title: 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.
authors.affiliation: National Center for Genetic Engineering and Biotechnology, 113 Thailand Science Park, Paholyothin Road, Khlong Nueng, Khlong Luang, Pathumthani, 12120, Thailand.
authors.forename: Jeremy R
authors.initials: JR
authors.lastname: Shearman
authors.affiliation: National Center for Genetic Engineering and Biotechnology, 113 Thailand Science Park, Paholyothin Road, Khlong Nueng, Khlong Luang, Pathumthani, 12120, Thailand.
authors.forename: Chutima
authors.initials: C
authors.lastname: Sonthirod
authors.affiliation: National Center for Genetic Engineering and Biotechnology, 113 Thailand Science Park, Paholyothin Road, Khlong Nueng, Khlong Luang, Pathumthani, 12120, Thailand.
authors.forename: Chaiwat
authors.initials: C
authors.lastname: Naktang
authors.affiliation: National Center for Genetic Engineering and Biotechnology, 113 Thailand Science Park, Paholyothin Road, Khlong Nueng, Khlong Luang, Pathumthani, 12120, Thailand.
authors.forename: Wirulda
authors.initials: W
authors.lastname: Pootakham
authors.affiliation: National Center for Genetic Engineering and Biotechnology, 113 Thailand Science Park, Paholyothin Road, Khlong Nueng, Khlong Luang, Pathumthani, 12120, Thailand.
authors.forename: Thippawan
authors.initials: T
authors.lastname: Yoocha
authors.affiliation: National Center for Genetic Engineering and Biotechnology, 113 Thailand Science Park, Paholyothin Road, Khlong Nueng, Khlong Luang, Pathumthani, 12120, Thailand.
authors.forename: Duangjai
authors.initials: D
authors.lastname: Sangsrakru
authors.affiliation: National Center for Genetic Engineering and Biotechnology, 113 Thailand Science Park, Paholyothin Road, Khlong Nueng, Khlong Luang, Pathumthani, 12120, Thailand.
authors.forename: Nukoon
authors.initials: N
authors.lastname: Jomchai
authors.affiliation: National Center for Genetic Engineering and Biotechnology, 113 Thailand Science Park, Paholyothin Road, Khlong Nueng, Khlong Luang, Pathumthani, 12120, Thailand.
authors.forename: Somvong
authors.initials: S
authors.lastname: Tragoonrung
authors.affiliation: National Center for Genetic Engineering and Biotechnology, 113 Thailand Science Park, Paholyothin Road, Khlong Nueng, Khlong Luang, Pathumthani, 12120, Thailand.
authors.forename: Sithichoke
authors.initials: S
authors.lastname: Tangphatsornruang
mesh_terms: D032461:Chromosomes, Plant; D054629:Genome, Mitochondrial; D054643:INDEL Mutation; D010802:Phylogeny; D020641:Polymorphism, Single Nucleotide; D011995:Recombination, Genetic; D031786:Saccharum / Q000145:classification / Q000235:genetics*