Plant mitochondrial genome has unique features such as large size, frequent recombination
and incorporation of foreign DNA. Cytoplasmic male sterility (CMS) is caused by
rearrangement of the mitochondrial genome, and a novel chimeric open reading frame (ORF)
created by shuffling of endogenous sequences is often responsible for CMS. The Ogura-type
male-sterile cytoplasm is one of the most extensively studied cytoplasms in Brassicaceae.
Although the gene orf138 has been isolated as a determinant of Ogura-type CMS, no
homologous sequence to orf138 has been found in public databases. Therefore, how orf138
sequence was created is a mystery. In this study, we determined the complete nucleotide
sequence of two radish mitochondrial genomes, namely, Ogura- and normal-type genomes,
and analyzed them to reveal the origin of the gene orf138.
Ogura- and normal-type mitochondrial genomes were assembled to 258,426-bp and 244,036-
bp circular sequences, respectively. Normal-type mitochondrial genome contained 33
protein-coding and three rRNA genes, which are well conserved with the reported
mitochondrial genome of rapeseed. Ogura-type genomes contained same genes and
additional atp9. As for tRNA, normal-type contained 17 tRNAs, while Ogura-type contained
17 tRNAs and one additional trnfM. The gene orf138 was specific to Ogura-type
mitochondrial genome, and no sequence homologous to it was found in normal-type genome.
Comparative analysis of the two genomes revealed that radish mitochondrial genome consists
of 11 syntenic regions (length >3 kb, similarity >99.9 %). It was shown that short repeats and
overlapped repeats present in the edge of syntenic regions were involved in recombination
events during evolution to interconvert two types of mitochondrial genome. Ogura-type
mitochondrial genome has four unique regions (2,803 bp, 1,601 bp, 451 bp and 15,255 bp in
size) that are non-syntenic to normal-type genome, and the gene orf138 was found to be
located at the edge of the largest unique region. Blast analysis performed to assign the unique
regions showed that about 80 % of the region was covered by short homologous sequences to
the mitochondrial sequences of normal-type radish or other reported Brassicaceae species,
although no homology was found for the remaining 20 % of sequences.
Ogura-type mitochondrial genome was highly rearranged compared with the normal-type
genome by recombination through one large repeat and multiple short repeats. The
rearrangement has produced four unique regions in Ogura-type mitochondrial genome, and
most of the unique regions are composed of known Brassicaceae mitochondrial sequences.
This suggests that the regions unique to the Ogura-type genome were generated by
integration and shuffling of pre-existing mitochondrial sequences during the evolution of
Brassicaceae, and novel genes such as orf138 could have been created by the shuffling
process of mitochondrial genome.