Scripts used to analyze spectra from scallop retinochrome in manuscript, "Widespread variation in retinochrome spectral absorbance across scallop phylogeny".
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.
- spectra_analysis.R: script to estimate lmax from dark and difference spectrum
- spectra_multi_panel.R: accessory script to make multipanel figure of spectral results
- spectra_overlay_variants.R: accessory script to make a figure with mutant difference spectra overlaying each other with wild-type values indicated
- spectra_overlay_WT.R: accesory script to overal the wild-type difference spectra, with visible light bar for refernce