Lifestyle-Dependent Intron Divergence and Conserved Multi-Scale Genomic Organization Patterns Across 28 Nematode Genome
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# 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 requestAfter 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 Tanigawatanigawa@oita-u.ac.jpDepartment 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. introns2. nematodes3. comparative genomics4. genome organization5. parasitism6. Caenorhabditis elegans7. lifestyle evolution8. intron architecture9. multi-scale analysis10. WormBase ParaSite11. sequence-based inference12. scale invariance``` ### **1-8. Additional information**```Version: v1.0 Language: English NotesThis dataset is embargoed during peer review and will be made publicly available upon manuscript acceptance.``` ---
