Discovery of endogenous retroviruses in the genome of the red panda ( Ailurus fulgens )

ABSTRACT Endogenous retroviruses (ERVs) are viral genomes that originate from the integration of exogenous retroviruses into host germ cells and can be stably inherited across generations. Despite being mostly incomplete and silent, several ERVs have been observed to play potential pathological roles in numerous diseases, including multiple sclerosis, rheumatoid arthritis, and notably, cancer. Research has revealed the presence of ERVs in the genomes of nearly all mammals. However, the distribution and diversity of these retroviral genes in the endangered red panda ( Ailurus fulgens ) remain largely unexplored. This study aimed to identify and characterize ERV sequences in the red panda genome using bioinformatic methods. The results revealed the presence of 11 ERV sequences in the red panda genome, among which 6 contain complete viral sequences with long terminal repeats (LTRs), indicating proviral structures. Furthermore, phylogenetic analysis based on crucial retroviral protein structures (GAG, POL, and ENV) showed that nine ERVs belonged to the Gammaretrovirus genus and two to the Betaretrovirus genus, suggesting stable clustering within their respective taxonomic groups. Notably, the red panda ERVs clustered with retroviral sequences from various hosts, including Muridae, Felidae, and Cervidae. LTR divergence dating indicated that the integration of these ERVs occurred after the divergence of their respective host lineages, providing strong evidence for cross-species transmission events. This study not only deepens our understanding of red panda ERV classification but also provides a more comprehensive foundation for analyzing cross-species transmission events in mammalian retroviral evolution and offers a new perspective on ERV diversity and evolutionary mechanisms. IMPORTANCE This study reports the discovery of complete endogenous retrovirus (ERV) sequences in the genome of the endangered red panda. We have annotated the genomic structures of these ERVs, which significantly enhance our understanding of their genetic composition and evolutionary history. Furthermore, by constructing host phylogenetic trees and performing LTR divergence dating, we identified trans-species transmission events of ERVs, shedding new light on the evolutionary interactions between ERVs and their hosts. These findings contribute to a broader understanding of microbial and viral diversity in the context of wildlife health and conservation, providing critical information to the scientific community.