The origin and maintenance of the small repeat in the bean mitochondrial genome

The genesis of small repeats involved in infrequent recombinations in plant mitochondrial genomes remains unclear. We propose that at least some of the small repeats are generated in a similar way to the large, highly recombinogenic, plant mitochondrial repeats. A 314-bp sequence was detected as a small, rarely recombining mitochondrial repeat in the genus Phaseolus. Two of the recombinational forms were predominant, while two others were found in substoichiometric amounts in the species P. vulgaris, P. polyanthus and P. coccineus. However, the pairs of predominant and substoichiometric forms were distinct in each genome, indicating that a mechanism other than recombination is responsible for their maintenance in high or low copy number. In P. lunatus, which is phylogenetically quite remote from the other species examined, only one form of the 314-bp repeat was predominant, while the other forms were present in substoichiometric amounts. In this genome, we also identified sequences containing the terminal 11 or 7 bp of the 314-bp repeat. These configurations could serve as intermediates during generation of the repeat. We presume that two site-specific recombinations between the intermediates and the predominant form found in P. lunatus resulted in creation of the two new forms of the repeat. The fourth form of the repeat appeared after a further recombination that occurred at the substoichiometric level. The nature of this recombination, whether site-specific or homologous, is discussed. Beyond the evident similarities between the model presented in this work and the three-recombination models previously proposed to explain the formation of large, frequently recombining repeats, we did not detect any specific deletion associated with generation of the repeat.