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Background All-inclusive DNA-barcoding libraries in the storage and analysis platform of the BOLD (Barcode of Life Data) system are essential for the study of the marine biodiversity and are pertinent for regulatory purposes, including ecosystem monitoring and assessment, such as in the context of the EU Water Framework Directive (WFD) and the Marine Strategy Framework Directive (MSFD). Here, we investigate knowledge gaps in the lists of DNA barcoded organisms within two inventories, Cnidaria (Anthozoa and Hydrozoa) and Ascidiacea from the reference libraries of the European Register of Marine Species (ERMS) dataset (402 ascidians and 1200 cnidarian species). ERMS records were checked species by species, against publicly available sequence information and other data stored in BOLD system. As the available COI barcode data adequately cover just a small fraction of the ERMS reference library, it is of importance to employ quality control on existing data, to close the knowledge gaps and purge errors off BOLD. Results Results revealed that just 22.9% and 29.2% of the listed ascidians and cnidarians species, respectively, are BOLD barcodes of which 58.4% and 52.3% of the seemingly barcoded species, respectively, were noted to have complete BOLD pages. Thus, only 11.44% of the tunicate and 17.07% of the cnidarian data in the ERMS lists are of high quality. Deep analyses revealed seven common types of gaps in the list of the barcoded species in addition to a wide range of discrepancies and misidentifications, discordances, and errors primarily in the GenBank mined data as with the BINs assignments, among others. Conclusions Gap knowledge in barcoding of important taxonomic marine groups exists, and in addition, quality management elements (quality assurance and quality control) were not employed when using the list for national monitoring projects, for regulatory compliance purposes and other purposes. Even though BOLD is the most trustable DNA-barcoding reference library, worldwide projects of DNA barcoding are needed to close these gaps of mistakes, verifications, missing data, and unreliable sequencing labs. Tight quality control and quality assurance are important to close the knowledge gaps of Barcoding of the European recommended ERMS reference library.

Gap analysis of DNA barcoding in ERMS reference libraries for ascidians and cnidarians