Lessons from the Analysis of WGS and RNA-Seq of a Sugarcane Cultivar

Despite the major importance of sugarcane (Saccharum spp) for biofuel production, its complex polyploid genome yet remains vastly unexplored both from structural and functional points of view. In this talk, we will present current progress in the assembly of whole genome shotgun sequencing data from sugarcane cultivar SP80-3280 and discuss its state as compared to assemblies of other polyploid and diploid species.

1 - Alignment of shotgun short reads against the sorghum (Sorghum bicolor) genome, the known diploid genome most closely related to sugarcane, indicated that up to 30% of the sugarcane genome has a counterpart in this diploid relative, with dispersed islands of conservation between the two species.

2 - From a functional standpoint, RNA sequencing provided evidence that many of the predicted sugarcane genes lack introns, as observed by the complete alignment of the majority of full-length RNA-seq reads.

3 - Differential gene expression analyses between tissues of SP80-3280 further showed a weak but significant local effect on gene expression, potentially indicating that genes located close to each other may share expression control mechanisms.

4 - Finally, we compared SNP allele frequencies among DNA and RNA reads on a gene-by-gene basis and found that as much as half of the predicted genes displayed some level of preferential allele expression, substantiating observations that gene expression underwent significant modifications during the polyploidization events of sugarcane.