Phylogenetic and recombination analysis of 286 RdRp gene fragments sampled from three Brazilian orange trees. (A) Largely recombination free maximum likelihood phylogeny of 269 RdRp gene fragment sequences. Sequences sampled from trees C3, C5 (both with CSD) and C6 (without CSD) are represented by blue, green and red dots respectively. Multiple dots on particular branches represent identical sequences. Whereas branches with more than 75% bootstrap support are labeled with filled black diamonds, those with between 50 and 74% support are labeled with unfilled black diamonds. Sequence lineages R1a, R1b, R2, R3 and R4 are indicated. (B) The mosaic structures of obviously recombinant sequences excluded from the phylogenetic analysis. The mosaics are colour coded according to the main sequence lineages from which they have probably been derived. Grey areas represent sequence tracts that were not clearly derived from one of the five identified sequence lineages in A. Coloured dots beside the schematic representations of the recombinant sequences represent the numbers and origins of recombinant sequences sharing similar mosaics. (C) The relative population representation of different major RdRp lineages identified in A.