Tity of each and every residue pair in each and every column, with green bars representing identical JNJ-47965567 Purity & Documentation residues and missing bars highlighting regions exactly where sequences differ. Finish gaps within the alignments have solid green bars. Amino acids are shaded depending on similarity, with black representing identical residues between the two sequences, grey representing similar residues, and white representing dissimilar residues. A = arrestin, B = cGMP gated channel alpha, C = cGMP gated channel beta, D = Goprotein alpha subunit, E = Gtprotein alpha subunit, F = Gprotein beta subunit, G = Gprotein gamma subunit, H = opsin, I = PDE alpha, J = PDE beta, K = protein kinase A, L = rhodopsin kinase. (PDF) Figure S3 Amino acid alignments of scallop circadian clock genes to identified homologs. Circadian clock gene sequences in the Placopecten magellanicus adult eye transcriptome have been translated and aligned to identified homologs from Drosophila, mouse, or Crassostrea gigas. Alignments had been completed and exported from Geneious v. five.6 (www.geneious.com). The graph above the alignment represents imply pairwise identity of each and every residue pair in every column, with green bars representing identical residues and missing bars highlighting locations where the sequences differ. End gaps within the alignments have strong green bars. Amino acids are shaded according to similarity, with black representingidentical residues involving the two sequences, grey representing comparable residues, and white representing dissimilar residues. A = clock, B = cryptochrome, C = cycle, D = doubletime, E = period, F = timeless. (PDF)Table SList of phototransduction and circadian clock protein sequences applied in blasts to recognize homologs inside each and every scallop eye transcriptome. All protein sequences had been downloaded from NCBI and blasted against the transcriptomes applying Geneious v. five.5 (Biomatters). (XLSX)Table S2 Genes annotated with Gene Ontology (GO) terms associated with neural processes, vision, or retina(l) in the adult eye transctriptome of A. irradians. (XLSX) Table S3 Genes annotated with Gene Ontology (GO) terms related to neural processes, vision, or retina in the adult eye transcriptome of P. magellanicus. (XLSX) Table S4 List of genes identified in KEGG pathways related to light detection inside the adult eye transcriptomes of A. irradians and P. magellanicus. KEGG pathways have been identified utilizing the KEGG Automatic Annotation Server (www. genome.jp/tools/kaas). (XLSX)AcknowledgmentsBrad Fleming kindly assisted with MATLAB scripts to organize data files and Fadi Towfic assisted using the InParanoid analyses. Figure 1 was made by Samantha Butler. The photo for Figure 1A was taken by Anita Krause. We thank Keithanne Mockaitis for her support with production of the Argopecten irradians transcriptome dataset. We also thank members in the D.C. Adams, N. Valenzuela, and J.M. Serb labs and three anonymous reviewers for their helpful comments on earlier drafts of this manuscript.Author ContributionsConceived and created the experiments: ANP JMS. Performed the experiments: ANP. Analyzed the data: ANP JMS. Contributed reagents/ materials/analysis tools: JMS. Wrote the paper: ANP JMS. Completed the scallop eye tissue dissections: ANP JMS.
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