Sugarcane cultivars (Saccharum spp.) have probably the most complex genome among crops. They all derived from a few interspecific hybridization events performed a century ago between two polyploid species, the sugar producing species S. officinarum (2n=8x=80, x= 10) and the wild species S. spontaneum (2n=5x=40 to 16x=128 and aneuploid; x=8), followed by backcrossing with S. officinarum. The resulting cultivars are highly polyploid (2n ~ 12x ~ 120, ~10Gb), highly heterozygous and aneuploid which make an assembly of the whole genome very challenging. We developed a strategy based on the global synteny and collinearity conservation between sugarcane and sorghum. Whole genome profiling technology was applied on 20,736 sugarcane BAC clones, producing 455,656 unique sequence tags that allowed the anchoring of 11,732 BAC onto the gene-rich part of the sorghum genome. A minimum tiling path of 4,688 sugarcane BAC clones was selected, sequenced and assembled in a Single Tiling Path of 382 Mb of high-quality sequence. A total of 25,316 protein-coding gene models were predicted, 17% of which display no collinearity with their sorghum orthologs. We showed that the two species, S. officinarum and S. spontaneum, involved in modern cultivars differ by their transposable element content explaining their distinct basic genome size. A SNP-based genetic map was built and revealed a few large chromosomal rearrangements between S. officinarum and S. spontaneum, explaining their distinct basic chromosome numbers while also suggesting that polyploidization arose in both lineages after their divergence.

This BAC-based sugarcane reference sequence represents an essential resource to explore hom(oe)ologous allelic variation and perform genetic and genomic studies in cultivars and sugarcane germplasm.

BAC sequencing was done through international collaborations involving DOE-JGI, CSIRO, SASRI, QAAFI and USP and with the financial support of the ICSB (International Consortium for Sugarcane Biotechnology).

• Garsmeur et al., 2018. A mosaic monoploid reference sequence for the highly complex genome of sugarcane. Nature Communications. doi:10.1038/s41467-018-05051-5.