Ocular and extraocular expression of opsins reveals evolutionary trends underlying visual and non-visual functions in bivalves (Pteriomorphia)
Data files
Apr 14, 2026 version files 7.34 MB
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Bash_commands.txt
3.17 KB
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bivalve_opsins_updated.csv
1.93 KB
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comparative_opsins_GLMM.R
15.41 KB
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comparative_opsins_plots.R
11.45 KB
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expression_rank.txt
5.19 KB
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opsin_ali_trim_auto.fasta
171.22 KB
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opsin_ali.fa
685.52 KB
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opsin_full.treefile
29.91 KB
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opsin_pruned_expressed_only.tree
14.04 KB
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rank-based_comparison_opsin.R
2.79 KB
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README.md
5.28 KB
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species_tree.fasta
6.40 MB
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species_tree.tre
448 B
Abstract
Opsin proteins are central to photoreception and have diversified extensively to support both visual and nonvisual functions in animals. While the molecular conservation is striking, the evolutionary pathways that shaped opsin diversity, particularly in relation to visual and extraocular roles, remain poorly understood. To address this gap, we examined opsin repertoires in Pteriomorphia, a diverse group of mostly sessile marine bivalves with multiple photoreceptor systems and ecologies. We generated transcriptomes for 12 species, including eyed and eyeless adults, and analyzed published RNA-seq data from five additional species, covering all taxonomic orders and eye types. We identified and classified opsins expressed in the photosensitive mantle margin and eyes using phylogenetically informed annotation. We tested whether opsin diversity is associated with eye presence or mobility and determined which opsins are widely used. Our results suggest that bivalve eyes generally express more opsins than extraocular tissues. Additionally, opsin expression in photosensitive tissues suggests an ancestral repertoire for the mantle margin, with convergent changes in repertoire size. Curiously, differences in mobility among species do not influence opsin repertoire. Our findings further support that the rhodopsin-retinochrome system is pervasive across bivalves and identify visual and nonvisual opsins used in both eyes and dermal photoreception.
Dataset DOI: 10.5061/dryad.kd51c5bhj
Description of the data and file structure
We compare 17 species based on transcriptomic data to determine opsin profiles from photosensitive tissues, including eyes from eyed species and mantle margin (extraocular tissue) from eyeless species. We generated transcriptomes for 12 species, including eyed and eyeless adults, and analyzed published RNA-seq data from five additional species, covering all taxonomic orders and eye types. We identified and classified opsins expressed in the photosensitive mantle margin and eyes using phylogenetically informed annotation. We tested whether opsin diversity is associated with eye presence, photoreception class, or mobility, and determined which opsins are widely used.
Files and variables
File: species_tree.fasta
Description: amino acid sequences derived from single-copy ortholog genes (BUSCO) for 17 pteriomorphian species.
File: species_tree.tre
Description: species phylogenetic tree based on BUSCO genes for 17 pteriomorphian species.
File: bivalve_opsins_updated.csv
Description: dataset for opsin counts and types in bivalve ocular and extraocular tissues.
Variables
- Species: pteriomorphian species.
- total: total number of expressed opsins in the sample.
- opnGx: total number of expressed xenopsins.
- opnGo: total number of expressed Go-opsins.
- opn5: total number of expressed neuropsins.
- RTC: total number of expressed retinochrome.
- pero: total number of expressed peropsins.
- opnGq: total number of expressed canonical r-opsins.
- opnGq-nc: total number of expressed noncanonical r-opsins.
- mobility-3: mobility organized in three levels (1) no mobility, (2) partial mobility, and (3) full mobility.
- mobility-bi: mobility organized in two levels (1) no mobility and (2) full mobility.
- eye: eye presence or absence.
- complexity: photoreception class in thee levels (1) non-directional, (2) directional, and (3) low-resolution vision.
- Gx: expression of xenopsin (presence or absence).
- Go: expression of Go-opsin (presence or absence).
- neuro: expression of neuropsin (presence or absence).
- retino: expression of retinochrome (presence or absence).
- per: expression of peropsin (presence or absence).
- Gq: expression of canonical r-opsin (presence or absence).
- Gq-nc: expression of noncanonical r-opsin (presence or absence).
File: comparative_opsins_GLMM.R
Description: Bayesian generalized mixed models with a Markov chain Monte Carlo (MCMC) approach used to determine whether eyes, photoreception class, and mobility are evolutionarily associated with the number of expressed opsins. Script in R.
File: comparative_opsins_plots.R
Description: Comparative analysis, phylo-PCA, and options for plotting data related to expressed opsins across samples (eye and mantle margin of 17 pteriomorphian species). Script in R.
File: expression_rank.txt
Description: dataset with global rank and percentile ranks for each opsin gene in each species based on TPM values.
Variables
- sequence: opsin expressed in the sample.
- rank: global rank of expression for the gene.
- percentage: percentile ranks obtained by ordering all genes by expression value and dividing their ranks by the total number of genes with non-zero values.
- type: opsin type.
- species: one of the 17 pteriomorphian species included in the study.
- tissue: eye or mantle margin.
File: opsin_full.treefile
Description: phylogenetic tree of bivalve opsins used for phylogenetic classification of opsin candidates expressed in the samples.
File: opsin_pruned_expressed_only.tree
Description: opsin phylogenetic tree after pruning the complete phylogeny and keeping only the opsins known to be expressed.
File: rank-based_comparison_opsin.R
Description: code to plot the dataset related to percentile ranks of opsin expression using R.
File: opsin_ali.fa
Description: amino acid sequences of all opsins used in the phylogenetic analysis after MAFFT alignment.
File: opsin_ali_trim_auto.fasta
Description: amino acid sequences of all opsins used in the phylogenetic analysis after trimming.
File: Bash_commands.txt
Description: example bash scripts used for trimming, assembling, screening of predicted proteins, and gene expression quantification.
Code/software
For de novo transcriptome assembly: Trinity v2.1.1.
For maximum likelihood phylogenetic analysis: IQ-TREE2 v2.1.3.
For sequence alignment: MAFFT v7.453.
For sequence trimming: trimal v1.4.
For analysis and plotting using R (v4.5.2) code, the following packages were used: phytools v2.4-4, geomorph v4.0.9, MCMCglmm v2.36, coda v0.19-4.1, geiger v2.0.11, dplyr v1.1.4, purrr v1.2.0, ggplot2 v4.0.0, reshape2 v1.4.5, xlsx v0.6.5, and viridis v0.6.5.
Access information
Other publicly accessible locations of the data:
- nothing to declare.
Data was derived from the following sources:
- nothing to declare.
We compare 17 species based on transcriptomic data to determine opsin profiles from photosensitive tissues, including eyes from eyed species and mantle margin (extraocular tissue) from eyeless species. Individuals of 12 species were collected, dissected, preserved, and immediately stored at -80 ºC. In addition, five other pteriomorphian species with publicly available RNA-seq data from either the mantle margin or the eyes were included. Raw reads were downloaded, and transcriptomes were generated. All five Pteriomorphia orders were sampled, totaling 17 species from 10 families. Our dataset also covers the five eye types, i.e., pigmented cup, cap eyespot, invaginated eye, compound eye, and mirror eye, occurring in the group.
Total RNA was extracted from dissected mantle margins and eye samples. All libraries were prepared and sequenced (300 cycles) on an Illumina NovaSeq 6000. Details on quality checking, de novo assembly, protein prediction, and other relevant information are listed in the manuscript. Sequence data generated in this study have been deposited in the Sequence Read Archive (NCBI) with accession numbers listed in the supplementary materials of the article.
We inferred a pteriomorphian species tree based on BUSCO genes from the 17 transcriptomes to provide a phylogenetic framework to examine opsin diversity. Opsin candidates were aligned, trimmed, and submitted to ML phylogenetic analysis. Comparative data and expression data were analyzed using R packages.