Probing of plant transcriptomes unveils the hitherto hidden genetic diversity of the family Secoviridae

Abstract

Abstract Secoviridae family contains single stranded RNA genome-containing viruses that infect plants. In the present study, we mined publicly available plant transcriptomes and identified sixty-one putative novel secoviral sequences in various plant species ranging from bryophytes to trees, which increased the known secoviral diversity by approximately 0.5-fold. Of the identified viral sequences, 13 were monopartite and 48 were bipartite, and sequences of 52 secoviruses were coding-complete and nine were partial. Except for small open reading frames (ORFs) determined in waikaviral genomes and RNA2 of torradoviruses, all the recovered genomes/genome segments contained a large ORF encoding a polyprotein. Based on genome organization, sequence similarity to known members, phylogeny and secovirus species demarcation criteria, all but three identified novel secoviruses were assigned to different secoviral genera- Cheravirus (3), Comovirus (2), Fabavirus (5), Nepovirus (29), Sadwavirus (3), Sequivirus (1), Stralarivirus (1), Torradovirus (4) and Waikavirus (10). Genome organization of two of the identified waika-like viruses resembled that of the recently identified waika-like virus- Triticum aestivum secovirus. Phylogenetic analysis revealed the host-waikavirus co-evolution pattern in a few waika- and waika-like viruses, the increased phylogenetic diversity of nepoviruses and the phylogenetic clustering of waika-like viruses. The study paves way for further studies on understanding the biological properties of identified novel secoviruses.