Adaptive evolution of traits for parasitism and pathogen transmission potential in bat flies

Deciphering the mechanisms underlying the transmission and spillover of zoonoses from reservoir hosts is essential in preventing future global pandemics. Bat flies, obligate blood-feeding ectoparasites of bats, are known carriers of diverse viruses. Here, we conducted a de novo assembly of a chromosome-level genome for the bat fly species Phthiridium sp. Comparative genomic analysis unveiled genes associated with specialized traits, such as the loss of eyes and wings, as well as elongated legs, which have adapted to parasitism on the dense fur of bats. Utilizing small RNA (sRNA) sequencing, we identified a spectrum of known and previously unclassified viruses in bat flies. Notably, experimental evidence indicated that bat flies can also feed on mammalian hosts other than bats, suggesting the potential for the spillover of bat-borne viruses. Furthermore, we demonstrated the role of the bat fly's RNA interference pathway in influencing the diversity and evolution of viruses. In summary, this study not only presents a new genome catalog to unveil the evolutionary mechanisms underpinning bat fly parasitism, but also provides a novel research system that can be used to investigate the mechanisms of cross-species transmission of bat-borne viruses and the co-evolution of bats and viruses.