Data from: Genomic structural variation rescues a classic biological invader from a population bottleneck
Data files
Jun 11, 2026 version files 477.11 MB
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Boiga_irregularis_hapW_geneModels.gff3.gz
4.75 MB
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Boiga_irregularis_hapZ_geneModels.gff3.gz
5.30 MB
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Boiga_irregularis_pangenome.gfa.gz
467.06 MB
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README.md
2.57 KB
Abstract
Invasion genetics presents a classic paradox: how do species successfully establish and spread despite severe population bottlenecks? The brown treesnake (Boiga irregularis) in Guam represents a striking example of this phenomenon, having been introduced with only a handful of individuals. We show that the population endured an extreme bottleneck and high levels of inbreeding, with roughly half of the genome exhibiting runs of homozygosity, comparable to species of conservation concern. Despite this, we uncovered extensive diversity in the form of nearly 19,000 genomic structural variants, which affect almost eight times more of the genome than single-nucleotide variants and provide material for ‘rescuing’ the population from inbreeding-driven declines. This diversity is not randomly distributed across chromosomes, but rather are enriched in genes vital for immunity and olfaction, suggesting genomic diversity in key chromosomal regions can rescue populations from inbreeding. This work has critical implications for invasion biology and conservation genetics practitioners.
This dataset contains the structural variation-based pangenome and haplotype-specific gene annotations associated with the study of the Brown Treesnake invasion. These data provide a high-resolution look at the genomic architecture and structural diversity of this invasive species.
Contact Information:
Corresponding Authors: Trevor Krabbenhoft and Christopher Osborne
Institution: University at Buffalo
Email: tkrabben@buffalo.edu, caosborn@buffalo.edu
Dataset Overview: This repository contains two primary types of data:
- A Pangenome Graph: Representing structural variations (SVs) across the sampled population.
- Haplotype-Resolved Annotations: High-quality gene models for both haplotypes of a single diploid individual.
File List and Descriptions
File Name: Boiga_irregularis_pangenome.gfa.gz.gfa
Description: Pangenome graph containing structural variants (SVs) integrated into a reference backbone.
File Name: Boiga_irregularis_hapW_geneModels.gff3.gz.gff3
Description: Gene models for the resolved assembly that contained the W chromosome.
Filne Name: Boiga_irregularis_hapZ_geneModels.gff3.gz.gff3
Description: Gene models for the resolved assembly that contained the Z chromosome.
Methodological Information
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Pangenome Construction
The pangenome was constructed to capture large-scale structural diversity that traditional linear references often miss.SV Detection: Structural variants were identified using NextSV3, optimized for long-read sequencing data to ensure high sensitivity and precision.
Graph Integration: The resulting VCF file of SVs was converted into a Graphical Fragment Assembly (GFA) format. This was achieved using SVJedi-Graph, which utilizes Minigraph to anchor SV sequences into the graph structure, allowing for a comprehensive representation of the brown treesnake pangenome.
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Gene Annotation
Annotations were generated for a single, haplotype-resolved diploid assembly.Annotation Pipeline: Gene models were predicted independently for each haplotype to preserve phase-specific variations. The entire genome annotation pipeline can be found on the Krabbenhoft Lab GitHub at https://github.com/KrabbenhoftLab/genome_annotation_pipeline
Software and Versions: NextSV3: v3.2.0, SVJedi-Graph: v1.2.1, GFF3 Specification: Version 3
