Using PacBio reads to sequence and assemble mitochondrial genome of a sugarcane cultivar

Sugarcane is the major source of processed sugar in the world and therefore an important crop species. 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.

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BIOTEC researchers have used the PacBio RSII, a sequencer that is able to sequence single molecules in real time without any sample amplification, 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 study was conducted by researchers from BIOTEC Genomic Research Laboratory.

 

Ref: Shearman, J.R., Sonthirod, C., Naktang, C., Pootakham, W., Yoocha, T., Sangsrakru, D., Jomchai, N., Tragoonrung, S. and Tangphatsornruang, S (2016). The two chromosomes of the mitochondrial genome of a sugarcane cultivar: assembly and recombination analysis using long PacBio reads. Scientific Reports, 6, 31533.

 

Posted on 30 November 2016.