Figure 3

Detection of recombination events. (A) Schematic representation of four recombination events identified by RDP3. Each gray bar represents a concatenated sequence of a recombinant. Colour bars indicate the insertion of foreign sequences. The event numbers and the putative origins of foreign sequences are shown in the box. The gene order of the concatenated sequence is shown on the top and the borders are shown as vertical lines. (B) Mosaic structure in recombination event 2. The alignment was conducted on the concatenated sequences of one recombinant (Strain 1062) and two parental STs (Kerr Seringe and Uganda S001). Only the polymorphic sites are shown, and the position on the sequence is shown above each site. A foreign sequence is indicated as red on yellow. The gene order of the concatenated sequence is shown on the top and the borders are shown as vertical lines.