A novel endogenous retrovirus in slow lorises (Nycticebus) and its role in species identification

Abstract

Endogenous retroviruses (ERVs) are the result of an exogenous infectious retrovirus becoming integrated within the host genome through infection of germline cells. The majority of ERV research has been conducted on humans and other great apes, and research of them within other primates can provide unique insights. Screening the reference genomes of two endangered slow lorises, Nycticebus bengalensis and N. coucang, a novel ERV family (LERV1) was identified within their genomes with multiple loci represented by full length proviruses with varying levels of completeness and numerous solo LTRs (long-terminal repeats). Phylogenetic analysis of the genes of LERV1 indicates that it is a betaretrovirus most closely related to HERV-K, the most recently active retroviral family in the human genome. LERV1 is only found in Asian lorises and absent in all other primates. The remarkable similarity of the LERV1 loci between the two species of slow loris indicate that the current N. coucang reference genome may actually be a hybrid of the two species, or a N. bengalensis from a different population as the N. bengalensis reference genome. The similarity of LERV1 loci between the two reference genomes indicate that the two genomes belong to the same species rather than two distinct species, as currently labelled (further supported by mtDNA phylogenetic analysis). This study highlights that studying ERVs in cryptic species can be informative in species identification.