ArticleMolecular ecology resources2019
Diurnal variation in opsin expression and common housekeeping genes necessitates comprehensive normalization methods for quantitative real-time PCR analyses.
Article in Molecular ecology resources, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 21 papers, 1 of them a synthesis that pooled it.
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Who cites it
21 citing papers in PubMed, 1 synthesis or guideline pooled it, 40 citations in OpenAlex.
- Phenotypic plasticity in visual opsin gene expression: a meta-analysis in teleost fish.The Journal of experimental biology · 2025Pooled it
- Genomic and regulatory basis of visual opsin genes in the cleaner wrasse behavior: features, expression, and enhancer mechanisms.Molecular biology reports · 2026Article
- Opsin gene evolution in aquatic, amphibious and terrestrial blennies (Blenniidae).Biology open · 2026Article
- Seeing in the Deep: Evolution of the Opsin Gene Expression in Bermin Crater Lake Cichlids.Molecular biology and evolution · 2025Article
- Genetic and Environmental Factors Shape Rates of Plasticity: The Temporal Dynamics of Opsin Gene Expression in Aquatic Environments.Molecular biology and evolution · 2025Article
- Robust Sensory Traits Across Light Habitats: Visual Signals but Not Receptors Vary in Centrarchids Inhabiting Distinct Photic Environments.Molecular ecology · 2025Article
- Damsels in Disguise: Development of Ultraviolet Sensitivity and Colour Patterns in Damselfishes (Pomacentridae).Molecular ecology · 2025Article
- Bifidobacterium animalis subsp. lactis BB-12 attenuates diabetic retinopathy through gut microbiota modulation: evidence for the gut-retinal axis.Frontiers in cellular and infection microbiology · 2025Article
- Visual pigment chromophore usage in Nicaraguan Midas cichlids: phenotypic plasticity and genetic assimilation ofHydrobiologia · 2025Article
- Long-wavelength-sensitive (lws) opsin gene expression, foraging and visual communication in coral reef fishes.Molecular ecology · 2023Article
- Developing and adult reef fish show rapid light-induced plasticity in their visual system.Molecular ecology · 2023Article
- Development of dim-light vision in the nocturnal reef fish family Holocentridae. I: Retinal gene expression.The Journal of experimental biology · 2022Article
- Contribution of opsins and chromophores to cone pigment variation across populations of Lake Victoria cichlids.Journal of fish biology · 2022Article
- Transcriptomic evidence for visual adaptation during the aquatic to terrestrial metamorphosis in leopard frogs.BMC biology · 2022Article
- Seeing Picasso: an investigation into the visual system of the triggerfish Rhinecanthus aculeatus.The Journal of experimental biology · 2022Article
- Correlated Expression of the Opsin Retrogene LWS-R and its Host Gene in Two Poeciliid Fishes.Zoological studies · 2022Article
- Public transcriptome database-based selection and validation of reliable reference genes for breast cancer research.Biomedical engineering online · 2021Article
- Molecular Evolution of Ultraviolet Visual Opsins and Spectral Tuning of Photoreceptors in Anemonefishes (Amphiprioninae).Genome biology and evolution · 2021Article
- Axes of visual adaptation in the ecologically diverse family Cichlidae.Seminars in cell & developmental biology · 2020Review
- Tbx2a Modulates Switching of RH2 and LWS Opsin Gene Expression.Molecular biology and evolution · 2020Article
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Authors and funding
10 authors at 1 institution in 1 country.
Funding
Abstract
To determine the visual sensitivities of an organism of interest, quantitative reverse transcription-polymerase chain reaction (qRT-PCR) is often used to quantify expression of the light-sensitive opsins in the retina. While qRT-PCR is an affordable, high-throughput method for measuring expression, it comes with inherent normalization issues that affect the interpretation of results, especially as opsin expression can vary greatly based on developmental stage, light environment or diurnal cycles. We tested for diurnal cycles of opsin expression over a period of 24 hr at 1-hr increments and examined how normalization affects a data set with fluctuating expression levels using qRT-PCR and transcriptome data from the retinae of the cichlid Pelmatolapia mariae. We compared five methods of normalizing opsin expression relative to (a) the average of three stably expressed housekeeping genes (Ube2z, EF1-α and β-actin), (b) total RNA concentration, (c) GNAT2, (the cone-specific subunit of transducin), (d) total opsin expression and (e) only opsins expressed in the same cone type. Normalizing by proportion of cone type produced the least variation and would be best for removing time-of-day variation. In contrast, normalizing by housekeeping genes produced the highest daily variation in expression and demonstrated that the peak of cone opsin expression was in the late afternoon. A weighted correlation network analysis showed that the expression of different cone opsins follows a very similar daily cycle. With the knowledge of how these normalization methods affect opsin expression data, we make recommendations for designing sampling approaches and quantification methods based upon the scientific question being examined.
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