Fig. 3.

The Chlamydomonas transcriptome is highly dynamic and rhythmic over one diurnal cycle. (A) PCA of the Chlamydomonas transcriptome over the diurnal cycle: samples collected at night (●), samples collected during the day (○). The time of sample collection is indicated next to the corresponding circle. (B) Heatmap representation of gene expression for 10,465 differentially expressed genes over the diurnal cycle. Genes were included if at least 1,000 counts were detected in the experiment, and there was a Benjamini–Hochberg-adjusted P value < 0.01 for differential expression. Genes were grouped into 16 clusters of nuclear genes, 3 clusters of chloroplast genes, and 1 mitochondrial cluster. For easier visualization, the vertical scale of the organellar transcriptomes (chloroplast transcriptome, Middle; mitochondrial transcriptome, Bottom) is enlarged 50 times relative to the nuclear transcriptome. (C) Heatmap representation of gene expression for 6,916 genes based on peak time (phase) of expression, as determined by the algorithm JTK_CYCLE, with minimal expression of 1 FPKM for at least one time-point. For easier visualization, the vertical scale of the organellar transcriptomes (chloroplast transcriptome, Middle; mitochondrial transcriptome, Bottom) is enlarged 25 times relative to the nuclear transcriptome. The green vertical lines indicate the timing of cell division.