Data from: Rapid light-induced shifts in opsin expression: finding new opsins, discerning mechanisms of change, and implications for visual sensitivity
Fuller, Rebecca C, University of Illinois at Urbana Champaign
Claricoates, Kristin M, Virginia–Maryland College of Veterinary Medicine
Published Aug 20, 2015 on Dryad.
Cite this dataset
Fuller, Rebecca C; Claricoates, Kristin M (2015). Data from: Rapid light-induced shifts in opsin expression: finding new opsins, discerning mechanisms of change, and implications for visual sensitivity [Dataset]. Dryad. https://doi.org/10.5061/dryad.k8073
Light induced shifts in cone frequency and opsin expression occur in many aquatic species. Yet little is known about how quickly animals can alter opsin expression and, thereby, track their visual environments. Similarly, little is known about whether adult animals can alter opsin expression or whether shifts in opsin expression are limited to critical developmental windows. We took adult wild caught bluefin killifish (Lucania goodei) from three different lighting environments (spring, swamp, variable), placed them under two different lighting treatments (clear vs. tea-stained water), and monitored opsin expression over four weeks. We measured opsin expression for five previously described opsins (SWS1, SWS2B, SWS2A, RH2-1, LWS) as well as RH2-2 which we discovered via 454 sequencing. We used two different metrics of opsin expression. We measured expression of each opsin relative to a housekeeping gene and the proportional expression of each opsin relative to the total pool of opsins. Population and lighting environment had large effects on opsin expression which were present at the earliest time points indicating rapid shifts in expression. The two measures of expression produced radically different patterns. Proportional measures indicated large effects of light on the SWS1 expression whereas relative measures indicated no such effect. Instead, light had large effects on the relative expression of SWS2B, RH2-2, RH2-1, and LWS. We suggest that proportional measures of opsin expression are best for making inferences about color vision, but that measures relative to a house keeping gene are better for making conclusions about which opsins are differentially regulated.
This Excel file contains the main data from Fuller & Claricoates. We list the population (population), the water treatment (water), and the day on which fish were sampled after being introduced into the lighting treatments (day). Due to low sample sizes, we had to pool these into “early, middle, and late” sampling periods which we refer to as (time). We also list the (sample name) and (sex) of the individual. We then list the mean critical threshold cycle for each individual for the following genes: elongation factor 1-alpha (CT-ef 1a), LWS (CT-LWS), RH2-1 (CT-RH2-1), RH2-2 (CT-RH2-2), SWS1 (CT-SWS1), SWS2A (CT-SWS2A), and SWS2B (CT-SWS2B). Based on these data and the efficiencies listed in our manuscript, we calculated the expression of each opsin gene relative to our housekeeping gene, elongation factor 1 alpha. These are listed as (rel-lws_ef), (rel-rh2-1_ef), (rel-rh2-2_ef), (rel-sws1_ef), (rel-sws2a_ef), and (rel-sws2b_ef). We also calculated the natural log of the relative expression of each opsin. These are listed in this file as (log(relsws1-ef)), (log(relsws2b-ef)), (log(relsws2a-ef)), (log(relrh21-ef)), (log(relrh22-ef)), and (log(rellws-ef)). We also calculated the proportional expression of each opsin gene relative to the total opsin pool. These are listed in this file as (propLWS), (propRH2-1), (propRH2-2), (propSWS1), (propSWS2a), and (propSWS2b). Finally, we also calculated the proportion expression of each opsin gene relative to all of the opsins, but excluding RH2-2. These are listed in this file as (propSWS1(noRH2-2)), (propSWS2b(noRH2-2)), (propSWS2a(noRH2-2)), (propRH2-1(noRH2-2)), and (propLWS(noRH2-2)). For other inquiries about these data, please contact Becky Fuller – email@example.com.
Lucania goodei EF1 -alpha
This is a fasta file that contains the sequence data for elongation factor 1 alpha in Lucania goodei. Genbank would not accept this data because we used cDNA that was pooled from several populations. However, we are analyzing new sequence data from a single population and should soon have an EF-1-alpha sequence submitted to Genbank.
Lucania goodei RH2-2
This is a fasta file that contains the sequence data for the RH2-2 opsin in Lucania goodei. Genbank would not accept this data because we used cDNA that was pooled from several populations. However, we are analyzing new sequence data from a single population and should soon have an RH2-2 sequence submitted at Genbank.