Complete genome and leaf RNA-seq analysis for the model facultative CAM plant Kalanchoë gracilipes

Crassulacean acid metabolism (CAM) is a highly water use efficient (WUE) metabolic adaptation of photosynthetic CO2 assimilation that is found in at least 38 plant families. Here, we report a chromosome-scale genome assembly and de novo annotation for the drought-inducible facultative CAM species Kalanchoë gracilipes (Baker) Baillon, an epiphytic member of the Crassulaceae that is endemic to rainforests in Central and Eastern Madagascar. We also report data from a quantitative RNA-seq experiment that compared leaves of well-watered K. gracilipes, which use C3 photosynthesis, to drought-stressed leaves that had induced weak CAM. For the RNA-seq, leaf pair 1 and 2 were sampled separately from leaf pairs 3, 4 and 5, to capture the developmental gradient of CAM inducibility, and both leaf ages were sampled every 4-h over a 12-h-light/ 12-h-dark cycle, starting at 02:00, 2-h into the 12-h-light period. Together, these resources provide a comprehensive insight into the genomic and transcriptome-level regulatory underpinnings of environmentally flexible CAM and its diurnal regulation in K. gracilipes.