Fig. 5

Characteristics of novel (−)ssRNA viruses classified in family Rhabdoviridae from the present study. a Photographs of samples that tested positive for selected novel rhabdoviruses in RT-PCR assays. b–d Heatmaps showing the pairwise identities of species in genus Alphanucleorhabdovirus (b), Betanucleorhabdovirus (c), and Cytorhabdovirus (d), based on full genome nucleotide sequences. Virus acronyms in blue bold font are the novel rhabdoviruses, while those in black bold font are known rhabdoviruses from the present study. Indicated after virus names and acronyms are the isolate IDs. e Genome organization of novel rhabdoviruses with their genome lengths or position shown to scale. Open reading frames (ORFs) and the proteins they code for are color coded accordingly. f Co-phylogenetic tree (tanglegram) showing the phylogenetic relationships of novel rhabdoviruses among known species (left tree), which are linked with associated plant host(s) indicated in GenBank, shown on the right tree. Links of well-supported clade of viruses to taxonomically related plants are highlighted in red. Maximum likelihood phylogenetic tree of rhabdoviruses was constructed based on the conserved amino acid sequence of the RdRp. Branch length scale represents amino acid substitution per site. The host cladogram was made in phyloT (www.phylot.biobyte.de). In the virus tree, viruses associated with at least two plant hosts are indicated by a blue circle. In the host tree, green circles are used to indicate plants that are associated with two or more rhabdoviruses, and the host species names in bold green font are those that have representative samples in the present study. The clades are separately color coded and annotated for each tree. Full virus names of those abbreviated in the pairwise identity matrices (b–d) can be found in the genome organization and phylogenetic trees (e, f)