Dictyostelium Genome Annotation, Assembly & tgr Locus Analysis

This repository contains a collection of scripts and workflows to:

1. Annotate new Dictyostelium genome assemblies (tandem repeats, telomeres, transposable elements, rRNA, and mtDNA)
2. Assemble and polish long‐read genome assemblies
3. Quality-control variant calls and structural errors
4. Extract and analyze the tgrBC self/non-self recognition locus, including its intersections with transposable elements and structural errors

Assembled genomes and annotations have been deposited in NCBI under:

• BioProject: PRJNA1300491
• Zenodo: 10.5281/zenodo.17955877

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Table of Contents

• Installation
  • Requirements
  • Steps
• Repository Structure
  • annotation
  • assembly
  • quality-control
  • tgr_locus
• Citation

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Installation

Requirements

To use this repository, ensure the following requirements are met:

• Operating System: Linux
• Python Version: Python 3.10+ (tested on 3.12)
• Python Packages: pandas, numpy
• External Tools: SAMtools, Bedtools, Minimap2, BWA, BLAST+, TRF, CRAQ, BCFtools

Steps

1. Clone this repository:

   git clone https://github.com/MayarMAhmed/dicty_genome.git
   cd dicty_genome

2. Install Python dependencies (recommended using conda):

   conda create -n dicty_env python=3.10 
   conda activate dicty_env
   conda install numpy pandas

3. Install external tools via conda or your package manager.

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Repository Structure

├── annotation
│   ├── 01_run_trf.sh                # Run Tandem Repeat Finder on genome FASTA
│   ├── 02_extract_telomere_motif.sh # Search for putative telomere motifs 
│   ├── 03_filter_telomeres.py       # Filter and process telomere motif hits
│   ├── 04_find_TE.sh                # Identify transposable elements (RepeatMasker/BLAST)
│   ├── 05_generate_TE_bedgraph.py   # Generate bedGraph of TE density
│   ├── 06_run_rrna_blast.sh         # Extract rRNA transcripts via BLAST
│   ├── 07_map_rrna_summary.py       # Summarize rRNA BLAST results
│   ├── 08_search_mtdna_dna.sh       # Identify mtDNA‐containing contigs with BLASTn
│   ├── 09_search_mtdna_prot.sh      # Identify mtDNA proteins with tblastn
│   ├── 10_parse_mtdna_prot.py       # Parse mtDNA protein BLAST output
│   └── contig_mapping.txt           # Contig name mapping for AX4 reference and TNS-C-14 
├── assembly                         # De novo assembly & polishing workflows
├── quality-control
│   ├── 01_variant_calling.sh        # Call variants with bcftools/GATK
│   └── 02_run_craq.sh               # Detect structural errors using CRAQ
└── tgr_locus
    ├── 01_tgr_extraction.py         # Extract tgrBC syntenic locus from GFF & bedGraph
    ├── 02_tgr_TE_intersection.py    # Intersect TEs with tgr loci (optional gene annotation)
    ├── 03_tgr_CSE_intersection.py   # Intersect tgr loci with CRAQ-identified structural errors
    └── tgrBClocus_wacA2chdB.bedgraph.txt  
                                    # BedGraph of tgrBC locus coordinates across species

Each subdirectory contains a driver script and helper scripts. You can execute steps individually or chain them into a pipeline.

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Citation

If you use these scripts or the assemblies/annotations generated with them, please cite:

Holland M, Ahmed M, Young JM, Drurey JR, McFadyen S, Ostrowski EA, Levin TC. (2025) Hypermutable hotspot enables the rapid evolution of self/non-self recognition genes in Dictyostelium. Proc Natl Acad Sci U S A 122(51): e2520843122. https://doi.org/10.1073/pnas.2520843122