Diel transcriptome response of sugarcane (Saccharum sp.) under regular and short day reveals distinct rhythmic behavior

Diel rhythms occur in response to a light-dark cycle and are major players synchronizing the endogenous rhythms to external stimuli such as photoperiods. Perfect matching between photoperiod and rhythms is of great importance for plants, resulting in competitive advantages. Sugarcane comprises about 75% of the world's sugar production and has an enormous potential for biofuel industry because of its high capacity of sucrose storage in the stems, which reaches about 670 mM. Most of the knowledge of rhythmic expression came from Arabidopsis studies, a starch-accumulating diploid C3 plant, while sugarcane runs C4 photosynthesis, accumulates sucrose and is highly polyploid. Here we report a RNA-seq transcriptomic survey from sugarcane subjected to regular and short day. We showed a different phase profile related to each photoperiod, with an enrichment in the middle of the night under short day. We organized transcripts in functional groups related to characteristics of commercial interest for sugarcane and discussed their relationships. Gene ontology analysis revealed evidence of a significant enrichment of genes related to negative regulation of defense response in regular day, notably in groups of genes shared between Arabidopsis and sugarcane. We also report a set of rhythmic long non-coding RNAs and emphasize their level of conservation to other crops, and the establishment of gene co-expression to better understand the gene networks under a diel control, including many lncRNAs. Finally, we also detected several genes related to photosynthesis that were enriched in sugarcane subjected to different photoperiods, in a similar manner to other plants showing the plasticity of photosynthesis in response to abiotic stress.