Sugarcane is an Ancient Allopolyploid

Comparative analysis of sugarcane and Miscanthus using synonymous substitution rates provided some evidence that the two closely related species share a whole genome duplication (Kim et al., 2014). A whole genome reference sequencing project for sugarcane provides rich new data to evaluate these findings. We performed a comparative analysis of allelic dosage by aligning sugarcane unitigs generated by the SUGESI (Sugarcane Genome Sequencing Initiative) to the sorghum physical map. Although we aligned all possible sugarcane unitigs to the sorghum genome, gene-rich regions of sorghum were a focus due to voluminous data as well as the fact that major allelic variations may reside in coding regions. The four possible levels of allelic dosage are defined based on the four nucleotide bases. Aside from regions where unitigs were monomorphic, two-base variations were predominant in the sugarcane genome, consistent with our previous evidence that sugarcane has genomic compartmentation caused by an ancient allopolyploidization. Despite a recent lineage-specific autopolyploidization to confer its current octoploidy, chromosomes formed by the more ancient allopolyploidy appear to have been somehow retained and have imparted on sugarcane a partially allopolyploid nature.