Fig. 5: GC development networks under darkness and light.

a, RNA velocity inferred for SL cells of light-grown samples. The colours indicate different subtypes. b, RNA velocity inferred for SL cells of dark-grown samples. The colours indicate different subtypes. c, Cell atlases for SL of Light samples. Transcript distributions of development factors in SL cells are highlighted by different colours. d, Cell atlases for SL of Dark samples. Two replicates of Dark samples are merged. Transcript distributions of development factors in SL cells are highlighted by different colours. e, Visualization of SL cells during the de-etiolation process. The orange and black arrows indicate canonical and dark-specific trajectories, respectively, for GC development. f, Latent time inferred for SL cells during the de-etiolation process; a darker colour represents earlier development stages. g, Expression trends of candidate regulators involved in SL development in dark and light conditions along the inferred pseudotime. h, Regulatory models for GC development. The black dots represent the respective cell clusters (0–9). Cells belonged to different clusters were coloured in respective colours: dark-grown precursors: 0, 4, 6; de-etiolating precursors: 1, 3; light-grown precursors: 2, 5; light-grown pavement cell: 9; light-grown GC: 8; dark-grown and de-etiolating GC: 7. The black edges between the black dots represent probabilities for cell state transitions. The size of the edges corresponds to the approval rate (the frequency of occurence for edges). The candidate genes involved in the respective trajectories are listed.