Exploring endogenous retroviruses in ruminant genomes: They might not be all dead after all

International audience

English. Endogenous retroviruses (ERVs) are traces of ancestral retroviral infections, constituting an important portion of mammalian genomes and playing crucial roles in host evolution. Some ERVs have retained their coding capacities, enabling them to act as active transposable elements, capable of duplicating within host genomes and influencing genomic architecture. Despite their extensive research in human genomics, ERVs remain understudied in livestock species, notably in ruminants. Using de novo repeat identification approaches, we charac- terized ERV elements belonging to 24 families across reference assemblies of domestic and wild sheep and goats, and cattle. Among these families, 13 were shared across the five analyzed species, eight were exclusive to small ruminants and three to cattle. The evolu- tionary origin of these families was traced by identifying similar elements in other ruminant genomes and revealed multiple endogenization events over the last 40 million years. A high- resolution annotation of 100,534 ERV insertions was generated, representing 0.5 to 1% of the ruminant genomes. The number of copies varied among ERV families and between species, with a significantly higher number of copies from two specific families in the domestic goat. Population-level analyses of over a hundred domestic goat genomes from 37 different breeds, revealed an abundance of low-frequency copies from these two families, indicative of recent insertions. Whereas the youngest family includes insertions with complete coding capacities and is closely related to oncogenic circulating exogenous oncogenic retroviruses circulating in small ruminants; the second family displays uncomplete elements; suggesting different duplication mechanisms associated to a potential ongoing endogenization. These findings demonstrate recent transpositional activity of ERV copies in the domestic goat genome and highlight distinct ERV evolutionary dynamics among ruminant species. This study under- scores the significance of ERVs as models for understanding species evolution and host-virus interactions and calls for further research into their impact on the genomic landscapes of livestock species.