Meta-Fish-Lib

Meta-Fish-Lib curates a dynamic mitochondrial DNA reference library and associated computational tools for fish species identification from environmental DNA (eDNA) metabarcoding data.

Key Features:

• Extensive Reference Library: Curated mitochondrial DNA sequence data for marine and freshwater fishes with 93% coverage of common U.K. species for the MiFish-12S fragment.
• Support for Multiple Metabarcoding Markers: Accommodates various metabarcoding markers to enable diverse marker-based analyses.
• Taxonomic Validation and Synonym Searches: Searches species synonyms and validates taxonomic names to improve identification accuracy.
• Phylogeny-Assisted Quality Control: Uses phylogenetic data to identify and remove misannotated sequences.
• Automated Coverage Reports: Generates coverage reports automatically with each new release update from GenBank.
• Citable DOIs: Provides versioned, citable Digital Object Identifiers (DOIs) for reference sequences.
• New Sequences and Primer Sets: Includes 241 newly generated MiFish-12S sequences for 88 U.K. marine species and new primer sets optimized for these markers.

Scientific Applications:

• Large-scale metabarcoding surveys: Enables scaling of fish metabarcoding studies across wide spatial gradients.
• Biodiversity assessment: Supports more accurate fish biodiversity assessments using a high-coverage reference library.
• Aquatic ecosystem monitoring: Facilitates monitoring of aquatic ecosystems via eDNA metabarcoding.
• Species distribution and biogeography: Improves study of species distribution patterns and biogeographic analyses.

Methodology:

Downloads mitochondrial DNA sequences from NCBI and BOLD, performs sequence cleaning and annotation, conducts taxonomic validation including synonym searches and phylogeny-assisted quality control to remove misannotations, generates automated coverage reports triggered by GenBank releases, and assigns versioned DOIs to reference sequences.