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Updated: Nov 11, 2025

A Bioinformatics Pipeline for Investigating Molecular Evolution and Gene Expression using RNA-seq

A Bioinformatics Pipeline for Investigating Molecular Evolution and Gene Expression using RNA-seq

Published on: May 28, 2021

Evolutionary Constraint on Visual and Nonvisual Mammalian Opsins.

Brian A Upton^1,2,3,4, Nicolás M Díaz⁵, Shannon A Gordon⁵

¹Visual Systems Group, Abrahamson Pediatric Eye Institute, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio.

Journal of Biological Rhythms

|March 26, 2021

Summary

Mammalian opsins, crucial for light detection, show diverse evolutionary patterns. Some, like OPN5 and rhodopsin, are highly conserved, while others, such as RGR and OPN4, exhibit significant diversity across species.

Keywords:

RGR-opsin atypical encephalopsin melanopsin neuropsin peropsin

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Area of Science:

Evolutionary biology
Genomics
Molecular biology

Background:

Opsins are light-sensitive G protein-coupled receptors essential for visual and nonvisual functions in animals.
Mammalian opsins have adapted to specific lighting environments, with known variations in rod and cone opsins, but less understanding of atypical opsins.
Atypical opsins include photoisomerases (RGR, RRH), encephalopsin (OPN3), melanopsin (OPN4), and neuropsin (OPN5).

Purpose of the Study:

To investigate the evolutionary patterns of various mammalian opsins, including atypical ones.
To compare the conservation and diversity of different opsin families across mammalian lineages.
To understand the evolutionary constraints and functional implications of opsin evolution in mammals.

Main Methods:

Genomic data analysis from over 400 mammalian species across 22 orders.
Identification and comparison of evolutionary patterns for photoisomerases (RGR, RRH), OPN3, OPN4, and OPN5.
Assessment of sequence conservation and diversity, including lineage-specific gene loss.

Main Results:

Rhodopsin and OPN5 exhibit extreme conservation across all mammalian lineages.
Cone opsins (SWS1, LWS), OPN3, and RRH show moderate conservation with some gene loss.
RGR and OPN4 display high sequence diversity within mammals, with conserved residues for chromophore binding.
Observed conservation patterns are consistent in human populations.

Conclusions:

Mammalian opsins display distinct evolutionary trajectories, reflecting adaptation to diverse functions and environments.
The retention of key amino acid residues ensures the light-sensing capability of all mammalian opsins.
Understanding these evolutionary patterns provides insights into the functional roles of atypical opsins in physiology, such as circadian and metabolic regulation.