Figure 9.

Examples of 3 nanopore reads from radA mitochondrial replicate 1 that capture repeat-mediated recombination. Nanopore reads that derive from recombination between inverted repeats map with two hits, one in the forward orientation and the other in the reverse orientation, both flanked by the sequence of a repeat, as shown in A where the 29-kb read is flanked by repeats I-1 and I-2. Recombination between direct repeats results in two hits in the same orientation with a deletion of the intervening sequence (B). The alternative product of recombination between direct repeats is the production of a small circular molecule. We identified a number of putative circular molecules or tandem duplications mediated by recombination between repeats EE-1 and EE-2, which map with two hits in the same orientation, but with a section of the end of the read mapping in front of the end of the read (C).