Find research datasets worth reusing
Search datasets from major research repositories and use ShareScore to quickly assess how well each record supports discovery, access, and reuse.
30
datasets available to search
ShareScore release 0.9.0
Dataset results
30 results for “opsin genes”
PAML data from: Evolutionary ecology of the visual opsin gene sequence and its expression in turbot (Scophthalmus maximus)
Open the record for dataset details and reuse information.
Data from: Novel opsin gene variation in large-bodied, diurnal lemurs
Open the record for dataset details and reuse information.
Data from: Variation in opsin genes correlates with signaling ecology in North American fireflies
Open the record for dataset details and reuse information.
Microhabitat partitioning correlates with opsin gene expression in coral reef cardinalfishes (Apogonidae)
<ol> <li>Fish are the most diverse vertebrate group, and they have evolved equally diverse visual systems, varying in terms of eye morphology, number and distribution of spectrally distinct photoreceptor types, visual opsin genes and opsin gene expression levels.</li> <li>This variation is mainly due to adaptations driven by two factors: differences in the light environments and behavioural tasks. However, while the effects of large-scale habitat differences are well described, it is less clear whether visual systems also adapt to differences in environmental light at the microhabitat level.</li> <li>To address this, we assessed the relationship between microhabitat use and visual system features in fishes inhabiting coral reefs, where habitat partitioning is particularly common.</li> <li>We suggest that differences in microhabitat use by cardinalfishes (Apogonidae) drive morphological and molecular adaptations in their visual systems. To test this, we investigated diurnal microhabitat use in 17 cardinalfish species and assessed whether this correlated with differences in visual opsin gene expression and eye morphology.</li> <li>We found that cardinalfishes display six types of microhabitat partitioning behaviours during the day, ranging from specialists found exclusively in the water column to species that are always hidden inside the reef matrix.</li> <li>Species predominantly found in exposed microhabitats had higher expression of the short-wavelength sensitive violet opsin (<i>SWS2B</i>) and lower expression of the dim-light active rod opsin (<i>RH1</i>). Species of intermediate exposure, on the other hand, expressed opsins that are mostly sensitive to the blue-green central part of the light spectrum (<i>SWS2As</i> and <i>RH2s</i>), while fishes entirely hidden in the reef substrate had a higher expression of the long-wavelength sensitive red opsin (<i>LWS</i>).</li> <li>We also found that eye size relative to body size differed between cardinalfish species, and relative eye size decreased with an increase in habitat exposure.</li> <li>Retinal topography did not show co-adaptation with microhabitat use, but data suggested co-adaptation with feeding mode.</li> <li>We suggest that, although most cardinalfishes are nocturnal foragers, their visual systems – and possibly those of other (reef) fishes – have also adapted to the light intensity and the light spectrum of their preferred diurnal microhabitats.</li> </ol>
Data from: Analysis of the opsin repertoire in the tardigrade Hypsibius dujardini provides insights into the evolution of opsin genes in Panarthropoda
<p>Screening of a deeply sequenced transcriptome using Illumina sequencing as well as the genome of the tardigrade <em>Hypsibius exemplaris </em>(referred to as <em>Hypsibius dujardini </em>in the published article) revealed a set of five opsin genes.To clarify the phylogenetic position of these genes and to elucidate the evolutionary history of opsins in Panarthropoda (Onychophora +Tardigrada+Arthropoda), we reconstructed the phylogeny of broadly sampled metazoan opsin genes using maximum likelihood and Bayesian inference methods in conjunction with carefully selected substitution models. According to our findings, the opsin repertoire of <em>H. exemplaris</em> comprises representatives of all three major bilaterian opsin clades, including one r-opsin, three c-opsins, and a Group 4 opsin (neuropsin/opsin-5). The identification of the tardigrade ortholog of neuropsin/opsin-5 is the first record of this opsin type in a protostome,but our screening of available metazoan genomes revealed that it is also present in other protostomes. Our opsin phylogeny further suggests that two r-opsins, including an "arthropsin", were present in the last common ancestor of Panarthropoda. Although both r-opsin lineages were retained in Onychophora and Arthropoda, the arthropsin was lost in Tardigrada. The single (most likely visual) r-opsin found in <em>H. exemplaris</em> supports the hypothesis of monochromatic vision in the panarthropod ancestor, whereas two duplications of the ancestral panarthropod c-opsin have led to three c-opsins in tardigrades. Although the early-branching nodes are unstable within the metazoans, our findings suggest that the last common ancestor of Bilateria possessed six opsins: Two r-opsins, one c-opsin, and three Group 4 opsins, one of which (Go opsin) was lost in the ecdysozoan lineage.</p>
Microhabitat partitioning correlates with opsin gene expression in coral reef cardinalfishes (Apogonidae)
Open the record for dataset details and reuse information.
Data from: Analysis of the opsin repertoire in the tardigrade Hypsibius dujardini provides insights into the evolution of opsin genes in Panarthropoda
Open the record for dataset details and reuse information.
Data from: Functional preservation and variation in the cone opsin genes of nocturnal tarsiers
Open the record for dataset details and reuse information.
A New Model Organism to Investigate Extraocular Photoreception: Opsin and Retinal Gene Expression in the Sea Urchin Paracentrotus lividus
GEO Series GSE211842. Paracentrotus lividus. 2 samples. Type: Expression profiling by high throughput sequencing.
Expression of Extraocular opsin Genes and Light-Dependent Basal Activity of Blind Cavefish
<p><strong>Background. </strong>Animals living in well-lit environments utilize optical stimuli for detecting visual information, regulating the homeostatic pacemaker, and controlling patterns of body pigmentation. In contrast, many subterranean animal species without optical stimuli have evolved regressed binocular eyes and body pigmentation. Interestingly, some fossorial and cave-dwelling animals with regressed eyes still respond to light. These light-dependent responses may be simply evolutionary residuals or they may be adaptive, where negative phototaxis provides avoidance of predator-rich surface environments. However, the relationship between these non-ocular light responses and the underlying light-sensing Opsin proteins has not been fully elucidated.</p> <p><strong>Methods. </strong>To highlight the potential functions of opsins in a blind subterranean animal, we used the Mexican cave tetra to investigate opsin gene expression in the eyes and several brain regions of both surface and cave-dwelling adults.<strong> </strong>We performed database surveys, expression analyses by quantitative reverse transcription PCR (RT-qPCR), and light-dependent locomotor activity analysis using pinealectomized fish, one of the high-opsin expressing organs of cavefish.</p> <p><strong>Results. </strong>Based on conservative criteria, we identified 33 opsin genes in the cavefish genome. Surveys of available RNAseq data found 26 of these expressed in the surface fish eye as compared to 24 expressed in cavefish extraocular tissues, 20 of which were expressed in the brain. RT-qPCR of 26 opsins in surface and cavefish eye and brain tissues showed the highest opsin-expressing tissue in cavefish was the pineal organ, which expressed exo-rhodopsin at 72.7 % of the expression levels in surface fish pineal. However, a pinealectomy resulted in no change to the light-dependent locomotor activity in juvenile cavefish and surface fish. Therefore, we conclude that, after 20,000 or more years of evolution in darkness, cavefish light-dependent basal activity is regulated by a non-pineal extraocular organ.</p>
ScienceDex guides
Understand access before you commit
These curated guides explain access requirements, typical timelines, costs, and reuse considerations for widely used research datasets.
Allen Brain Atlas
Allen Brain Atlas is an Allen Institute collection of brain map atlases, datasets, APIs, and analysis tools covering mouse, human, and non-human primate brain resources.
Annotated Behaviour and Observability Dataset (ABODe)
ABODe is a University of Edinburgh DataShare dataset for behavior classification in group-housed mice using home-cage video, identities, bounding boxes, ground-plate positions, and annotator labels.
DANDI Archive for NWB datasets
DANDI is a BRAIN Initiative archive for publishing and sharing neurophysiology data, including electrophysiology, optophysiology, and behavioral data packaged as NWB and related standards.
International Brain Laboratory public data
The International Brain Laboratory public data releases expose standardized mouse decision-making experiments, including Neuropixels recordings, widefield calcium imaging, behavior, and session metadata accessed through the ONE API.
OpenNeuro
OpenNeuro is a free, open platform for sharing neuroimaging datasets, with public search, dataset pages, and download paths for web, S3, DataLad, and the OpenNeuro CLI.