Novel viruses of the genus Amalgavirus from crown imperial Fritillaria imperialis transcriptome

In an in silico investigation, genome sequences of three RNA viruses were identified in the crown imperial Fritillaria imperialis L. transcriptome dataset. Sequence comparison and phylogenetic analyses revealed that these three novel viruses belong to the genus Amalgavirus. They were tentatively named Crown imperial amalgavirus (CIAV), Iranian amalgavirus (IrAV), and Koohrang amalgavirus (KAV). The RNA-dependent RNA polymerases (RdRps) of CIAV, IrAV, and KAV showed 69.53%, 42.26%, and 37.46% amino acid sequence identities with the homologous RdRp of the most closely related virus, respectively, suggesting that they are novel viruses. Also, the conserved motifs of RdRp were detected in the RdRp of each CIAV, IrAV, and KAV. Genomes of both CIAV and IrAV were complete and contained two overlapping Open Reading Frames (ORFs). A + 1 programmed ribosomal frameshifting (PRF) motif, which matches the conserved amalgaviruses consensus sequence UUU_CGN was found at the ORF1/ORF2 boundary of CIAV and IrAV. The current study reports three novel viruses for the first time from crown imperial, and these findings enrich our understanding of new plant dsRNA virus species, which may also be helpful for the study of amalgaviruses.