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Figure 1. Schematic pathway and components of retinoic acid (RA) signaling in echinoderms. The signaling pathway is divided into three steps: RA synthesis/degradation, RA transport, and gene expression regulation. Dotted arrows indicate the direction of signaling transduction; orange and gray indicate canonical and non-canonical pathways, respectively. Squares indicate enzymes and retinal derivatives; blue, brown indicate enzymes with canonical and non-canonical pathways, respectively, and yellow indicates retinol derivatives. Solid arrows indicate enzyme functions.
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Figure 2. Maximum-likelihood phylogenetic tree for RDH genes (A: sdr7 and B: adh3). All sequences are presented in Tables S1 and S2 and Supplementary Datasets 1 and 2. Sequences were aligned using the MAFFT v7 software with the default parameters [20]. Amino acid sites for tree construction were selected using the trimAl (1.2rev59) tool with a gap threshold of 0.8 [21]. A best-fitting amino acid substitution model and a maximum-likelihood tree were inferred using the RaxML v8.2.12 software [22]. Confidence values shown at nodes were calculated after 1000 bootstrap runs. Yellow box and arrows, respectively, indicate sdr7 (A), adh3 (B) gene clade and the genes retrieved from dataset of echinoderms. Abbreviation: Human; Homo sapiens, Mouse; Mus musculus, Bovine; Bos taurus, Frog; Xenopus tropicalis, Frog; Xenopus leavis, Zebrafish; Danio rerio, Amphioxus; Branchiostoma floridae, Acorn worm; Saccoglossus kowalevskii, Sea cucumber; Holothuria glaberrima, Scallop; Mizuhopecten yessoensis, Oyster; Crassostrea gigas, Annelid; Platynereis dumerilii, Annelid; Capitella teleta, Limpet; Lottia gigantea and Sea anemone; Nematostella vectensis.
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Figure 3. Maximum-likelihood phylogenetic tree for aldh1a, -1b and 2 genes. We retrieved the gene dataset of aldh1a, -1b and 2 (Table S3, Supplementary Dataset 3) and constructed phylogenetic tree as described above. Yellow box and arrows, respectively, indicate aldha1 gene clade and aldha1 genes retrieved from dataset of echinoderms. Abbreviation: Tunicate; Ciona intestinalis.
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Figure 4. Maximum-likelihood phylogenetic tree for aldh5–9 genes. We retrieved the gene dataset of aldh5–9 (Table S4, Supplementary Dataset 4) and constructed phylogenetic tree as described above. Yellow box and arrows, respectively, indicate aldh8a1 gene clade and aldh8a1 genes retrieved from dataset of echinoderms.
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Figure 5. Maximum-likelihood phylogenetic tree for cyp genes. We retrieved the gene dataset of cyp (Table S5, Supplementary Dataset 5) and constructed phylogenetic tree as described above. In addition, construct phylogenetic tree, respectively. Yellow box and arrows, respectively, indicate cyp26 gene clade and cyp26 genes retrieved from dataset of echinoderms.
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Figure 6. Maximum-likelihood phylogenetic tree for iLBP genes. We retrieved the dataset of iLBP genes (Table S6, Supplementary Dataset 6) and constructed phylogenetic tree as described above. Each color box indicates the gene clade of crabp (blue), fabp-like1 (orange), fabp-like2 (green) and fabp-like3 (yellow). Abbreviation: Fly; Drosophila melanogaster, Locust; Schistocerca gregaria and Moth; Bombyx mori.
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Figure 7. Maximum-likelihood phylogenetic tree for nuclear receptor genes. We retrieved the dataset of nuclear receptor genes (Table S7, Supplementary Dataset 7) and constructed phylogenetic tree as described above. Each color box indicates the gene clade of ppar (orange), rar (green) and rxr (yellow). Arrows indicate the genes retrieved from dataset of echinoderms. Abbreviation: thr; thyroid hormone receptor, Amphioxus (Bl); Branchiostoma lanceolatum, Tunicate (Pm); Polyandrocarpa misakiensis, Snail (Rc); Reishia clavigera, Snail (Ls); Lymnaea stagnalis and Jellyfish; Tripedalia cystophora.
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Figure 8. Summary of gene identification of RA signaling components in echinoderms. Yellow boxes indicate the presence of ortholog genes. On the other hand, gray and white boxes indicate the absence of ortholog genes in the search of transcriptomic and genomic dataset, respectively.
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Figure 9. The function of RA signaling in life cycle transition of echinoderms and cnidarians. The involvement of RA signaling in metamorphosis is reported in the starfish P. pectinifera [9], A. latespinosus [10] and the feather star A. serrata [11]. RA is also known as the regulator of strobilation in the jellyfish Aurelia aurita [12].
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