Alternative repeat arrangements and mitochondrial genomic conformations. (A) Each of the three large repeats (R1, R2, and R3) is shown in all four possible arrangements (a, b, c, and d). Coexisting arrangements found within particular genomic conformations are paired together as recombination products (a + b and c + d). (B) Eight complete conformations (C1–C8) are possible for the Mimulus mitochondrial genome as the result of homologous recombination between one of the three large repeat pairs (direction of black arrows on genome maps indicates orientation between repeat copies). Recombination between inverted repeats leads to inversions of genomic segments in different conformations (gray arrows), whereas recombination between direct repeats causes genomic fission or fusion events (brown arrows). The repeat facilitating a particular recombination event is labeled on each arrow. The six single-copy genomic regions are shown in gradients of color; the same color for each single-copy region was used in all conformations.