Complete Telomere-to-Telomere Genome Assembly for the Gila Monster

2026 release provides the first public, complete T2T squamate genome for the Gila monster (Heloderma suspectum). The dataset includes final reference assemblies for autosomes, Z and W sex chromosomes, and the mitogenome, along with annotation files for gene features, telomeres, and variant calls. It is published by author Brendan J. Pinto under a CC BY 4.0 license.

Use Cases

• Conduct whole-genome alignments and synteny analysis using the final reference assembly FASTA file containing autosomes, Z/W chromosomes, and the mitogenome.
• Call accurate variants like indels and SNPs on sex chromosomes in female samples using the hard-masked PAR version of the reference assembly FASTA file.
• Analyze gene features and annotations across the genome using the provided GFF3 file generated with RNAseq, Iso-seq, and protein database evidence.
• Investigate structural variants and haplotype-specific small variants using the provided VCF files from ONT and HiFi data.
• Study genome assembly features like manual patches, gaps, telomeres, and low-complexity regions using the provided BED files.

Strengths

• Represents the first public, complete Telomere-to-Telomere (T2T) genome assembly for a squamate reptile.
• Includes multiple annotated file types (FASTA, GFF3, BED, VCF) totaling 2.5 GB for detailed genomic analysis.
• Provides two versions of the reference assembly (soft-masked and hard-masked PAR on chrW) tailored for different research applications.
• Gene annotations are supported by multiple evidence types including RNAseq, Iso-seq, and a custom protein database.

Limitations

• The dataset is specific to a single species, the Gila monster, limiting comparative analyses without external genomic data.
• One remaining assembly gap is present on the W chromosome, as noted in the assembly features BED file.
• Satellite arrays on chrW were hard-masked prior to gene annotation, meaning no gene annotations exist within those specific regions.

Provenance

Source

figshare, authored by Brendan J. Pinto.

Collection Method

Genome assembly and annotation using tools like EviAnn, Liftoff, longdust, anianns, and longcallD, with evidence from RNAseq, Iso-seq, and a custom protein database.

Freshness

Last updated on 2026-03-23.