Next-Generation Sequencing Reveals the Genetic Bases of Three Mitochondrial Mutants in Cucumber

Mitochondrial mutations are useful to study nuclear-organelle genomic interactions. The mosaic (MSC) mutants of cucumber (Cucumis sativus L.) appear after passage of highly inbred line B through cell culture and show paternal transmission.  MSC mutants have distinctive phenotypes with misshapen cotyledons, silvery/chlorotic spots on leaves, low germination and growth rates, and tolerance to abiotic stresses.  Three independently derived MSC lines (3, 12, and 16) were sequenced using Next-Generation Sequencing Roche/454 platform and compared to the mitochondrial genome of inbred B. Analyses of read depths revealed that the MSC lines have several deletions in their mitochondrial DNAs which were confirmed by quantitative-Polymerase Chain Reaction (q-PCR). Genes that showed to be “low-represented” and “equally-represented”, based on the read depths in the MSC lines, were evaluated for their expression. Mass Spectrometry was performed to corroborate the expression results.