An intact mitochondrial cox1 gene and a pseudogene with different genomic configurations are present in apple cultivars ‘Golden Delicious’ and ‘Delicious’: Evolutionary aspects

We have characterized the mitochondrial cox1 gene copies in two apple cultivars ‘Golden Delicious’ and ‘Delicious’. Both the cultivars contained an intact copy and a truncated copy of cox1. The intact ‘Golden Delicious’ and ‘Delicious’ cox1 genes, designated G-cox1 and D-cox1, respectively, were both found to be actually transcribed to give an RNA of approximately 1.7 kb. The two intact cox1 and two truncated copies (G-φcox1 and D-φcox1) shared a common 1115-bp segment flanked by four combinations of two different 5′- and 3′-sequences. PCR assay demonstrated that the configurations bearing G-cox1 and G-φcox1 existed in substoichiometric amounts within the mitochondrial genome of ‘Delicious’ whereas substoichiometric molecules carrying D-φcox1 were present in the ‘Golden Delicious’ mitochondrial genome. Although ancestor/descendant relationships cannot be inferred between the G-cox1 and D-cox1 arrangements, the results led us to hypothesize that (1) the 1115-bp segment containing part of the progenitor cox1 was duplicated, thereby generating a pseudo-cox1 copy, and (2) this was followed by homologous recombination across a portion of the 1115-bp repeats which gave rise to the descendant cox1 and pseudo-cox1 arrangements.