Mesophyll-Specific Circadian Dynamics of CAM Induction in the Ice Plant Unveiled by Single-Cell Transcriptomics

Crassulacean acid metabolism (CAM) is an evolutionary modification of the C3 photosynthetic carbon dioxide fixation pathway used by approximately 7% of terrestrial plants to live in drought-prone environments. Facultative CAM species, such as Mesembryanthemum crystallinum (common ice plant), possess the unique ability to switch from C3 to CAM photosynthesis in response to high-salinity and water-deficit stress. Here we characterized the environmentally-triggered transition from C3 to CAM in the ice plant using single nucleus RNA sequencing (snRNA-seq) to identify its putative regulators, supported by a novel high-quality assembled and annotated genome. Analysis of snRNA-seq datasets from ice plant leaves transitioning between C3 and CAM collected at dawn and dusk revealed substantial transcriptional changes in mesophyll cells at the onset of CAM induction. Notably, our findings identify mesophyll sub-cell types engaged in either CAM or C3 photosynthesis at dusk. Cell trajectory inference analysis reconstructed both 24-hour CAM and C3 cycles, enabling a direct comparison of gene expression profiles in these pathways. This comparative study uncovered divergent expression patterns of key circadian clock genes in CAM and C3 cell trajectories, pointing to a connection between circadian regulation and CAM induction.