Insights from a Long-Read Assembly of the Complex Sugarcane Genome

A complex polyploid and aneuploid genome has long hindered the advancement of genomic understanding and the application of modern genetic breeding approaches to sugarcane. Following recent technological developments, the capability of generating better genome reference assemblies is providing new clues into the nature and evolution of this important biofuel and energy crop. With the aid of high-quality long reads, we reconstructed partial homoeologue haplotypes of a hybrid sugarcane cultivar. Sugarcane commercial varieties derive from crosses of Saccharum officinarum and Saccharum spontaneous. We will describe allelic variation and allele clustering in an interspecific sugarcane hybrid, as well as gene conservation with sorghum.  We will also describe putative species-specific genes and alleles, which may afford information about the contributions of each ancestor species to commercially used sugarcane genotypes.