Comparative analysis of convergent jellyfish eyes reveals extensive differences in expression of vision-related genes

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 protot..., , # 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.

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## 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 info...,