Analysis of public domain plant transcriptomes expands the phylogenetic diversity of the family Secoviridae

Secoviruses are mono-/bi-partite plant-infecting RNA viruses that cause economically important diseases in plants. In the present study, nine secoviruses tentatively named as Ananas comosus secovirus (AcSV), Artocarpus altilis secovirus (AaSV), Boehmeria nivea secovirus (BnSV), Gynostemma pentaphyllum secovirus (GpSV), Orobanche cernua secovirus (OcSV), Paris polyphylla secovirus 1 (PpSV1), Paris polyphylla secovirus 2 (PpSV2), Rhododendron delavayi secovirus (RdSV) and Yucca gloriosa secovirus (YgSV) were identified by analysis of publicly available transcriptomes of eight plant species. Coding-complete genome/genome segments of all the identified viruses encoding a polyprotein were recovered. Two of the identified viruses- AcSV and GpSV were discovered in few of the small RNA libraries of respective plant species. Putative cleavage sites were predicted in polyproteins encoded by AcSV, GpSV, PpSV2 and YgSV genome segments. Phylogenetic and sequence similarity analyses showed that AcSV, GpSV and YgSV, PpSV1 and RdSV putatively belong to the genera- Sadwavirus (sub genus: Cholivirus ), Fabavirus , Nepovirus and Waikavirus , respectively while AaSV, BnSV and PpSV2 may represent a distinct group of viruses within the family Secoviridae as they could not certainly be assigned to a particular genera.