AChE Gene Evolution – Insect Transcriptome Pipeline

A Multi-Species Workflow for Acetylcholinesterase (AChE) Gene Analysis

This repository contains a complete R-based bioinformatics pipeline for collecting, filtering, aligning, and analyzing acetylcholinesterase (AChE) transcripts across locusts, crickets, and mosquitoes. The workflow identifies the longest isoforms, builds multi-species FASTA files, prepares alignments, constructs phylogenetic trees, and generates figures for research poster or manuscript preparation.

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🧬 Project Overview

Locusts possess unusually high AChE gene copy numbers yet fail to evolve organophosphate pesticide resistance, unlike mosquitoes. This project explores:

• AChE copy-number differences across key insects
• Whether locust AChE expansion is ancestral or derived
• How gene family size affects resistance evolution
• Whether AChE copies contain known resistance-associated mutations

This repository provides the complete computational workflow for that analysis.

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⚙️ Pipeline Summary

1. Download AChE sequences

File: scripts/01_download_AChE_sequences.R
Downloads all AChE CDS/mRNA isoforms from NCBI into data/raw/.

2. Extract longest isoforms

File: scripts/02_extract_longest_isoforms.R
Identifies the longest CDS per AChE gene and writes results to data/longest/.

3. Merge longest isoforms

File: scripts/03_merge_longest_fastas.R
Builds a unified multi-species FASTA in data/combined/.

4. Prepare alignment

File: scripts/04_run_alignment.R
Prepares or runs MAFFT/Clustal alignment and saves files to data/alignment/.

5. Build phylogenetic tree

File: scripts/05_build_tree_fasttree.R
Constructs a phylogenetic tree using FastTree or IQ-TREE, saved to data/tree/.

6. Plot phylogeny

File: scripts/06_plot_tree.R
Generates polished tree visualizations.

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🗂 Repository Structure

Top-level files

• AChE_Project.Rproj — RStudio project file
• README.md — documentation
• LICENSE — MIT license
• CITATION.cff — citation metadata
• .gitignore — ignored files

Folder: scripts/

• 01_download_AChE_sequences.R
• 02_extract_longest_isoforms.R
• 03_merge_longest_fastas.R
• 04_run_alignment.R
• 05_build_tree_fasttree.R
• 06_plot_tree.R

Folder: data/

• raw/ — raw NCBI downloads (ignored by Git)
• longest/ — longest isoform FASTAs (ignored by Git)
• combined/ — merged multi-species dataset (ignored by Git)
• alignment/ — alignment files (ignored by Git)
• tree/ — final tree outputs (tracked)

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🦗 Species Included

Locusts

• Schistocerca gregaria
• Schistocerca cancellata
• Schistocerca piceifrons

Cricket

• Anabrus simplex

Mosquitoes

• Anopheles gambiae
• Aedes aegypti
• Culex quinquefasciatus

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📦 Dependencies

R packages:

• rentrez
• seqinr
• dplyr
• stringr
• ape
• ggtree
• ggplot2
• readr

External tools:

• MAFFT — alignment
• FastTree / IQ-TREE — phylogenetics

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🚀 Quickstart

1. Clone the repository git clone https://github.com/Taylortxtt/AChE_Insect_Transcriptome.git

2. Open the project

• Open AChE_Project.Rproj in RStudio

3. Run the pipeline Run scripts in numerical order:

1 → 2 → 3 → 4 → 5 → 6

Each script outputs files into the corresponding data/ subfolder.

4. Add new species

• Drop FASTA files into data/raw/
• Re-run the pipeline starting at script 02 or 03

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👩‍🔬 Author

Taylor M. Johnson
Department of Biochemistry
Mississippi State University

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📄 License

MIT License — see the LICENSE file.

📣 Citation

Please cite using the included CITATION.cff file.

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