An automated workflow to assess completeness and curate <scp>GenBank</scp> for environmental <scp>DNA</scp> metabarcoding: The marine fish assemblage as case study

To successfully implement environmental DNA-based (eDNA) diversity monitoring, the completeness and accuracy of reference databases used for taxonomic assignment eDNA sequences are among challenges to be tackled. Here, we have developed a workflow that evaluates current status GenBank marine fishes. For given combination species barcodes, gap analysis is performed potentially erroneous identified. Our based on four most genes (cytochrome c oxidase subunit 1, 12S rRNA, 16S cytochrome b) fish metabarcoding found COI, universal choice metazoans, gene covering highest number Northeast Atlantic fishes (70%), while preferred region fish-targeting studies, only covers about 50% species. The presence too close distant barcode as expected by their classification confirms existence in our can detect eliminate. Comparing assignments real samples with raw clean rRNA barcodes (teleo MiFish), confirmed both perform differently demonstrated application database cleaning result drastic changes community composition. Besides providing tool curation, this study need increase European evidences dangers directly querying GenBank. We