Evolution of endogenous retroviruses (ERVs) in the Bovinae subfamily

Endogenous retroviruses (ERVs) are remnants of ancient viral infections that have integrated into host genomes, significantly influencing genome evolution, adaptation, and disease. This study employed a genome-wide screening protocol to analyze 49 genomes, covering 17 species within the Bovinae subfamily, including 25 cattle genomes and 7 buffalo genomes. The identification of ERVs primarily employed RepeatModeler. To gauge ERV activity, Kimura divergence was applied, and PCR genotyping validated insertion polymorphisms across 12 international breeds, shedding light on the activity of selected potential ERVs. Intersection analyses mapped ERV integration in protein-coding (PC) and long noncoding RNA (lncRNA) genes. A total of 22 distinct ERV groups were identified, consisting of 20 beta-retroviruses (Class II) and two gamma-retroviruses (Class I). Notably, the abundance of ERVs varied significantly, with Bubalus bubalis (buffalo) housing 838 ERVs compared to 575 in Bos taurus (cattle). Five ERV groups showed recent activity (Kimura divergence < 5 %), and PCR genotyping revealed breed-specific polymorphisms in both cattle and buffalo, suggesting ongoing retroviral influence. Buffalo genomes demonstrated 33 % more ERV integrations than cattle, with ERVs enriched in PC (23.62-33.44 %) and lncRNA genes (24.34-30.76 %). Phylogenetic analysis traced the origins of these ERVs to approximately 15.89 million years ago, coinciding with the diversification of the Bovinae subfamily. While ERVs were depleted in transcribed regions likely due to purifying selection, they were enriched at regulatory loci, indicating their role in shaping host gene networks. Additionally, analysis of transposable elements (TEs) showed that LINEs are predominant in species such as Tragelaphus eurycerus (30.78 %), while SINEs varied, with Bubalus depressicornis at 7.78 % and Tragelaphus imberbis at 6.05 %. DNA transposons were present at 1.39 % in T. imberbis and 1.90 % in B. depressicornis. Species with higher non-repetitive DNA content, like T. buxtoni (68.72 %) and T. eurycerus (54.13 %), exhibited lower LINE abundance.