The Genome Sequence of a Sugarcane Hybrid: Exploring Gene Alleles, Transcripts and Regulatory Elements

Expansion of bioenergy use in the world, with practices that reduce CO₂ emissions and water requirement, is expected to contribute significantly to climate change mitigation. The understanding of regulatory networks that control sugarcane growth and maturation is increasingly necessary for its improvement. We are sequencing the sugarcane genome using several high-throughput platforms (454, HiSeq, Moleculo). Using Moleculo long reads technology, we obtained a total of 21.8 Gb of sequencing data, which roughly corresponds to 2.18 X coverage of the 10 Gbp polyploid genome. The assembly yielded 450,609 contigs, with contig length average of 9,452 bp and N50 of 13,157. Until now, we have observed that using Moleculo long reads we obtained a more than 5-fold increase in contiguity over the WGS assembly based on 454 data only. As sugarcane genome is highly polyploid, we are developing new algorithms to enable the recognition of allelic copies. Existing data on the sugarcane transcriptome is being integrated to validate gene models and infer gene function. We have full-length enriched cDNA libraries for S. officinarum, S. spontaneum and SP803280 and a first draft of the sugarcane ORFeome. We found 38,195 (19%) sugarcane-specific transcripts with less than 0.5% of all transcripts being ancestor-specific. This cDNA library comprises 17,563 full-length unique genes. The transcriptomic and genomic techniques that are being developed in our group associated with the physiological data are resulting in a more comprehensive understanding of sugar content, fibre and drought regulation that can aid through translational genomics efforts for the development of an Energycane.