Identification and expression profiling of genes involved in circadian clock regulation in red dragon fruit () by full-length transcriptome sequencing.

Crassulacean acid metabolism (CAM) plants fix CO at night, exhibiting a reversed regulatory pattern of metabolomic pathways compared with most model plants, which have C3 and C4 pathways. In this study, we used a valuable tropic fruit, red dragon fruit (), as model plant to identify and analyze the circadian regulation genes. Due to the absence of red dragon fruit's whole-genome dataset, we established a full-length transcriptome dataset using single-molecule real-time (SMRT) sequencing method. A 7.66-Gb dataset with 4,552,474 subreads was generated, with an average length of 1,683 bp and an N50 of 2,446 bp. Using this dataset, we identified center oscillator genes: ( ( ( ( (), and (); a gene for the input pathway: (); a gene for the output pathway: (); and genes related to the CAM pathway: ( (), and (). We further established the 24-h rhythmic expression pattern of these genes and classified these into three groups: , and have expression peaks during the day; , and have highest expression levels at night; The genes involved in the CAM pathways, namely, , and , have double expression peaks in the day and night. Comparison of these expression patterns between red dragon fruit and model plants could provide clues in understanding the circadian clock regulation and the activity of the CAM pathways in cactus plants.