Sugarcane is one of the world's most valuable crops and is responsible for 80% of the world's sugar production. Modern day sugarcane cultivars are derived from inter-specific hybridization between domesticated Saccharum officinarum and wild S. spontaneum, combining both high sugar production and environmental adaptability and disease resistance. The hybridization of two complex polyploid progenitors however, has generated one of the most complex plant genomes sequenced and assembled to date.

Using a combination of multiple genomic technologies (genetic map, Bionano optical map, single flow-sorted chromosome libraries, HiC, PacBio HiFi, Illumina RNAseq, PacBio IsoSeq), we generated a high quality assembly (5.04Gb; Contig N50: 12.6Mb) and annotation of cultivar R570, the most widely researched sugarcane cultivar in the world. The genome assembly enabled identification of candidate genes underlying a single copy brown rust resistance locus that has provided durable fungal pathogen resistance for the past three decades. This reference genome and analyses shed light on the genomic effects of breeding practices in sugarcane, and illustrate how R570 can be used for genomic improvement and breeding of modern sugarcane hybrids.