Analysis of the four cox2 genes found in turnip (Brassica campestris, Brassicaceae) mitochondria

In turnip mitochondria the cox2 gene is partially contained within a 2-kb (kilobase) direct repeat that is the site of homologous recombination events that generate subgenomic molecules. Because of its partial presence within the direct repeat, the turnip cox2 gene exists in four genomic contexts, two on the master chromosome and one on each of the subgenomic circles. In order to gain information on the expression of plant mitochondrial genes that exist in multiple genomic contexts and on plant mitochondrial recombination repeats in general we have characterized all four copies of the turnip 2-kb repeat and the cox2 gene. DNA sequence analysis indicates that the turnip high-frequency recombination repeat is 2424 bp in length. All but the last 58 bp of the cox2 gene is contained within the repeat, resulting in the presence of two intact cox2 genes and two pseudogenes. An intact cox2 gene and a pseudogene are found on the master chromosome (218 kb). An intact cox2 gene is also found on the 135-kb subgenomic circle, while a pseudogene is found on the 83-kb subgenomic circle. The turnip cox2, gene is unique because it lacks the first or 5' intron and contains the second or 3' intron previously found only in the carrot. The turnip intron is a group II intron that has high similarity (94.7%) with the second intron in carrot; also it is in precisely the same position within the gene. Transcript mapping studies using locus-specific probes reveal stable transcripts from the intact genes but not from the pseudogenes.