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

Abstract

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.

Figure 1. Chromosomes of the sugarcane mitochondrial genome.

Chromosomes 1 and 2 of the sugarcane mitochondrial genome with gene location and symbol shown. Exons are shown in colour with small introns indicated as white space. Genes shown on the inside are on the negative strand while genes shown on the outside are on the positive strand. The grey circle represents the GC content.

Figure 2. Phylogenetic tree comparing sugarcane with seven plant mitochondrial genomes.

Gene gain and loss are indicated by arrow direction toward or away from the branch, respectively. Gene names in red indicate genes that have been lost and then regained or vice versa.

Figure 3. Comparison of sugarcane and Sorghum bicolor mitochondrial genomes.

The S. bicolor genome is represented in full as the red circle. Similar sequence from the sugarcane assembly is represented in blue for chromosome 1 and purple for chromosome 2. The segmented nature of the two sugarcane chromosomes reflects the highly rearranged state of the sequence compared to S. bicolor.