We have sequenced the genome of the commercial sugarcane variety SP80 3280 using a shotgun approach. Commercial sugarcane is a highly polyploid and aneuploid species with a <10 Gbp genome. It is estimated that commercial sugarcane has 100 to 120 chromossomes, with 10 a 14 gene copies coming from Saccharum officinarum and S. spontaneum. Leaf DNA was broken into fragments of 500 bp to 1000 bp (average of 650 bp) and was sequenced using the Titanium 454 (Roche). A total of 27 runs were made, which generated 10.8 Gbp from 5 different shotgun libraries. When the 26 million reads were assembled using Newbler (40 bp coverage, 90% overlap), 1.1 million contigs were generated with an average of 830 bp and 18x coverage. We have been using the 9kbp sorghum gene GIGANTEA (SbGI) as a quality indicator of the assemblies. While 4 contigs would align to SbGI covering about 91% of the genome in the previous assembly, 3 contigs of the new assembly align to SbGI with 100% coverage as they would overlap between 50 to 100 bp. When we analyzed the flanking regions of this gene (3 kbp), only a 2kbp contig downstream the gene was found. A similar situation was observed in other analyzed genes. This is an indication that sorghum genome may be useful to identify coding regions in the sugarcane genome but may not be enough to identify their regulatory regions.