Fig. 1.

Genome organization and phylogenetic analyses (2 columns). A Map of the DWV-D genome showing the location and size of the major genomic regions: 5’ UTR and 3’ UTR (yellow), Lp gene (red), capsid proteins VP1, VP2, VP3 and VP4 (blue), and the non-structural proteins (green), including the helicase, VPg, 3C-protease and RdRp genes. Shown above the genome map are the conserved protease cleavage sites for DWV-A, DWV-B, DWV-C, DWV-D, and Darwin bee virus-3 for processing the polyprotein into functional units. B Plot of the nucleotide similarity between DWV-D and either DWV-A (black), DWV-B (red) or DWV-C (blue) across a sliding 200 bp window. C Phylogenetic relationships between the four major DWV variants relative to the closest known outgroup (Darwin bee virus 3) for the four major genomic regions: UTR (yellow), Lp gene (red), structural proteins (blue), and non-structural proteins (green) based on either the nucleotide sequence (left) or the amino acid sequence (right). The number of characters included in each phylogram is shown in Additional file 1: Table S2. The phylogenetic trees with the highest log likelihood (see Additional file 1: Table S2) are shown. All trees are drawn to scale, with branch lengths measured in the number of substitutions (nucleotide or amino acid) per site. The degree of confidence in the branching nodes, based on bootstrapping the alignment 500 times, is shown by the solid, shaded, and white circles. Nodes with less than 70% bootstrap support (no circle) are unreliable