Datasets for the project "High quality genome for the endangered Louisiana Pearlshell Margaritifera hembeli (Conrad, 1838)"

Whole-genome assembly of the federally threatened freshwater mussel Margaritifera hembeli.Data GenerationHigh molecular weight DNA extraction from foot tissue, short-read and long-read library preparation, and long-read and short-read sequencing were done by GENEWIZ (New Jersey, USA). Whole-genome short-read data was generated using 2 × 150 bp paired-end chemistry on an Illumina (San Diego, CA) HiSeq X. Pacific Biosciences (PacBio; Menlo Park, CA) long-read data was generated following the single-molecule real-time (SMRT) bell library preparation protocol. Four SMRT cells were sequenced on a PacBio Sequel. Frozen tissue of the mantle, gills, and additional tissue from the foot were also sent to GENEWIZ for RNA extractions and stranded RNA-seq library preparations. Each tissue library was sequenced using 2 x 150 bp paired-end chemistry on an Illumina Hiseq X.
For assembly and genome annotation details please see the Material and Methods section of the original publication "High quality genome for the endangered Louisiana Pearlshell Margaritifera hembeli (Conrad, 1838)".
Available Files on Figshare
Bivalvia_Hox_Proteins.fastaMargaritifera_hembeli_HoxGenes.fastaMargaritifera_margaritifera_HoxGenes.fastaMargHem_1.0.5.Unmasked.Genome.fasta.gzMargHem_1.0.5.SoftMasked.Genome.fasta.gzMargHem_1.0.5.Annotations.gff3MargHem_1.0.5.PredictedProteins.fastaOrthoFinder_and_Cafe5_Files/SMP_Biomineralization_Genes_July2025.fasta #Fasta File of Biomineralization Genes of InterestOrthoFinder_Files/Biomineral_Bivalve_Transcripts/ #Input Files for OrthofinderBivalve_Orthogroup_Sequences_PreProcessing.tar.gz #Output Fasta Files from OrthoFinderBivalve_Orthogroup_Sequences_PostProcessing.tar.gz #Fasta Files after Cleanup for Biomineralization IDBivalve_Orthogroup_GeneCounts.tsv #Output File with Gene Counts for each OrthogroupBivalve_SpeciesTree_Orthofinder.txt #Species Tree from Orthofinder of SpeciesCafe5_Files/Bivalve_SpeciesTree_Ultrametric_Tree.txt #Converted Species Tree, Rooted and in Newick FormatBivalve_Biomineral_Orthogroup_GeneCounts.txt #Gene Counts of Only Biomineral Orthogroups. Formatted for Cafe5.KEGG_Analysis_Graphing_FilesKegg_for_Graphing.csvKegg_for_Graphing_Names.csvGo_Enrichment_Graphing_FilesOrthovenn_Margaritiferaidae.csvOrthovenn_Margaritiferida_Names.csvOrthovenn_MargHem.csvOrthovenn_MargHem_Names.csvQuestions or Comments Contact Sam Donohoo at [e-mail] or [e-mail]