A monoploid reference sequence for the highly complex genome of sugarcane. Reference sequence for sugarcane genome

Sugarcane (Saccharum spp.) is a major crop for sugar and bioenergy production. Its genome poses challenges that have not been addressed in any prior sequencing project due to its highly polyploid, aneuploid, heterozygous and interspecific genome structure (2n ~ 12x ~ 120, ~10Gb). We exploited the colinearity with sorghum to produce a monoploid genome sequence of sugarcane. We applied whole genome profiling (WGPTM) to 20,736 sugarcane BAC clones and anchored 11,732 of them onto the sorghum genome. A minimum tiling path of 4,660 sugarcane BAC clones that best cover the gene-rich part of the sorghum genome was selected, sequenced and assembled in a 382 Mb single tiling path (STP) of high quality sequence. A total of 25,316 protein-coding gene models were predicted on the STP, 17% of which displayed no colinearity with their sorghum orthologs. A 12,468 SNP-based sugarcane genetic map revealed a few large chromosomal rearrangements in S. spontaneum as compared to S. officinarum and sorghum, which explain their distinct basic chromosome numbers and suggest that polyploidization in S. spontaneum and S. officinarum lineages arose after their divergence.This BAC-based monoploid sugarcane reference sequence represents a crucial resource for genetic and functional genomic studies while providing an essential framework for future whole genome sequence assembly programmes.