The genome of the vervet (Chlorocebus æthiops sabæus)

Wesley C. Warren, Anna J. Jasinska, Raquel García-Pérez, Hannes Svardal, Chad Tomlinson, Mariano Rocchi, Nicoletta Archidiacono, Oronzo Capozzi, Patrick Minx, Michæl J. Montague, Kim Kyung, La Deana W. Hillier, Milinn Kremitzki, Tina Graves, Colby Chiang, Jennifer Hughes, Nam Tran, Yu Huang, Vasily Ramensky, Oi Wa ChoiYoon J. Jung, Christopher A. Schmitt, Nikoleta Juretic, Jessica Wasserscheid, Trudy R. Turner, Roger W. Wiseman, Jennifer J. Tuscher, Julie A. Karl, Jörn E. Schmitz, Roland Zahn, David H. O'Connor, Eugene Redmond, Alex Nisbett, Béatrice Jacquelin, Michæla C. Müller-Trutwin, Jason M. Brenchley, Michel Dione, Martin Antonio, Gary P. Schroth, Jay R. Kaplan, Matthew J. Jorgensen, Gregg W.C. Thomas, Matthew W. Hahn, Brian J. Raney, Bronwen Aken, Rishi Nag, Juergen Schmitz, Gennady Churakov, Angela Noll, Roscoe Stanyon, David Webb, Francoise Thibaud-Nissen, Magnus Nordborg, Tomas Marques-Bonet, Ken Dewar, George M. Weinstock, Richard K. Wilson, Nelson B. Freimer

Research output: Contribution to journalArticle

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Abstract

We describe a genome reference of the African green monkey or vervet (Chlorocebus æthiops). 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. sabæus), whose numbers have expanded dramatically since Europeans introduced small numbers of their ancestors fromWest Africa during the colonial era. Weuse 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. sabæus population. Through comparative analyses withhuman and rhesus macaque,wecharacterize at high resolution the unique chromosomal fission events that differentiate the vervets and their close relatives frommost 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. sabæus vervets, comparedto vervets fromputatively ancestral West African regions. In the C. a. sabæus 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.

Original languageEnglish
Pages (from-to)1921-1933
Number of pages13
JournalGenome research
Volume25
Issue number12
DOIs
StatePublished - Dec 2015

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    Warren, W. C., Jasinska, A. J., García-Pérez, R., Svardal, H., Tomlinson, C., Rocchi, M., Archidiacono, N., Capozzi, O., Minx, P., Montague, M. J., Kyung, K., Hillier, L. D. W., Kremitzki, M., Graves, T., Chiang, C., Hughes, J., Tran, N., Huang, Y., Ramensky, V., ... Freimer, N. B. (2015). The genome of the vervet (Chlorocebus æthiops sabæus). Genome research, 25(12), 1921-1933. https://doi.org/10.1101/gr.192922.115