Possibly to increase the resonance of the plant’s rhythms with the environmental rhythms. These differences, however, did not impair the sugarcane circadian clock, which suggests that the interactions between the components of the sugarcane circadian clock may also show differences from Arabidopsis. It is worth noting that the presence of common components of the core oscillator between sugarcane and Arabidopsis does not necessarily mean that they will have the same function. It is also possible that there are more differences in the sugarcane circadian clock as we did not try to identify elements of the circadian clock that are present in sugarcane, or grasses, but not in Arabidopsis. One important question is how the circadian clock relays time information to other pathways. We have found 111 transcription factors, of a total of 356 identified in the SUCEST database, regulated by the circadian clock, including ScCCA1 and ScTOC1. Moreover, a large number of probes associated with histone regulation, spliceosome function, RNA degradation and transport are circadian clock regulated. These are mechanisms known to be involved in the control of transcript levels by the circadian clock. Another important regulatory mechanism is the expression of natural antisense transcripts. NATs have been shown to regulate their cognate transcript levels through gene methylation, direct control of transcription, alternative splicing and transcript stability. Widespread antisense transcription has been described in Arabidopsis. In this work, not only have we found AS that were co-regulated with their SS cognates, but AS that had expression levels that did not correlated with their SS cognates, as well. The circadian AS time courses had a tendency to peak towards subjective dawn, while the circadian SS time courses had a tendency to peak towards the subjective middle of the day, a difference that was also observed using tiling arrays in Arabidopsis. AS/SS pairs have been associated with gene plasticity and BIBW2992 EGFR/HER2 inhibitor responsiveness to stimuli, which could also be a strategy to increase the Gefitinib amplitude of circadian rhythms. Most of the circadian AS time courses identified did not have the time courses of their SS cognate considered circadian. These circadian AS may regulate the translation activity of their cognate SS in order to confer circadian behaviour in the protein level. Some AS/SS pairs show small changes in phase, such as violaxanthin deepoxidase and glucose 1-phosphate adenylyltransferase. It is possible that these AS act controlling the expression of their SS cognate, helping to regulate the timing of their expression. The sugarcane circadian transcriptome has shown some properties found in similar works, such as the clustering of transcripts with similar function, the anticipation of daily environmental changes and the temporal compartmentation of metabolic processes. Clustering can be observed in the light harvesting reactions of photosynthesis, in which probes associated with light harvesting complex and photosystem I cluster very tightly between ZT4 and ZT6, when sunlight is usually at its peak. Curiously, probes for synthesis of pigments precede the expression of pigment binding proteins. On the other hand, probes associated with the carbon fixing part of photosynthesis, including RuBisCo activase, tended to cluster between ZT22 and ZT2, in the beginning of the subjective day. Probes for sucrose and starch metabolism are co-ordinated during the day following the timing of the carbon fixing pathways. There is a strong association between the peaks of probes associated with sucrose synthesis, including sucrose phosphatase synthase, with the peaks of transcript for carbon fixation and the upper portion of glycolysis/gluconeogenesis, indicating that one of the destinations of the newly fixed carbon is sucrose.