Lifestyle-Dependent Intron Divergence and Conserved Multi-Scale Genomic Organization Patterns Across 28 Nematode Genome

# Dataset Description

This dataset contains comprehensive intron architecture and sequence-based genomic organization data from 28 nematode species (12 free-living, 16 parasitic) representing approximately 400 million years of evolution.

**Note**: This dataset is currently restricted during peer review. It will be made publicly available upon acceptance of the associated manuscript.

## Contents

- **Primary intron dataset**: 4,581,099 intron records with sequences, genomic coordinates, GC content, and splice site annotations (1.9 GB)
- **Species summary statistics**: Aggregated metrics for all 28 species
- **Analysis scripts**: Complete Python and R pipeline for data integration and multi-scale genomic organization analysis
- **Documentation**: Detailed data dictionary, README, and reproducibility instructions

## Data Source

All genome assemblies and gene annotations were obtained from WormBase ParaSite release WBPS19 (https://parasite.wormbase.org/), accessed October 2022.

## Associated Publication

This dataset accompanies the manuscript:

**"Lifestyle-Dependent Intron Divergence and Conserved Multi-Scale Genomic Organization Patterns Across 28 Nematode Genomes"**

Submitted to PeerJ, November 2025

## Access

During peer review: Access available to editors and reviewers upon request
After acceptance: Full public access with CC BY 4.0 license

## Key Findings

- Parasitic nematodes show 35% longer introns and 11% lower GC content compared to free-living species
- Multi-scale genomic organization patterns remain remarkably conserved across lifestyle transitions
- Power-law scaling exponents exhibit near-perfect conservation

## File Structure
```
zenodo_package/
├── data/
│   ├── introns_28species_integrated.csv (primary dataset)
│   ├── species_summary_statistics.csv
│   └── additional summary tables
├── scripts/ (analysis pipeline)
├── documentation/ (data dictionary)
└── README.md (detailed documentation)
```

## Reproducibility

All analyses are fully reproducible using the provided scripts and publicly available genome data from WormBase ParaSite WBPS19.

## License

Creative Commons Attribution 4.0 International (CC BY 4.0)
(License will be fully activated upon public release)

## Contact

Masato Tanigawa
tanigawa@oita-u.ac.jp
Department of Biophysics, Fuculty of Medicine, Oita University
```

### **1-6. License**
```
選択:Creative Commons Attribution 4.0 International

注:Restrictedでも選択可能。論文受理後に有効化される。
```

### **1-7. Keywords**
```

1. introns
2. nematodes
3. comparative genomics
4. genome organization
5. parasitism
6. Caenorhabditis elegans
7. lifestyle evolution
8. intron architecture
9. multi-scale analysis
10. WormBase ParaSite
11. sequence-based inference
12. scale invariance
```

### **1-8. Additional information**
```
Version: v1.0

Language: English

Notes
This dataset is embargoed during peer review and will be made 
publicly available upon manuscript acceptance.
```

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