The genome of the vervet (Chlorocebus æthiops sabæus)

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.