Systematic identification and characterization of viral small RNAs from small RNA-Seq data

Virus-encoded small RNAs (vsRNAs) have been reported to play an important role in viral infections. Unfortunately, there is still a lack of a systematic characterization and resource of vsRNAs. Herein, we identified a total of 19 734 high-confidence vsRNAs including 2746 microRNAs (miRNAs) in 64 viral species from more than 800 samples of public small RNA-Seq data. The number of vsRNAs identified in viruses varied from 1 to 2489 with a median of 170. The length distribution of vsRNAs peaked at 21 and 22 nt. Plant viruses were found to express larger number and higher levels of vsRNAs than those of animal viruses. Besides, the number of vsRNAs identified increased as the viral infection persisted. Interestingly, the vsRNA showed strong expression specificity as little overlap was observed among vsRNAs identified in different strains of a virus, or in different hosts, cells, or tissues infected by the same virus. Little conservation was observed among vsRNAs of different viruses. The viral miRNAs were found to interact with host genes involved in multiple biological processes related to organization, development, action potential, polarity establishment, methylation, immune response, gene regulation, localization, and so on. To facilitate the usage of vsRNAs, a database named vsRNAdb was built for organizing and storing vsRNAs which is available at http://www.computationalbiology.cn/vsRNAdb/#/vsRNAdb/#/. Overall, the study deepens our understanding about the diversity and complexity of vsRNAs and provides a rich resource for further studies of vsRNAs.