Endogenous retroviruses (ERV) are LTR retrotransposons derived from ancient retroviral infections. In small ruminants, unlike in most species, an ERV family coexists with its exogenous counterparts. Apart from this family, no comprehensive study has been carried out on sheep and goat ERVs, and their co-evolutionary history with their host genomes remains largely unknown. 

In this study, we characterized 23 class I and II ERV families across four reference assemblies of domestic and wild sheep and goats, as well as one cattle assembly. Among these families, 15 were found to be shared among all ruminants, 6 were exclusive to small ruminants and 2 to cattle. The presence of these families has been assessed in other ruminant species, revealing different integration events before the Bovidae speciation 17 million years ago and more recently from 6 to 14 million years ago.

Between 0.5 to 1 % of small ruminant genomes were annotated as ERVs. Although class I ERVs showed comparable profiles between species, contrasting evolutionary dynamics were identified for class II ERVs. A prevalent family in the cattle genome, family-1, were only present as relics in small ruminants. Two other class II families designated as families-3 and -5, showed more abundant and conserved copies exclusively in domestic goat. Notably, family-5 is the family closely related to circulating exogenous retroviruses and was identified with 22 copies featuring fully identical LTRs and 7 having complete coding capacities. These findings collectively suggest that transposition and endogenization events may still be occurring in the domestic goat genome.

This study is the first comparative analysis of small ruminant ERVs and revealed that ERV families were shared among species but with lineage-specific insertion dynamics. Thus, small ruminants offer an incomparable model to compare the factors implicated in ERVs' expansion and decline across genomes.