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Sugarcane accounts for a large portion of the worlds sugar production. 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. The mitochondrial genome can be a useful way to identify the maternal origin of commercial cultivars. We have used the PacBio RSII to sequence and assemble the mitochondrial genome of a South East Asian commercial cultivar, known as Khon Kaen 3. The long read length of this sequencing technology allowed for the mitochondrial genome to be assembled into two distinct circular chromosomes with all repeat sequences spanned by individual reads. Comparison of five commercial hybrids, two  S. officinarum  and one  S. spontaneum  to our assembly reveals no structural rearrangements between our assembly, the commercial hybrids and an  S. officinarum  from New Guinea. The  S. spontaneum , from India, and one sample of  S. officinarum  (unknown origin) are substantially rearranged and have a large number of homozygous variants. This supports the record that  S. officinarum  plants from New Guinea are the maternal source of all modern commercial hybrids.

The two chromosomes of the mitochondrial genome of a sugarcane cultivar: assembly and recombination analysis using long PacBio reads