Genome-wide characterization of endogenous retroviral envelope genes across primate lineages reveals evolutionary diversity and recombination

Endogenous Retroviruses (ERVs) are remnants of ancient germline infections by now extinct exogenous retroviruses and constitute a substantial fraction of vertebrate genomes, serving as “fossil” records for the ancestral retroviral diversity and evolution. Among ERV genes, the characterization of env gene is particularly informative to understand ERVs’ evolutionary trajectory and infer their potential physiological/pathological role. However, detailed characterization has been performed for few domesticated env genes, while a comprehensive survey of their abundance and diversity among primates’ genomes is still lacking. Here, we reconstructed 32 representative Env consensus sequences from Class I, II, and III human ERVs and used them to screen 55 primate species across the Catarrhini and Platyrrhini parvorders. Similarity-based search, phylogenetic analysis, and recombination events detection revealed ERV diversification and broad distribution. Notably, we identified and extensively characterized in detail the presence of the HERV-K supergroup in the Platyrrhini parvorder, indicating initiation of its spread > 40 million years ago. Furthermore, we confirmed inter- and intra-class env recombination events, frequently involving LTR insertions within env coding regions, confirming the phenomenon of “ env snatching” among primates’ ERVs and domain disruption. Overall, our findings highlight the value of Env reconstruction for investigating ERV evolution and expands our current understanding of retroviral diversification, recombination dynamics, and primate genome evolution.