DOI: 10.6084/m9.figshare.29067578
title: Data from Widespread variation in retinochrome spectral absorbance across scallop phylogeny

description: <b>Abstract </b>(may differ from final publication)<br>Vision is a two-step process, including phototransduction initiated by a retinal-bound opsin photopigment, and subsequent photopigment regeneration following retinal release. In some animal lineages, a second opsin functions as a photoisomerase that converts retinal back to the proper conformation for the visual opsin, but very little is known about their spectral properties. We investigated spectral variation and spatial expression of scallop retinochrome, an opsin used for light-driven regeneration of molluscan visual photopigments. We show that retinochrome is expressed in scallop retina, along with visual opsins, indicating a conserved role in supporting vision. We compared retinochrome spectral absorption across six species with different ecologies, revealing considerable functional variation possibly associated with photic environments. Finally, we characterized multiple amino acid sites contributing to spectral tuning – shifts in the specific maximally sensitive wavelength of light - of this opsin. These results reveal retinochrome as a functionally dynamic component of the scallop visual cycle that may be adapted to different photic environments across species and highlights spectral tuning in an ocular but otherwise non-visual photopigment, which has been largely overlooked in studying the evolution of visual cycles.<br>This dataset includes wild-type retinochrome sequences from 4 species of scallops, along with mutants from site-directed mutagenesis targeting predicted spectral tuning sites. This dataset also includes the data underlying Figure 1 from the manuscript, a phylogenetic representation of different opsin groups.<br><b>Files included</b>Scallop_RTC_WT_muts.nt.fasta - scallop retinochrome (RTC) used for <i>in vitro</i> expressionOpsin_out_seqs.aa.mafft-einsi.fa - opsin amino acid sequences, aligned with MAFFTOpsin_out_seqs.aa.mafft-einsi.trimal-gappy.fa - opsin amino acid sequence alignment, trimmed with trimalOpsin_out_seqs.aa.mafft-einsi.trimal-gappy.fa.iqtree - run summary for IQ-TREE2 analysis of opsin sequencesOpsin_out_seqs.aa.mafft-einsi.trimal-gappy.fa.log - log file for IQ-TREE2 analysis of opsin sequencesOpsin_out_seqs.aa.mafft-einsi.trimal-gappy.fa.treefile - ML phylogenetic tree of opsins and outgroup sequences (newick format)SLURM_job_OpsinPhylo.bash - job script to perform sequence alignment, trimming, and phylogenetic analysis<b>Description of "</b><b>Scallop_RTC_WT_muts.nt.fasta"</b>Nucleotide sequences of scallop retinochrome expressed in cell culture for this study. These sequences represent gene inserts into the p1D4-hrGFP II expression vector, and therefore lack stop codons. These nucleotide sequences were not codon-optimized for expression in human cell culture.The wild-type sequences are:Apur-RTC: retinochrome from <i>Argopecten purpuratus</i>Aple-RTC: retinochrome from <i>Amusium pleuronectes</i>Cfar-RTC: retinochrome from <i>Chlamys farreri</i>Myes-RTC: retinochrome from <i>Mizuhopecten yessoensis</i>The mutant sequences are (site numbers refer to amino acid positions in the scallop retinochrome):Apur-RTC_W188Y: <i>Argopecten purpuratus </i>with W --&gt; Y amino acid substitution at site 188Apur-RTC_A193V: <i>Argopecten purpuratus </i>with A --&gt; V amino acid substitution at site 193Apur-RTC_W188Y-A193V: <i>Argopecten purpuratus</i> double mutant with W --&gt; Y amino acid substitution at site 188 and A --&gt; V amino acid substitution at site 193Cfar-RTC_G189S: <i>Chlamys farreri</i> with G --&gt; S amino acid substitution at site 189Myes-RTC_S189G: <i>Mizuhopecten yessoensis </i>with S --&gt; amino acid substitution at site 189<b>Phylogenetic tree</b>See "SLURM_job_OpsinPhylo.bash" for details on program versions and methods for alignment, trimming, and tree construction<br>