Anterior–posterior patterning in the chaetognath Spadella cephaloptera: insights into the evolution of the bilaterian nervous system and postanal tail

Supplementary code for “Anterior–posterior patterning in the chaetognath Spadella cephaloptera: insights into the evolution of the bilaterian nervous system and postanal tail”* Scripts used to download, assemble, and annotate transcriptomes for Hox gene mining in public SRA datasets. --- ## Hox gene mining pipeline from public transcriptomes This repository contains example scripts and a minimal walkthrough of the pipeline used to identify Hox genes from publicly available transcriptomes. The workflow has four main steps: 1. **Download RNA-seq reads from SRA** Script: `01_dowload_RNAseqData.sh` 2. **Trim and quality-filter reads, then assemble transcriptomes** Script: `02_qc_and_assemble.sh` 3. **Annotate assembled transcripts with DIAMOND against a custom Spiralian Hox database** Scripts: `03.1_03.1_makeHoxDB.sh` and `03.2_annot_diamonBlast.sh` 4. **Manually inspect and confirm candidate Hox genes by NCBI BLAST** - Filter DIAMOND hits for strong matches (e.g. e-value ≤ 1e-25) to identify candidate Hox transcripts. - Extract the corresponding transcript IDs from the assembly FASTA. - BLAST these candidates against NCBI (nt/nr) to confirm their identity and assign orthology. - Retain only well-supported Hox sequences for downstream phylogenetic analyses. The scripts are written for a SLURM-based HPC cluster using `module load`, but can be adapted to other environments. --- ## Requirements - Linux environment- SLURM (or adjust the `#SBATCH` lines)- Installed software: - [SRA Toolkit](https://github.com/ncbi/sra-tools) (tested with ≥ 3.2.0) - [Trimmomatic](http://www.usadellab.org/cms/?page=trimmomatic) (≥ 0.39) - [SPAdes](https://cab.spbu.ru/software/spades/) with RNA mode (`spades.py --rna`) - [DIAMOND](https://github.com/bbuchfink/diamond) (≥ 2.1.x)- Adapter FASTA for Trimmomatic (e.g. `TruSeq3-PE.fa`)- A FASTA file containing Spiralian Hox protein sequences to build the custom DIAMOND database