Alignment of the amino acid sequences in Carassius auratus, Danio rerio and Lepisosteus oculatus. The numbers at the nodes indicate the % significance of each internal node after 1000 Bootstrap replicates. The green diamonds represent duplications of “opn7” forms during the second (2R), third (3R), and fourth (4Rc) whole-genome duplications, and the purple circles represent tandem duplications (TD). The duplication 3R with question marks does not fit the phylogenetic history of the species due to the “long-branch attraction effect”; hence, the blue dashed line proposes how the branches should be arranged. The optimal tree is shown. The tree is drawn to scale, with branch lengths in the same units as those of the evolutionary distances used to infer the phylogenetic tree. The evolutionary distances were computed using the Poisson correction method and are in the units of the number of amino acid substitutions per site. This analysis involved 21 amino acid sequences. All ambiguous positions were removed for each sequence pair (pairwise deletion option). There was a total of 530 positions in the final dataset

Tissue distribution of representative opn7 paralogs in goldfish. (a) Agarose gel showing amplification on opn7a in the retina, but not in the liver. gDNA: genomic DNA control (no amplification because the amplicon is between two exons). Relative abundance (the value 1 was assigned to the lowest value) of opn7b (b), opn7c (c), and opn7d (d) transcripts in central and peripheral tissues. Data are expressed as mean + SEM (N = 5)

Effect of the 4 h exposure of live goldfish to light of different wavelengths during the night (ZT 14), on the mRNA abundance of per1a, per2a, and cry1a in the retina (a,c,e) and in the liver (b,d,f). Data are expressed as mean ± SEM (N = 8). One-way ANOVA or Kluskal-Wallis * p < 0.05, *** p < 0.001, n.s. p > 0.05. Different letters indicate statistically significant differences according to Student-Newman-Keuls or Dunn’s post-hoc test

Effect of 6-h direct light exposure to different wavelengths on the mRNA abundance of per2a (a), and cry1a (d) in the retina; and of per2a (b), per1a (c), and cry1a (e) in the liver. Effect of dexamethasone (DX, 100 mM) on the mRNA abundance of per1a in cultured goldfish liver (f). Data are expressed as mean ± SEM (N = 8). Paired t-test was performed when only two groups were compared * p < 0.05, ** p < 0.01 (a,d,f), and One-way ANOVA when there were more than two groups, n.s. p > 0.05 (b,c,e)