Probing the plant transcriptomes for novel waikaviral sequences broadens the host range and genetic diversity of waikaviruses

Abstract

Waikaviruses (family: Secoviridae) are monopartite, positive sense, single-stranded RNA viruses that cause economically important diseases in plants. Despite their importance, waikaviruses are poorly understood and only ten members are currently recognized. In the present study on Sequence Read Archive (SRA)-based data-driven virus discovery (DDVD), we identified twenty-two putative novel waikaviruses, nearly doubling the number of known waikaviruses, in SRA libraries of diverse plant species, starting from ferns to trees. Besides, a highly divergent secoviral sequence with distinct genome features, yet related to waikaviruses, was identified in a wheat transcriptome. Other significant findings of the study include identification of a novel waikavirus in a library derived from diseased water chestnut sample wherein a novel caulimovirus was reported, prediction of coiled-coils in the hypothetical protein region of waikaviral polyprotein alignment and phylogenetic clustering of tree-infecting waikaviruses in a single sub-group. The findings of the study not only reiterates the importance of DDVD in unveiling the hitherto hidden viral sequences in plant SRA libraries but also deepens our understanding of waikaviral diversity.