Genome-Wide Identification of MicroRNAs and Immune-Related Proteins Provides Insights into Antiviral Adaptations in Common Vampire Bat

Bats are natural reservoirs for diverse viruses, yet they rarely develop disease, suggesting unique antiviral adaptations. In this study, we performed a comprehensive genome-wide analysis in the common vampire bat (<i>Desmodus rotundus</i>), integrating comparative genomics, functional annotation, microRNA (miRNA) discovery, target prediction, and network-based analyses. Comparative genomic analysis revealed that <i>Phyllostomus discolor</i> exhibits the highest protein homology (97.4%) with <i>D. rotundus</i>. Alignment of interferon regulatory factors (IRFs) indicated strong conservation of IRF1, IRF5, and IRF8, while IRF4 and IRF7 showed divergence, reflecting bat-specific modulation of interferon signaling. Functional annotation of previously uncharacterized proteins identified immune-related elements, including toll-like receptor 4, syncytin-1, and endogenous retroviral sequences, highlighting the integration of viral components into host immunity. We further identified 19 novel miRNAs in <i>D. rotundus</i>, with high-confidence target genes such as <i>SOD2</i>, <i>TRIM28</i>, and <i>FGFR1</i> involved in antiviral defense, apoptosis regulation, and oxidative stress response. Functional enrichment analyses revealed processes associated with wound healing, apoptosis suppression, infection response, and longevity. Network entropy analysis highlighted central regulatory hubs, including <i>MYC</i>, <i>BCL2</i>, and <i>KIF1B</i>, influencing cell cycle, survival, and immune balance. Collectively, these results demonstrate that <i>D. rotundus</i> employs an integrated regulatory network combining conserved immune factors, lineage-specific gene divergence, and miRNA-mediated fine-tuning to achieve viral tolerance without pathology. This study expands our understanding of bat antiviral biology and provides candidate molecular targets for future functional and translational research.