An apple atp9 pseudogene is maintained at high copy number in ‘Golden Delicious’-type mitochondria but is present substoichiometrically in ‘Delicious’-type mitochondria

In this study, the mitochondrial atp9 gene sequence of an apple cultivar ‘Golden Delicious’ was found to exist in one intact version and two truncated versions (termed φatp9-1 and φatp9-2). Interestingly, the φatp9-1 sequence is maintained at high copy number in the six ‘Golden Delicious’-cytotype cultivars examined but present substoichiometrically in eight ‘Delicious’-cytotype cultivars. Our data also suggest that φatp9-1 originated in a homologous recombination event mediated by the short repeat in a common ancestral mitochondrial genome of ‘Golden Delicious’ and ‘Delicious’, and was preferentially amplified in an evolutionary lineage that gave rise to the ‘Golden Delicious’-type genome. On the other hand, φatp9-2 was revealed to be present in high abundance in all 14 cultivars examined.

► An apple cultivar ‘Golden Delicious’ mitochondria contains one intact atp9 gene and two truncated copies (termed φatp9-1 and φatp9-2).
► The φatp9-1 sequence is maintained at high copy number in the six ‘Golden Delicious’-cytotype cultivars.
► In the eight ‘Delicious’-cytotype cultivars, however, φatp9-1 is present substoichiometrically.
► A homologous recombination was a possible cause to generate φatp9-1 using the short repeat in a common ancestral mitochondrial genome of ‘Golden Delicious’ and ‘Delicious’.
► The φatp9-2 was revealed to be present in high abundance in all 14 cultivars.