Structural Variations on Mitochondrial Genome that Specify CMS Cytoplasm in Chili Pepper (Capsicum annuum L.)

Cytoplasmic male sterility (CMS), which is a reproductive characteristics spread among wide range of higher plant species, infers to maternally inherited inability to produce functional pollens. Comparative analyses on CMS and normal mitochondrial genomes in several species have shown structural differences between genomes which include extensive rearrangements caused by illegitimate recombinations. However, the overall mitochondrial genome structure and the unique DNA rearrangement patterns that specify CMS cytoplasm have not been characterized completely in chili pepper. To determine CMS-specific mitochondrial DNA structures and elucidate the mechanism by which CMS mitochondrial genome was originated, we analyzed the mitochondrial genome sequence of a pepper CMS line, FS4401 and a fertile line, Jeju Jaerae, respectively, using 454 GS-FLX sequencing method. A total of 58,113,817 bp and 64,752,391 bp sequences were generated from these lines, respectively, and sequence assembly was carried out using Newbler2.0 program. In addition, genome walking and conventional PCRs were performed to fill gaps between separated contigs which were generated due to complexity of mitochondrial genome. The comparative analysis using draft sequences of FS4401 and Jeju mitochondrial genome showed that overall genome structure is highly different between two mitochondrial genomes. Especially, extensive rearrangements and insertions of aberrant sequences were detected on the DNA region between cox2 and atp6-2 genes. We expect that unique DNA recombinations which are detected on this region may play important role in the evolution of CMS cytoplasm in pepper.