Figure 2. The location of recombination events in isolates IDU1 (A) and IDU3 (B), determined by using the bootscanning program of Simplot. Possible tree topologies (a, b, and c) are shown (C). The phylogenetically informative sites and the tree topologies supported at each of those sites are indicated over each plot. In the tree topologies, Q, A, and H indicate query sequences (IDU1 or IDU3), genotype A, and genotype H (outgroup) consensus sequences, respectively. S indicates consensus sequence of genotype D and genotype C for IDU1 and IDU3, respectively. Possible crossover points are indicated by solid triangles. A sliding window size of 60 bp, step size of 10 bp, Kimura-2 parameter, 1,000 bootstrap replicates, and neighbor-joining method were used for the analysis of recombination.
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