Recombining repeats in the Silene latifolia mitochondrial genome. (A) A stylized version of the master circle undergoing one of many possible recombination events. The black boxes represent the 6-copy repeat with numbering corresponding to Figure 2. The lettered sections represent intervening single-copy regions. The "left" and "right" probes used in Southern blot hybridizations are indicated with small gray bars and labeled L and R, respectively. The dotted gray lines indicate a crossover event between repeat copies that produces 2 sub-genomic molecules. Given all possible recombination events, each left flanking sequence has the potential to be paired with 6 different right flanking sequences (and vice versa), and therefore, each probe is expected to hybridize to 6 restriction fragments. (B) Southern blot hybridizations with "left" and "right" probes each show 6 strong bands, corresponding to the sizes predicted based on recombination among the 6 large repeats (see Additional File 1 for a more resolved replicate of the "left" probe blot). The left pair of lanes contain DNA samples from one full-sib family, while the right pair contain DNA samples from a second full-sib family. The size standards are indicated by the values between the two blots. The values on either side represent the predicted fragment sizes with the corresponding single-copy flanking sequence noted in parentheses. The black triangle indicates an unexpected 1.8 kb fragment detected in some but not all individuals with the "right" probe.