Detection and characterization of endogenous retroviruses in the horse genome by in silico analysis

Endogenous retroviruses (ERVs) are proviral phases of exogenous retroviruses that have become incorporated into the host genome. Little is known about ERVs in the horse genome. By combining 3 bioinformatic approaches, we detected 1947 putative ERVs in the horse genome. These equine ERVs are not scattered randomly across the genome and are especially abundant in the X chromosome. Based on phylogenetic relationships, some of these equine ERVs were classified into 15 previously uncharacterized families of Classes I, II and III. Compared with the cow and other species, the horse genome appears to container fewer ERVs. Although this could be due to limitations of the detection process, it could also stem from characteristics of the horse genome or the effect of the domestication process.

► 1947 putative equine endogenous retroviruses were detected combining 3 approaches.
► Equine endogenous retroviruses were not distributed randomly across the genome.
► Equine endogenous retroviruses were clustered in 15 families of Class I, II or III.
► Compared with other animal genomes, the horse genome appears to contain fewer ERVs.