Cucumber mitochondria have three unique characteristics: paternal transmission, huge genome size, and mitochondrially encoded mosaic phenotypes. The cucumber mitochondrial DNA is enormous at 1.6 Mb, one of
largest among angiosperms, and is divided into three chromosomes of 1.5 Mb, 84 Kb and 45 Kb. Paternally transmitted mitochondrial mutants show strongly mosaic (MSC) phenotypes on cotyledons and true leaves, slow growth and low germination rates. The Roche 454 platform was used to sequence mitochondrial DNAs from the highly inbred line ‘B’ and three MSC lines (MSC3, MSC12 and MSC16) independently derived from B and reads were aligned to the mitochondrial assembly of the cucumber cultivar ‘Calypso’ (Plant Cell DOI 10.1105.tpc.111.087189). Compared to B and Calypso, the MSC lines had five deleted regions in the 1.5 Mb chromosome. The 85 kb chromosome was completely absent in MSC12 and MSC16 and approximately one-half was present in MSC3. Importantly none of the MSC lines possessed identical deletions, indicating that they do not trace back to the same sublimon in inbred B. Analysis of the mitochondrial genes in the deleted regions should reveal the genetic lesion responsible for the MSC phenotypes.