Endogenous retroviruses in livestock and poultry: From genomic invaders to beneficial allies.

Endogenous retroviruses (ERVs), the genomic remnants of ancient retroviral infections, constitute a significant and dynamic component of livestock and poultry genomes. This review synthesizes current knowledge on the dual roles of ERVs, from drivers of genomic instability and disease to essential agents of evolution and innovation in domesticated species. We detail the classification, structure, and life cycle of ERVs, highlighting the distinct genomic landscapes and host-silencing strategies that differentiate avian and mammalian lineages, with poultry genomes maintaining lower ERV loads through persistent repression compared to livestock. A critical examination reveals the "dark side" of ERVs, including their capacity for insertional mutagenesis, contribution to diseases like avian leukosis, and zoonotic risks, exemplified by porcine endogenous retroviruses (PERVs). Conversely, we talk over how ERVs have been harnessed as allies, where their insertions create structural variants that shape economically vital traits-such as metabolism, growth, and unique phenotypes-and where domesticated viral genes support crucial functions like placental development and innate immunity. Finally, we discuss the transformative potential of CRISPR-Cas9 genome editing as a precise tool for silencing hazardous ERVs and exploiting their beneficial aspects. A comprehensive understanding of ERV biology is thus pivotal for advancing genetic improvement, disease resistance, and the sustainability of livestock and poultry production systems.