Figure 1
Maximum likelihood phylogenetic trees (both constructed with the GTR+G 4 nucleotide substitution model) indicating possible evolutionary relationships between 23 PanSV isolates. (a) Tree constructed using complete genome sequences. Virus names take the form "Strain [country-region-year of isolation]" (b) A tree constructed using recombination-free portions of the genome indicated beneath the genome map and recombination mosaic cartoons in c. (c) Linearised genome cartoons depicting unique recombinant mosaics detected amongst the PanSV sequences. Colours represent as best as possible the origins of different genome regions. Letters below the depicted recombination events correspond to detailed descriptions of each of the events given in Additional file 7. For labels on the genome map: mp = movement protein gene, cp = coat protein gene, rep = replication associated protein gene, repA = RepA gene. Whereas branches marked with filled and open circles were supported in >90% and 70-89% of bootstrap replicates, respectively, branches with <50% bootstrap support have been collapsed. The tree was rooted on the Sugarcane streak Reunion virus isolate SSRV-Bas (not shown).