Evolutionary changes in the structures of the cox2 and atp6 loci in the mitochondrial genome of soybean involving recombination across small interspersed sequences

Mitochondrial DNA (mtDNA) fragments that contained cox2 or atp6 loci were cloned from three accessions of wild soybean (Glycine soja) in order to understand the evolutionary changes of mitochondrial genomes in the genus Glycine subgenus Soja. Cox2 was cloned as a single configuration, while atp6 was cloned as either one or two configurations from each accession. Structural variations were detected in the 5' upstream region of cox2 and in both the 5' upstream and 3' downstream regions of atp6. These variations appeared to be the results of recombination events. A comparison of the mtDNA fragments previously cloned from a cultivated soybean (G. max) and a wild soybean revealed various sites of recombination, as well as various combinations of the 5' and 3' regions, at the cox2 and atp6 loci. Some of the cloned fragments were found to contain a set of repeated sequences, namely 299-bp and 23-bp repeats in the 5' region of cox2 or atp6, which were interspersed in the mitochondrial genome in the subgenus Soja. Recombination events involving the 299-bp or 23-bp repeated sequences were shown to account for the generation of structural variations in the 5' regions of these loci.