Table 1.
Clock genes that cycled according to MetaCycle.
Fig 1.
Brain expression profile of clock and arntl family members in endogenous (720 dd) and exogenous (920 dd) feeding Atlantic salmon.
A) The clock2a expression at 920 dd was significantly cyclic. B) clock2b had a significantly high and cyclic expression at 920 dd compared to the non-cyclic at 720 dd. C) At 920 dd arntl1a.2 had a significantly cyclic expression pattern. D) The significantly higher and cyclic expression of arntl2c at 920 dd, with an acrophase late in the night. E) arntl1b.1 with a significantly lower and cyclic expression level at 920 dd. F) A significantly lower and cyclic expression level of arntl1b.2 at 920 dd compared to 720 dd. Plots are outputs of CircaCompare with a cosinusoidal curve drawn between the circadian sampling points. Bars at the x-axis indicate the light conditions. * 24 h, ** 28 h cycling period according to MetaCycle with p-value < 0.05.
Table 2.
Genes in the KEGG pathway circadian rhythm, hepatic leukaemia factors (hlf) and thyrotroph embryonic factors (tef) cycling according to MetaCycle.
Table 3.
Genes in the KEGG pathway cell cycle cyclic according to MetaCycle.
Fig 2.
The expression profile of aanat2.1 and asmt2 in the brain of endogenous (720 dd) and exogenous (920 dd) feeding Atlantic salmon.
A) The expression of aanat2.1 at 920dd cycled significantly with a period of 28 h and had a similar expression level as in 720 dd. B) The expression of asmt2 at 920 dd was significantly higher and cyclic, with a period of 28 h, at 920 dd compared to 720 dd. Plots are outputs of CircaCompare with a cosinusoidal curve drawn between the circadian sampling points. Bars at the x-axis indicate the light conditions. ** 28 h cycling period according to MetaCycle.
Fig 3.
Acrophase of cyclic genes at endogenous and exogenous feeding according to MetaCycle.
Rose plots of circadian cyclic genes at 720 and 920 dd with color coding of the bars indicating whether the acrophase occurs during the light period (white) or dark period (grey) (LD 14:10). The size of the bars indicates the number of genes with an acrophase at the given timepoint, with number shown with an increasing value of 30 for each circle. Clock genes (light blue), KEGG pathway circadian rhythm genes, hepatic leukaemia factor (hlf) (dark blue) and genes of the KEGG pathway cell cycle (magenta) are listed under the respective acrophase. A) Distribution by acrophase of 215 genes cyclic with a period of 24 h at 720 dd. B) Distribution by acrophase of 864 genes cyclic with a period of 24 h at 920 dd.
Table 4.
Number of differentially expressed genes (DEGs) at 720 dd and 920 dd.
Fig 4.
The circadian expression pattern of members of the clock and arntl family and their Ss4R paralogues at 920 dd.
A) Both clock2a and clock2b had a significantly cyclic expression pattern but clock2a had a higher expression level. B) Only the paralogue arntl1a.2 was significantly cyclic with a high expression level. C) Both Ss4R paralogues arntl1b.1 and arntl1b.2 were cycling with a period of 24 h and an acrophase 22.00. D) The paralogue arntl2c was significantly cyclic with an acrophase at 06:00, while the arntl2b expression was low. The acrophases for clock2a, clock2b, arntl1a.2, arntl1b.1 and arntl1b.2 were all late in the light phase or early dark phase. Plots are outputs of CircaCompare with a cosinusoidal curve drawn between the circadian sampling points. Bars at the x-axis indicate the light conditions. * 24 h, ** 28 h cycling period according to MetaCycle with p-value < 0.05.
Fig 5.
Heatmap of the differentially expressed genes.
The heatmap shows DEGs among the clock genes, genes of the circadian rhythm KEGG pathway, hlfs and tefs and genes in the melatonin synthesis. Each sampling point is given by mean normalized counts and white or black bars indicate the light:dark period. The heatmap shows that in the brain of feeding fry dd, 16 clock genes were upregulated and 17 were downregulated, 26 genes of the circadian rhythm KEGG pathway, hlfs and tefs and genes were upregulated and 17 downregulated. Five genes of the melatonin synthesis were upregulated and one downregulated. The heatmap is scaled by row and genes are annotated as in S6 Table.