MargHem 1.0.5: Genome Assembly and Annotation for the Louisiana Pearlshell Mussel

This dataset provides the whole-genome assembly and annotation for the federally threatened freshwater mussel Margaritifera hembeli (Louisiana Pearlshell). It includes PacBio long-read and Illumina short-read sequencing data, a soft-masked genome assembly (MargHem_1.0.5), predicted protein sequences, and gene annotations in GFF3 format. Supplementary files contain Hox gene sequences for bivalves and data from orthology analyses focused on biomineralization genes.

Use Cases

• Comparative genomics analysis based on the provided Hox gene sequences for Margaritifera hembeli and related species.
• Studying biomineralization pathways using the provided fasta file of biomineralization genes of interest and orthology analysis outputs.
• Gene annotation and genome browser visualization using the provided GFF3 annotation file.
• Phylogenetic analysis of bivalve relationships using the OrthoFinder output files containing orthogroup sequences.

Strengths

• Includes a hybrid genome assembly combining PacBio long-read and Illumina short-read sequencing data, which likely improves contiguity and accuracy.
• Provides functional annotation (GFF3) and predicted protein sequences, adding biological context to the genomic data.
• Contains curated supplementary data for specific gene families (Hox, biomineralization) useful for targeted evolutionary studies.

Limitations

• The dataset size (1.93 GB) and specific assembly statistics (e.g., contig N50, BUSCO scores) are not detailed in the provided metadata, limiting initial assessment of assembly quality.
• Metadata completeness is medium; detailed column names for structured files are not provided, and the exact row/record counts are unknown.
• The temporal coverage of the source biological sample is not specified, only the dataset publication date.

Provenance

Source

Sequencing and initial data generation performed by GENEWIZ (New Jersey, USA). Dataset authored by Samantha Donohoo.

Collection Method

High molecular weight DNA extracted from foot tissue; sequencing performed on Illumina HiSeq X and PacBio Sequel platforms; genome assembly and annotation details are in the associated publication.

Freshness

Last updated on 2026-03-21.

Geography

Species (Margaritifera hembeli) is native to North America (Louisiana, USA), but specific collection location for the sequenced specimen is not provided.