The Saccharum Mitochondrial Genome

Modern commercial cultivars are complex hybrids of S. officinarum and several other Saccharum species. Historical records identify New Guinea as the origin of S. officinarum and that a small number of plants originating from there were used to generate all modern commercial cultivars. We have used the PacBio RSII to sequence and assemble the mitochondrial genomes of a South East Asian commercial cultivar, known as Khon Kaen 3, and a haploid clone of S. spontaneum (SES208). The long read length of this sequencing technology allowed for the mitochondrial genome of Khon Kaen 3 to be fully assembled into two discrete circular sequences, totalling 444 kb, with no repeats that would facilitate recombination. The mitochondria of S. spontaneum has a more dynamic arrangement with several subgenomic circles, totalling 523 kb, and multiple shared repeats that would facilitate recombination. We mapped Illumina sequence from DDBJ of five commercial hybrids, two S. officinarum and one S. spontaneum to the assemblies of Khon Kaen 3 and SES208. The results identify an interesting chance event that shaped the mitochondrial genome of the commercial hybrids.