Insights into Signaling and Regulation of Gene Expression in the Highly Polyploid Sugarcane

Sugarcane is of global importance in the field of renewable energy, including biofuels, bioelectricity and as a biomass feedstock for bioprocessing into a wide range of chemicals. The study and improvement of sugarcane through genetic diversity and its adaptation to the environment is a major challenge, mainly because of the complex genome that is polyploid and aneuploid, and the great allelic variation. The CaneRegNet framework is the most complete reference for studies on the Sugarcane transcriptome allowing to associate gene expression profiles, gene functions and now structural and functional genomic information. We previously described an assembled sugarcane genome of 450,609 scaffolds with NG50 of 41,394Kb and 373,869 predicted genes. The integration of the sugarcane genome and the transcriptome data within CaneRegNet is now allowing to study how the expression profile differs among the alleles, if all of them are expressed in similar levels and if allele expression is tissue-specific. Genome annotation improved the Signal Transduction (SUCAST), Transcription Factors and Cell Wall catalogues. From the predicted genes, 15,737 genes were annotated and classified into 57 TF families including 12 new families in relation to those obtained within the SUCEST Project. MYB-related and CSD TF families had also an impressive increase in the number of identified members (762 and 2,209 genes respectively). A total of 4,661 genes were classified into 20 Cell Wall categories, an increase of 3,936 genes. The most identified and represented Cell Wall categories were “Internal Signal Transduction”, “Phenylpropanoid biosynthesis” and “Other glycan degradation”. The CaneRegNet framework will be presented as well as analysis tools for the application of Systems Biology approaches.