Hypsibius Dujardini: Tardigrade Genome Assembly and Annotation

The Genome Of The Tardigrade Hypsibius Dujardini accompanies a bioRxiv preprint from the University of Edinburgh. It includes the Edinburgh genome assembly version 2.3, spanning 140 megabases with median coverage of 86X, and gene model annotations from Augustus and MAKER. The dataset contains assembly files, gene prediction files in GFF and FASTA formats, and blobDB JSON files for contamination analysis.

Use Cases

• Studying tardigrade genome structure and evolution based on the 140 Mb assembly.
• Training or benchmarking gene prediction algorithms using the Augustus and MAKER annotation files.
• Analyzing genome assembly contamination using the provided blobDB JSON files and coverage/GC content information.
• Comparative genomics research using the protein and transcript sequences generated from the annotation.

Strengths

• The final genome assembly spans 140 megabases with a median coverage of 86X.
• Includes both final annotation files (from Augustus) and intermediate files (from MAKER) for transparency.
• Describes a multi-step assembly and contamination screening process using tools like blobtools, Velvet, and SSPACE.

Limitations

• Column-level documentation is absent; field semantics must be inferred after download.
• Row count is unknown, which may limit suitability assessment for some analyses.
• Last update date is unknown; freshness unverified.

Provenance

Source

University of Edinburgh

Collection Method

Genomic reads were assembled and annotated using a pipeline involving CLC, Velvet, GapFiller, SSPACE, blobtools, Augustus, and MAKER.