Leveraging multiple sequencing technologies to generate a haplotype specific assembly of sugarcane R570. [W1018]

While sugarcane is one of the world's most important economic grasses for its sugar production and biofuel potential, tools and resources to understand its genetics are lacking. This is owed to the complexity of its genome which is highly polyploid, aneuploidy and heterozygous. Additionally, modern sugarcane cultivars are the result of interspecific hybridization and repeated backcrossing between domesticated S. officinarium and wild S. spontaneum parents. Cultivar R570 is best characterized sugarcane genome to date with the release of the BAC clone single tiling path, but this assembly represents a gene-rich and collapsed view of each of R570's homeologous chromosomes. To generate a haplotype specific assembly of R570, we devised a strategy that combines two de novo assemblies of R570 (Illumina; Pacbio), 96 selfed offspring (15X cov), single chromosome libraries and HiC to sequence and separate each homeologous chromosome. Using Illumina libraries, we generated a 5 Gb de novo genome assembly, using it to extract 55 Million unique 80bp genetic markers. Genotyping these markers in 96 selfed offspring isolated 1.9 million simplex (single dose) markers that were projected onto the 7.4 Gb PacBio assembly to generate a genetic map and anchor contigs onto separate linkage groups. Contigs that cannot be anchored by simplex markers will be ordered and oriented using HiC contact maps and single chromosome libraries. This strategy of combining multiple sequencing technologies will generate a more complete assembly for one of the most complex genomes to date in the Plant Kingdom.