A comprehensive map of the bovine mobilome and their epigenetic regulation of mastitis.

Retrotransposons are major components of mammalian genomes, yet their genome-wide annotation and epigenetic regulation in cattle remain incompletely characterized. Here, we present a comprehensive annotation and integrative epigenomic analysis of major retrotransposon classes in the bovine genome, with emphasis on DNA methylation patterns and their potential roles in subclinical mastitis. Using a multi-step de novo pipeline, we identified and classified long interspersed nuclear elements (LINEs), short interspersed nuclear elements (SINEs), and endogenous retroviruses (ERVs) in the bovine reference genome, including three LINE families, seven SINE families, and 20 ERV families. Retrotransposons accounted for ~ 40% of the genome, with LINEs representing the largest fraction. Evolutionary analysis suggested that BosL1A1, BosSINEL, BosERV1, and BosERV16 are the most recently active families. DNA methylation profiles in milk somatic cells showed consistently high levels across retrotransposons, with widespread hypermethylation in cows with Staphylococcus aureus-induced subclinical mastitis. We identified 20,839 differentially methylated retrotransposons, 3,306 of which overlapped differentially expressed genes. Promoter- and exon-overlapping elements showed inverse correlations between methylation and gene expression, and enriched genes are involved in immune and transport pathways. These results provide a comprehensive bovine mobilome resource and indicate that retrotransposon methylation is associated with gene regulation and host responses to mastitis.