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The genome of the vervet ( Chlorocebus aethiops sabaeus )

Wesley Warren 1, * Anna Jasinska 2, 3 Raquel García-Pérez 4, 5 Hannes Svardal 6 Chad Tomlinson 1 Mariano Rocchi 7 Nicoletta Archidiacono 7 Oronzo Capozzi 7 Patrick Minx 1 Michael Montague 1 Kim Kyung 1 Ladeana 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 Jung 2 Christopher Schmitt 2 Nikoleta Juretic 9 Jessica Wasserscheid 9 Trudy Turner 10, 11 Roger Wiseman 12 Jennifer Tuscher 12 Julie Karl 12 Jörn Schmitz 13 Roland Zahn 14 David O'Connor 12 Eugene Redmond 15 Alex Nisbett 15 Béatrice Jacquelin 16 Michaela Muller-Trutwin 16 Jason Brenchley 17 Michel Dione 18 Martin Antonio 18 Gary Schroth 19 Jay Kaplan 20 Matthew Jorgensen 20 Gregg Thomas 21 Matthew Hahn 21 Brian Raney 22 Bronwen Aken 23 Rishi Nag 23 Juergen 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 Weinstock 28 Richard Wilson 1 Nelson Freimer 2
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.
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Wesley Warren, Anna Jasinska, Raquel García-Pérez, Hannes Svardal, Chad Tomlinson, et al.. The genome of the vervet ( Chlorocebus aethiops sabaeus ). Genome Research, Cold Spring Harbor Laboratory Press, 2015, 25 (12), pp.1921-1933. ⟨10.1101/gr.192922.115⟩. ⟨pasteur-01960687⟩

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