Figure 4

Unequal recombination breakpoints within the RGA08 gene cluster. (A) An intragenic unequal recombination event between RGA08X and RGA08W results in the actual structure of the RGA08R sequence. The RDP software detected the region of sequence identity between RGA08X and RGA08R and indicated a recombination breakpoint on RGA08X. Manual inspection of RGA08 sequence alignments indicated RGA08W and RGA08X as likely parental sequences. The percent nucleotide identity of RGA08X (red curve) and RGA08W (blue curve) is plotted along the sequence of RGA08R. A shift in sequence identity levels (black arrows) is observed indicating a putative recombination event. (B) Unequal recombination mediated by duplicated 1 kb intergenic sequences (orange boxes). Intergenic sequences between RGA08K - RGA08L and RGA08O-RGA08P in B1 (top) have recombined to produce the actual intergenic sequence structure between RGA08K - RGA08P in B2 (bottom). Percent of nucleotide identity between 1 kb intergenic sequences of B1 is plotted along the B2 sequence. High sequence identity is visible at the beginning of the RGA08K - RGA08L intergenic sequence (red curve) and at the end of the RGA08O-RGA08P intergenic sequence (blue curve). Black arrows indicate breakpoint position.