RT Journal
A1 Warren, Wesley C.
A1 Jasinska, Anna J.
A1 García-Pérez, Raquel
A1 Svardal, Hannes
A1 Tomlinson, Chad
A1 Rocchi, Mariano
A1 Archidiacono, Nicoletta
A1 Capozzi, Oronzo
A1 Minx, Patrick
A1 Montague, Michael J.
A1 Kyung, Kim
A1 Hillier, LaDeana W.
A1 Kremitzki, Milinn
A1 Graves, Tina
A1 Chiang, Colby
A1 Hughes, Jennifer
A1 Tran, Nam
A1 Huang, Yu
A1 Ramensky, Vasily
A1 Choi, Oi-wa
A1 Jung, Yoon J.
A1 Schmitt, Christopher A.
A1 Juretic, Nikoleta
A1 Wasserscheid, Jessica
A1 Turner, Trudy R.
A1 Wiseman, Roger W.
A1 Tuscher, Jennifer J.
A1 Karl, Julie A.
A1 Schmitz, Jörn E.
A1 Zahn, Roland
A1 O'Connor, David H.
A1 Redmond, Eugene
A1 Nisbett, Alex
A1 Jacquelin, Béatrice
A1 Müller-Trutwin, Michaela C.
A1 Brenchley, Jason M.
A1 Dione, Michel
A1 Antonio, Martin
A1 Schroth, Gary P.
A1 Kaplan, Jay R.
A1 Jorgensen, Matthew J.
A1 Thomas, Gregg W.C.
A1 Hahn, Matthew W.
A1 Raney, Brian J.
A1 Aken, Bronwen
A1 Nag, Rishi
A1 Schmitz, Juergen
A1 Churakov, Gennady
A1 Noll, Angela
A1 Stanyon, Roscoe
A1 Webb, David
A1 Thibaud-Nissen, Francoise
A1 Nordborg, Magnus
A1 Marques-Bonet, Tomas
A1 Dewar, Ken
A1 Weinstock, George M.
A1 Wilson, Richard K.
A1 Freimer, Nelson B.
T1 The genome of the vervet (Chlorocebus aethiops sabaeus)
JF Genome Research 
JO Genome Research 
YR 2015 
FD December 01 
VO 25 
IS 12 
SP 1921 
OP 1933 
DO 10.1101/gr.192922.115 
UL http://genome.cshlp.org/content/25/12/1921.abstract 
AB 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.