Plant (meta)transcriptome data mining identified twenty-two putative novel taxa in the family Closteroviridae

Abstract The family Closteroviridae comprises filamentous, RNA genome-containing viruses that infect plants. In the present study, public domain SRA libraries derived from plants were mined for novel closteroviral sequences, resulting in the identification of twenty-two putative novel closterovirids across twenty-one plant genera. The identified viruses were represented by eighteen coding-complete and four partial genomes. Based on genome organization, pairwise sequence identity and phylogenetic analysis, the viruses were classified in the following genera: Ampelovirus (6), Bluvavirus (1), Closterovirus (7), Olivavirus (2) and Velarivirus (2), while four other viruses may represent four novel genera within the family. Other significant findings of the study include: (i) the identification of a 3’→5’ exonuclease-like protein in ampeloviruses and olivaviruses, (ii) the identification of an ampelovirus that encodes a polyprotein containing an RNA-dependent RNA polymerase motif without employing a + 1 ribosomal frameshift, (iii) the identification of a virus with the largest known genome among closterovirids, and (iv) the identification of a monopartite crini-like virus in Musa hosts potentially representing a novel genus. Besides, expanding the known closterovirid diversity by 0.25-fold, this study provides a base for future research aimed at understanding the biology and distribution of the identified novel viruses.