Annotation of 21 unannotated public bat genomes

Background Despite harboring diverse pathogenic viruses, bats rarely exhibit clinical symptoms of the diseases. Previous research has reported evolutionary characteristics in key antiviral gene families in bats, such as natural killer cell receptors, MHC class I genes, and type I interferons, leading to the hypothesis that bats may possess an immune tolerance that allows them to host viruses asymptomatically. However, this hypothesis is based on limited datasets and requires more comprehensive examinations.Results We assembled a chromosome-level reference genome of the Chinese horseshoe bat (Rhinolophus sinicus), a recognized reservoir for SARS-like coronaviruses. By combining this genome with data from 37 other bat species spanning major lineages, we have discovered that the evolutionary signatures of these antiviral gene families exhibit lineage-specific characteristics in gene repertoire, genomic distribution, signaling modes, and expression patterns. Furthermore, we found that the evolutionary diversification of these antiviral gene families is largely influenced by the richness and diversity of viruses, particularly in bats that host more viruses.Conclusions Our findings offer insights into the immune adaptations of bats in response to viral infections and reveal a greater interspecies evolutionary heterogeneity in their antiviral immune systems than previously recognized.