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Genome Res. 2015 Dec;25(12):1921-33. doi: 10.1101/gr.192922.115. Epub 2015 Sep 16.

The genome of the vervet (Chlorocebus aethiops sabaeus).

Author information

1
The Genome Institute, Washington University School of Medicine, St. Louis, Missouri 63108, USA;
2
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;
3
ICREA at Institut de Biologia Evolutiva, (UPF-CSIC) and Centro Nacional de Analisis Genomico (CNAG), PRBB/PCB, 08003 Barcelona, Spain;
4
Gregor Mendel Institute, Austrian Academy of Sciences, Vienna Biocenter (VBC), 1030 Vienna, Austria;
5
Department of Biology, University of Bari, Bari 70126, Italy;
6
Whitehead Institute, Cambridge, Massachusetts 02142, USA;
7
Center for Neurobehavioral Genetics, Semel Institute for Neuroscience and Human Behavior, University of California Los Angeles, Los Angeles, California 90095, USA;
8
Department of Human Genetics, McGill University, Montreal QC H3A 1B1, Canada;
9
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;
10
Department of Laboratory Medicine and Pathology, University of Wisconsin-Madison, Madison, Wisconsin 53705, USA;
11
Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Boston, Massachusetts 02115, USA;
12
Crucell Holland B.V., 2333 CN Leiden, The Netherlands;
13
St. Kitts Biomedical Research Foundation, St. Kitts, West Indies;
14
Institut Pasteur, Unité de Régulation des Infections Rétrovirales, 75015 Paris, France;
15
National Institute of Allergy and Infectious Diseases (NIAID), NIH, Bethesda, Maryland 20892-9821, USA;
16
Medical Research Council, Fajara, The Gambia;
17
Illumina Inc., San Diego, California 92122, USA;
18
Center for Comparative Medicine Research, Wake Forest School of Medicine, Winston-Salem 27157-1040, USA;
19
Department of Biology, Indiana University, Bloomington, Indiana 47405, USA;
20
University of California Santa Cruz, Santa Cruz, California 95060, USA;
21
European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SD, United Kingdom;
22
Institute of Experimental Pathology (ZMBE), University of Münster, 48149 Münster, Germany;
23
Institute of Experimental Pathology (ZMBE), University of Münster, 48149 Münster, Germany; Institute for Evolution and Biodiversity, University of Münster, 48149 Münster, Germany;
24
Department of Biology, University of Florence, 50122 Florence, Italy;
25
National Center for Biotechnology Information, Bethesda, Maryland 20894, USA;
26
The Jackson Laboratory for Genomic Medicine, Farmington, Connecticut 06001, USA.

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.

PMID:
26377836
PMCID:
PMC4665013
DOI:
10.1101/gr.192922.115
[Indexed for MEDLINE]
Free PMC Article

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