Circadian co-regulation of metabolic pathways. (a) Metabolic pathways for the production of the key intermediate geranylgeranyl diphosphate (GGDP), carotenoids, tocopherols, and the phytohormone abscisic acid (ABA). The three rate-limiting enzymes CLA1 (At4g15560), PSY (At5g17230), and NCED3 (At3g14440) are indicated next to the corresponding arrows. The pathways are color-coded to match the circadian expression profiles for genes involved in the synthesis of (b) GGDP, (c) tocopherols, (d) carotenoids, and (e) ABA. Large colored arrows in panel a represent steps carried out by enzymes encoded by circadian-regulated genes (shown as thick lines in panels b to e). Medium-sized colored arrows in panel a represent a gene determined to be rhythmically expressed based on visual inspection, but that does not pass the stringent cut-off for being considered circadian regulated (pMMC-β < 0.05; shown as thin line in panel d). Thin black arrows shown in panel a represent genes that do not appear to be circadian regulated. Dashed arrows in panel a and dashed data series in panels b to d represent circadian genes that do not match the consolidated phase of expression of the other circadian genes in the pathways. The dashed data series in panel d corresponds to NPQ1 (At1g08550), which is the gene responsible for the conversion of violaxanthin back to zeaxanthin (shown as dashed arrow in panel a). The dashed line in panel b corresponds to IPP1 (At5g16440) and that in panel c corresponds to VTE2 (At2g18950). Panel e shows the mean circadian expression profiles of genes that are both circadian regulated and ABA induced (black; n = 492) and circadian-regulated ABA biosynthetic genes (green). The data shown in panels b to e are from the combined Covington plus Edwards dataset CCEE. Expression levels are plotted on the y-axes and time in constant light is plotted on the x-axes. For panels b to e, white and gray shading represent subjective day and night, respectively.