DOI: 10.5061/dryad.bvq83bknd
title: Data from: Comparative analysis of convergent jellyfish eyes reveals extensive differences in expression of vision-related genes

description: Quantifying gene expression across convergent origins of traits clarifies
 the degree to which those traits arise from shared versus distinct genetic
 programs, revealing how gene re-use relates to the repeatability of
 evolution. Eyes are important traits that evolved in many distantly
 related lineages, including at least nine times within cnidarians. Here,
 we investigate gene expression in eye-bearing and non-visual tissues from
 three cnidarian species representing long-diverged lineages where eyes
 evolved convergently (Cubozoa, Scyphozoa, and Hydrozoa). We find gene
 expression in eye-bearing tissues to be mostly lineage-specific, with only
 a small proportion of genes having convergent expression across species.
 Nevertheless, all species express homologs of deeply conserved
 vision-related genes known from Bilateria, which likely reflects deep
 homology (parallel evolution across vast phylogenetic distances) of a
 metazoan phototransduction toolkit. A gene tree analysis of opsins—the
 prototypical animal photosensors—shows that convergent eyes recruited
 different opsin paralogs, with the potential exception of an opsin
 ortholog shared between scyphozoan and cubozoan eyes. Our results suggest
 that eyes have mostly lineage-specific patterns of gene expression, yet
 some key phototransduction components are repeatedly recruited across
 multiple independent eye origins in Medusozoa.
description: # RNA-Seq Workflow Resources This repository contains Snakemake workflows
 and data files used in the analysis of RNA-seq data for ***Sarsia***,
 ***Tripedalia***, and ***Aurelia***, including the generation of
 low-redundancy transcriptome references and downstream analyses. --- ##
 Contents `readme.txt`: copy of this readme file's contents ### 🔧
 Workflow Archives #### `sarsia_workflow.tar.gz` This archive contains the
 Snakemake workflow used to generate a low-redundancy transcriptome
 reference for *Sarsia* and to map RNA-seq reads. **Directory Structure:**
 * **`workflow/`** * `Snakefile`: Main workflow file. * `envs/`: Conda
 environment YAML files. * `rules/`: Snakemake rules for each analysis
 step. * `scripts/`: Custom Bash and Python scripts. * **`config/`** *
 `config.yaml`: General configuration file with file paths and variable
 definitions. * `samples.tsv`, `conditions.tsv`: Metadata about samples and
 conditions. * **`resources/`** * `GO_terms.gtf`: GO term information. *
 `pia/`: Accessory files for `get_opsins` rule in `workflow/rules/pia.smk`.
 * `reference/`: Includes `Trinity_20210112.fasta` used as the base
 transcriptome. * `rawdata/`: Raw RNA-seq reads. &gt; **Note:** When using
 SRA data, set `mergeReads: False` in `config.yaml` and update
 `config/units.tsv` accordingly, as technical replicates were already
 merged during SRA submission. --- #### `tripedalia_workflow.tar.gz`
 Snakemake workflow for generating a low-redundancy transcriptome for
 *Tripedalia* and mapping RNA-seq reads. * Automatically downloads raw data
 from SRA to `resources/rawdata`. * Reference transcriptome corresponds to
 TSA accession **GHAQ00000000.1**. * Structure is similar to
 `sarsia_workflow`. --- #### `aurelia_workflow.tar.gz` Workflow for mapping
 RNA-seq reads to the *Aurelia aurita* genome. * Structure mirrors the
 *Sarsia* workflow. * Technical replicates merged during SRA submission;
 set `mergeReads: False` in `config.yaml` and update `units.tsv`
 accordingly. --- ## 🧬 Result Files *
 **`aurelia_ARSv1_proteins.opsins.fasta`**\ Opsins from *Aurelia* genome
 protein models. *
 **`sarsia_Trinity_20210112_longestORFperGene.opsins.fasta`**\ Opsins from
 low redundancy reference assembly *Sarsia* longest ORFs. *
 **`tripedalia_GHAQ01.1.fsa_nt.fasta.fixed_longestORFperGene.opsins.fasta`**\ Opsins from low redundancy reference assembly *Tripedalia* longest ORFs. --- ## 📦 Reference Archives * **`sarsia_lowredundancy_reference.tar.gz`**\ Protein and nucleotide sequences for the low redundancy *Sarsia* reference. * **`tripedalia_lowredundancy_reference.tar.gz`**\ Protein and nucleotide sequences for the low redundancy *Tripedalia* reference. --- ## 📊 Expression Analysis * **`expression_analyses.tar.gz`**\ Contains R scripts and data for: * Differential expression * GO enrichment * Cross-species comparisons\ Includes count matrices and primary data files. --- ## 📫 Contact If you have questions or need assistance, please contact: * **Natasha Picciani** – [natasha.picciani@gmail.com](mailto:natasha.picciani@gmail.com) * **Cory Berger** – [cberger@ucsb.edu](mailto:cberger@ucsb.edu)