehavioral Genetics, Semel Institute for Neuroscience and Human Behavior, University of California Los Angeles, Los Angeles, California 90095, USA;
authors.forename: Yoon J
authors.initials: YJ
authors.lastname: Jung
authors.affiliation: Center for Neurobehavioral Genetics, Semel Institute for Neuroscience and Human Behavior, University of California Los Angeles, Los Angeles, California 90095, USA;
authors.forename: Christopher A
authors.initials: CA
authors.lastname: Schmitt
authors.affiliation: Department of Human Genetics, McGill University, Montreal QC H3A 1B1, Canada;
authors.forename: Nikoleta
authors.initials: N
authors.lastname: Juretic
authors.affiliation: Department of Human Genetics, McGill University, Montreal QC H3A 1B1, Canada;
authors.forename: Jessica
authors.initials: J
authors.lastname: Wasserscheid
authors.affiliation: Department of Anthropology, University of Wisconsin-Milwaukee, Milwaukee, Wisconsin 53705, USA; Department of Genetics Faculty of Natural and Agricultural Sciences, University of the Free State, Bloemfontein, 9300 South Africa;
authors.forename: Trudy R
authors.initials: TR
authors.lastname: Turner
authors.affiliation: Department of Laboratory Medicine and Pathology, University of Wisconsin-Madison, Madison, Wisconsin 53705, USA;
authors.forename: Roger W
authors.initials: RW
authors.lastname: Wiseman
authors.affiliation: Department of Laboratory Medicine and Pathology, University of Wisconsin-Madison, Madison, Wisconsin 53705, USA;
authors.forename: Jennifer J
authors.initials: JJ
authors.lastname: Tuscher
authors.affiliation: Department of Laboratory Medicine and Pathology, University of Wisconsin-Madison, Madison, Wisconsin 53705, USA;
authors.forename: Julie A
authors.initials: JA
authors.lastname: Karl
authors.affiliation: Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Boston, Massachusetts 02115, USA;
authors.forename: Jörn E
authors.initials: JE
authors.lastname: Schmitz
authors.affiliation: Crucell Holland B.V., 2333 CN Leiden, The Netherlands;
authors.forename: Roland
authors.initials: R
authors.lastname: Zahn
authors.affiliation: Department of Laboratory Medicine and Pathology, University of Wisconsin-Madison, Madison, Wisconsin 53705, USA;
authors.forename: David H
authors.initials: DH
authors.lastname: O'Connor
authors.affiliation: St. Kitts Biomedical Research Foundation, St. Kitts, West Indies;
authors.forename: Eugene
authors.initials: E
authors.lastname: Redmond
authors.affiliation: St. Kitts Biomedical Research Foundation, St. Kitts, West Indies;
authors.forename: Alex
authors.initials: A
authors.lastname: Nisbett
authors.affiliation: Institut Pasteur, Unité de Régulation des Infections Rétrovirales, 75015 Paris, France;
authors.forename: Béatrice
authors.initials: B
authors.lastname: Jacquelin
authors.affiliation: Institut Pasteur, Unité de Régulation des Infections Rétrovirales, 75015 Paris, France;
authors.forename: Michaela C
authors.initials: MC
authors.lastname: Müller-Trutwin
authors.affiliation: National Institute of Allergy and Infectious Diseases (NIAID), NIH, Bethesda, Maryland 20892-9821, USA;
authors.forename: Jason M
authors.initials: JM
authors.lastname: Brenchley
authors.affiliation: Medical Research Council, Fajara, The Gambia;
authors.forename: Michel
authors.initials: M
authors.lastname: Dione
authors.affiliation: Medical Research Council, Fajara, The Gambia;
authors.forename: Martin
authors.initials: M
authors.lastname: Antonio
authors.affiliation: Illumina Inc., San Diego, California 92122, USA;
authors.forename: Gary P
authors.initials: GP
authors.lastname: Schroth
authors.affiliation: Center for Comparative Medicine Research, Wake Forest School of Medicine, Winston-Salem 27157-1040, USA;
authors.forename: Jay R
authors.initials: JR
authors.lastname: Kaplan
authors.affiliation: Center for Comparative Medicine Research, Wake Forest School of Medicine, Winston-Salem 27157-1040, USA;
authors.forename: Matthew J
authors.initials: MJ
authors.lastname: Jorgensen
authors.affiliation: Department of Biology, Indiana University, Bloomington, Indiana 47405, USA;
authors.forename: Gregg W C
authors.initials: GW
authors.lastname: Thomas
authors.affiliation: Department of Biology, Indiana University, Bloomington, Indiana 47405, USA;
authors.forename: Matthew W
authors.initials: MW
authors.lastname: Hahn
authors.affiliation: University of California Santa Cruz, Santa Cruz, California 95060, USA;
authors.forename: Brian J
authors.initials: BJ
authors.lastname: Raney
authors.affiliation: European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SD, United Kingdom;
authors.forename: Bronwen
authors.initials: B
authors.lastname: Aken
authors.affiliation: European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SD, United Kingdom;
authors.forename: Rishi
authors.initials: R
authors.lastname: Nag
authors.affiliation: Institute of Experimental Pathology (ZMBE), University of Münster, 48149 Münster, Germany;
authors.forename: Juergen
authors.initials: J
authors.lastname: Schmitz
authors.affiliation: Institute of Experimental Pathology (ZMBE), University of Münster, 48149 Münster, Germany; Institute for Evolution and Biodiversity, University of Münster, 48149 Münster, Germany;
authors.forename: Gennady
authors.initials: G
authors.lastname: Churakov
authors.affiliation: Institute of Experimental Pathology (ZMBE), University of Münster, 48149 Münster, Germany;
authors.forename: Angela
authors.initials: A
authors.lastname: Noll
authors.affiliation: Department of Biology, University of Florence, 50122 Florence, Italy;
authors.forename: Roscoe
authors.initials: R
authors.lastname: Stanyon
authors.affiliation: National Center for Biotechnology Information, Bethesda, Maryland 20894, USA;
authors.forename: David
authors.initials: D
authors.lastname: Webb
authors.affiliation: National Center for Biotechnology Information, Bethesda, Maryland 20894, USA;
authors.forename: Francoise
authors.initials: F
authors.lastname: Thibaud-Nissen
authors.affiliation: Gregor Mendel Institute, Austrian Academy of Sciences, Vienna Biocenter (VBC), 1030 Vienna, Austria;
authors.forename: Magnus
authors.initials: M
authors.lastname: Nordborg
authors.affiliation: ICREA at Institut de Biologia Evolutiva, (UPF-CSIC) and Centro Nacional de Analisis Genomico (CNAG), PRBB/PCB, 08003 Barcelona, Spain;
authors.forename: Tomas
authors.initials: T
authors.lastname: Marques-Bonet
authors.affiliation: Department of Human Genetics, McGill University, Montreal QC H3A 1B1, Canada;
authors.forename: Ken
authors.initials: K
authors.lastname: Dewar
authors.affiliation: The Jackson Laboratory for Genomic Medicine, Farmington, Connecticut 06001, USA.
authors.forename: George M
authors.initials: GM
authors.lastname: Weinstock
authors.affiliation: The Genome Institute, Washington University School of Medicine, St. Louis, Missouri 63108, USA;
authors.forename: Richard K
authors.initials: RK
authors.lastname: Wilson
authors.affiliation: Center for Neurobehavioral Genetics, Semel Institute for Neuroscience and Human Behavior, University of California Los Angeles, Los Angeles, California 90095, USA;
authors.forename: Nelson B
authors.initials: NB
authors.lastname: Freimer
mesh_terms: D000818:Animals; D002522:Chlorocebus aethiops / Q000145:classification / Q000235:genetics*; D020223:Chromosome Painting; D019295:Computational Biology / Q000379:methods; D019143:Evolution, Molecular; D015321:Gene Rearrangement; D014644:Genetic Variation; D016678:Genome; D023281:Genomics / Q000379:methods; D059785:Karyotype; D008285:Major Histocompatibility Complex / Q000235:genetics; D058977:Molecular Sequence Annotation; D010802:Phylogeny; D058974:Phylogeography