Designing the Energy-Cane: Prospecting Genes and Regulatory Networks in Ancestor and Hybrid Sugarcane Genotypes Using WGS, RNA-Seq and Oligoarrays

Sugarcane is an important crop worldwide used for centuries as source of sugars for human consumption. Over the last few decades, sugarcane has also been used successfully for biofuels production. Despite its importance, biotechnology for sugarcane is not as developed as for other crops, its complete genome sequence is not available, and breeding tools are hard to apply due to many unknowns regarding the genetics of commercial cultivars that are interspecific hybrids derived from Saccharum officinarum and Saccharum spontaneum. In an attempt to define the sugarcane ORFeome, we developed a new protocol to produce full-length cDNA libraries and generated five libraries, three for a commercial hybrid and one for each of the ancestor genotypes S. officinarum and S. spontaneum. The libraries were sequenced on high-throughput platforms and assembled in 195,000 contigs (133 Mb). Results indicate at least 30,000 full-length transcripts. Contigs were aligned against the annotated transcriptome of six grasses and the most important sugarcane EST dataset, SUCEST. About 70-90% of grasses genes match the sugarcane contigs, but 40,000 contigs seem to be sugarcane specific. Furthermore, 78,000 contigs may represent new sugarcane transcripts. We also identified gene expression differences and antisense transcripts. This is the first large-scale analysis of full-length transcripts for sugarcane, an important step in the definition of the sugarcane ORFeome. In a preliminary analysis, the dataset was used together with whole-genome and oligoarrays data to infer regulatory networks associated to cell wall metabolism that can help identify specie-specific transcripts associated to biomass production and other important traits.