Fig. 2

Time-series transcriptomic analysis of autotrophic and mixotrophic Cylindrotheca sp. highlights the transition from light into darkness. a Sampling timepoints from autotrophic (AUTO) and mixotrophic (MIXO) culture with biological triplicates (A: half one hour before darkness; B: half one hour after darkness; C: half one hour before light); b distribution of gene expression level in log₁₀ (FPKM) in a box plot; FPKM: fragments per kilobase of transcript per million fragments mapped; c principal component analysis (PCA) of all collected samples; d, e differentially expressed genes (DEGs) from AUTO-A vs AUTO-B and AUTO-A vs MIXO-A displayed in volcano plots. Red, blue, and grey dots represent upregulated, downregulated and nonDEGs, respectively; FDR: false discovery rate; f–j representative common expression patterns of DEGs in autotrophic culture with significantly enriched KEGG pathways in each pattern noted (q < 0.05)