The genome of the vervet ( Chlorocebus aethiops sabaeus )

Wesley C Warren (1) , Anna J Jasinska (2, 3) , Raquel García-Pérez (4, 5) , Hannes Svardal (6) , Chad T Tomlinson (1) , Mariano Rocchi (7) , Nicoletta Archidiacono (7) , Oronzo Capozzi (7) , Patrick Minx (1) , Michael J Montague (1) , Kim Kyung (1) , Ladeana W Hillier (1) , Milinn Kremitzki (1) , Tina Graves (1) , Colby Chiang (1) , Jennifer Hughes (8) , Nam Tran (2) , Yu Huang (2) , Vasily Ramensky (2) , Oi-Wa Choi (2) , Yoon J Jung (2) , Christopher A Schmitt (2) , Nikoleta Juretic (9) , Jessica Wasserscheid (9) , Trudy R Turner (10, 11) , Roger W Wiseman (12) , Jennifer J Tuscher (12) , Julie A Karl (12) , Jörn E Schmitz (13) , Roland Zahn (14) , David O'Connor (12) , Eugene Redmond (15) , Alex Nisbett (15) , Béatrice Jacquelin (16) , Michaela Muller-Trutwin (16) , Jason M Brenchley (17) , Michel Dione (18) , Martin Antonio (18) , Gary P Schroth (19) , Jay R Kaplan (20) , Matthew J Jorgensen (20) , Gregg W.C Thomas (21) , Matthew W Hahn (21) , Brian J Raney (22) , Bronwen Aken (23) , Rishi Nag (23) , Juergen E Schmitz (24) , Gennady Churakov (24, 25) , Angela Noll (24) , Roscoe Stanyon (26) , David Webb (27) , Francoise Thibaud-Nissen (27) , Magnus Nordborg (6) , Tomas Marques-Bonet (4) , Ken Dewar (9) , George M Weinstock (28) , Richard E. Wilson (1) , Nelson B. Freimer (2)

1 MGI - The McDonnell Genome Institute
2 Semel Institute for Neuroscience and Human Behavior [Los Angeles, Ca]
3 Institute of Bioorganic Chemistry [Poznań]
4 ICREA - Institució Catalana de Recerca i Estudis Avançats = Catalan Institution for Research and Advanced Studies
5 CNAG - Centro Nacional de Analisis Genomico [Barcelona]
6 GMI - Gregor Mendel Institute of Molecular Plant Biology
7 UNIBA - Università degli studi di Bari Aldo Moro = University of Bari Aldo Moro
8 Whitehead Institute
9 McGill University = Université McGill [Montréal, Canada]
10 University of Wisconsin - Milwaukee
11 UFS - University of the Free State [South Africa]
12 University of Wisconsin-Madison
13 BIDMC - Beth Israel Deaconess Medical Center [Boston]
14 Crucell Holland B.V
15 St. Kitts Biomedical Research Foundation
16 Régulation des Infections Rétrovirales
17 NIAID-NIH - National Institute of Allergy and Infectious Diseases [Bethesda]
18 MRC - Medical Research Council Unit The Gambia
19 Illumina Incorporated [San Diego, CA, USA]
20 Wake Forest School of Medicine [Winston-Salem]
21 Indiana University [Bloomington]
22 UC Santa Cruz - University of California [Santa Cruz]
23 European Molecular Biology Laboratory [Hinxton]
24 ZMBE - Institute of Experimental Pathology
25 IEB - Institute for Evolution and Biodiversity
26 UniFI - Università degli Studi di Firenze = University of Florence = Université de Florence
27 NCBI - National Center for Biotechnology Information
28 JAX - The Jackson Laboratory [Bar Harbor]

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.

Domaines: Sciences du Vivant [q-bio]; Génétique; Génétique animale; Virologie; Sciences de l'environnement; Biodiversité; Evolution [q-bio.PE]; Biochimie, Biologie Moléculaire; Génomique, Transcriptomique et Protéomique [q-bio.GN]

Wesley C Warren, Anna J Jasinska, Raquel García-Pérez, Hannes Svardal, Chad T Tomlinson, et al.. The genome of the vervet ( Chlorocebus aethiops sabaeus ). Genome Research, 2015, 25 (12), pp.1921-1933. ⟨10.1101/gr.192922.115⟩. ⟨pasteur-01960687⟩