The genome of the vervet (Chlorocebus aethiops sabaeus)

  1. Nelson B. Freimer2
  1. 1The Genome Institute, Washington University School of Medicine, St. Louis, Missouri 63108, USA;
  2. 2Center for Neurobehavioral Genetics, Semel Institute for Neuroscience and Human Behavior, University of California Los Angeles, Los Angeles, California 90095, USA;
  3. 3Institute of Bioorganic Chemistry, Polish Academy of Sciences, 61-704 Poznan, Poland;
  4. 4ICREA at Institut de Biologia Evolutiva, (UPF-CSIC) and Centro Nacional de Analisis Genomico (CNAG), PRBB/PCB, 08003 Barcelona, Spain;
  5. 5Gregor Mendel Institute, Austrian Academy of Sciences, Vienna Biocenter (VBC), 1030 Vienna, Austria;
  6. 6Department of Biology, University of Bari, Bari 70126, Italy;
  7. 7Whitehead Institute, Cambridge, Massachusetts 02142, USA;
  8. 8Department of Human Genetics, McGill University, Montreal QC H3A 1B1, Canada;
  9. 9Department of Anthropology, University of Wisconsin-Milwaukee, Milwaukee, Wisconsin 53705, USA;
  10. 10Department of Genetics Faculty of Natural and Agricultural Sciences, University of the Free State, Bloemfontein, 9300 South Africa;
  11. 11Department of Laboratory Medicine and Pathology, University of Wisconsin-Madison, Madison, Wisconsin 53705, USA;
  12. 12Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Boston, Massachusetts 02115, USA;
  13. 13Crucell Holland B.V., 2333 CN Leiden, The Netherlands;
  14. 14St. Kitts Biomedical Research Foundation, St. Kitts, West Indies;
  15. 15Institut Pasteur, Unité de Régulation des Infections Rétrovirales, 75015 Paris, France;
  16. 16National Institute of Allergy and Infectious Diseases (NIAID), NIH, Bethesda, Maryland 20892-9821, USA;
  17. 17Medical Research Council, Fajara, The Gambia;
  18. 18Illumina Inc., San Diego, California 92122, USA;
  19. 19Center for Comparative Medicine Research, Wake Forest School of Medicine, Winston-Salem 27157-1040, USA;
  20. 20Department of Biology, Indiana University, Bloomington, Indiana 47405, USA;
  21. 21University of California Santa Cruz, Santa Cruz, California 95060, USA;
  22. 22European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SD, United Kingdom;
  23. 23Institute of Experimental Pathology (ZMBE), University of Münster, 48149 Münster, Germany;
  24. 24Institute for Evolution and Biodiversity, University of Münster, 48149 Münster, Germany;
  25. 25Department of Biology, University of Florence, 50122 Florence, Italy;
  26. 26National Center for Biotechnology Information, Bethesda, Maryland 20894, USA;
  27. 27The Jackson Laboratory for Genomic Medicine, Farmington, Connecticut 06001, USA
  1. Corresponding author: wwarren{at}genome.wustl.edu

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.

Footnotes

  • Received April 8, 2015.
  • Accepted September 10, 2015.

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/.

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  1. Published in Advance September 16, 2015, doi: 10.1101/gr.192922.115 Genome Res. 25: 1921-1933 © 2015 Warren et al.; Published by Cold Spring Harbor Laboratory Press

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