Dataset Information

The genome of the vervet (Chlorocebus aethiops sabaeus).

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.

SUBMITTER: Warren WC

PROVIDER: S-EPMC4665013 | biostudies-literature | 2015 Dec

REPOSITORIES: biostudies-literature

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The genome of the vervet (Chlorocebus aethiops sabaeus).

Warren Wesley C WC Jasinska Anna J AJ García-Pérez Raquel R Svardal Hannes H Tomlinson Chad C Rocchi Mariano M Archidiacono Nicoletta N Capozzi Oronzo O Minx Patrick P Montague Michael J MJ Kyung Kim K Hillier LaDeana W LW Kremitzki Milinn M Graves Tina T Chiang Colby C Hughes Jennifer J Tran Nam N Huang Yu Y Ramensky Vasily V Choi Oi-Wa OW Jung Yoon J YJ Schmitt Christopher A CA Juretic Nikoleta N Wasserscheid Jessica J Turner Trudy R TR Wiseman Roger W RW Tuscher Jennifer J JJ Karl Julie A JA Schmitz Jörn E JE Zahn Roland R O'Connor David H DH Redmond Eugene E Nisbett Alex A Jacquelin Béatrice B Müller-Trutwin Michaela C MC Brenchley Jason M JM Dione Michel M Antonio Martin M Schroth Gary P GP Kaplan Jay R JR Jorgensen Matthew J MJ Thomas Gregg W C GW Hahn Matthew W MW Raney Brian J BJ Aken Bronwen B Nag Rishi R Schmitz Juergen J Churakov Gennady G Noll Angela A Stanyon Roscoe R Webb David D Thibaud-Nissen Francoise F Nordborg Magnus M Marques-Bonet Tomas T Dewar Ken K Weinstock George M GM Wilson Richard K RK Freimer Nelson B NB

Genome research 20150916 12

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 Af ...[more]

PMID: 26377836

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Project description:OBJECTIVE:In humans, the ontogeny of obesity throughout the life course and the genetics underlying it has been historically difficult to study. We compared, in a non-human primate model, the lifelong growth trajectories of obese and non-obese adults to assess the heritability of and map potential genomic regions implicated in growth and obesity. STUDY POPULATION:A total of 905 African green monkeys, or vervets (Chlorocebus aethiops sabaeus) (472 females, 433 males) from a pedigreed captive colony. METHODS:We measured fasted body weight (BW), crown-to-rump length (CRL), body-mass index (BMI) and waist circumference (WC) from 2000 to 2015. We used a longitudinal clustering algorithm to detect obesogenic growth, and logistic growth curves implemented in nonlinear mixed effects models to estimate three growth parameters. We used maximum likelihood variance decomposition methods to estimate the genetic contributions to obesity-related traits and growth parameters, including a test for the effects of a calorie-restricted dietary intervention. We used multipoint linkage analysis to map implicated genomic regions. RESULTS:All measurements were significantly influenced by sex, and with the exception of WC, also influenced by maternal and post-natal diet. Chronic obesity outcomes were significantly associated with a pattern of extended growth duration with slow growth rates for BW. After accounting for environmental influences, all measurements were found to have a significant genetic component to variability. Linkage analysis revealed several regions suggested to be linked to obesity-related traits that are also implicated in human obesity and metabolic disorders. CONCLUSIONS:As in humans, growth patterns in vervets have a significant impact on adult obesity and are largely under genetic control with some evidence for maternal and dietary programming. These results largely mirror findings from human research, but reflect shorter developmental periods, suggesting that the vervet offers a strong genetic model for elucidating the ontogeny of human obesity.

Dataset Information

The genome of the vervet (Chlorocebus aethiops sabaeus).

Publications

The genome of the vervet (Chlorocebus aethiops sabaeus).

Similar Datasets

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