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Title: DNA barcode reference libraries for the monitoring of aquatic biota in Europe: Gap-analysis and recommendations for future work
Authors: Weigand, Hannah; Beermann, Arne J.; Ciampor, Fedor; Costa, Filipe O.; Csabai, Zoltan; Duarte, Sofia; Geiger, Matthias F. and Grabowski, Micha; Rimet, Frederic; Rulik, Bjoern; Strand, Malin; Szucsich, Nikolaus; Weigand, Alexander M.; Willassen, Endre; Wyler, Sofia A.; Bouchez, Agnes; Borja, Angel and Ciamporova-Zat'ovicova, Zuzana; Ferreira, Sonia; Dijkstra, Klaas-Douwe B.; Eisendle, Ursula; Freyhof, Joerg; Gadawski, Piotr; Graf, Wolfram; Haegerbaeumer, Arne; van der Hoorn, Berry B.; Japoshvili, Bella; Keresztes, Lujza; Keskin, Emre and Leese, Florian; Macher, Jan; Mamos, Tomasz; Paz, Guy; Pesic, Vladimir; Pfannkuchen, Daniela Maric; Pfannkuchen, Martin Andreas and Price, Benjamin W.; Rinkevich, Buki; Teixeira, Marcos A. L. and Varbiro, Gabor; Ekrem, Torbjrn
Citation: SCIENCE OF THE TOTAL ENVIRONMENT, 2019, 678, 499-524
Abstract: Effective identification of species using short DNA fragments (DNA barcoding and DNA metabarcoding) requires reliable sequence reference libraries of known taxa. Both taxonomically comprehensive coverage and content quality are important for sufficient accuracy. For aquatic ecosystems in Europe, reliable barcode reference libraries are particularly important if molecular identification tools are to be implemented in biomonitoring and reports in the context of the EU Water Framework Directive (WFD) and the Marine Strategy Framework Directive (MSFD). We analysed gaps in the two most important reference databases, Barcode of Life Data Systems (BOLD) and NCBI GenBank, with a focus on the taxa most frequently used in WFD and MSFD. Our analyses show that coverage varies strongly among taxonomic groups, and among geographic regions. In general, groups that were actively targeted in barcode projects (e.g. fish, true bugs, caddisflies and vascular plants) are well represented in the barcode libraries, while others have fewer records (e.g. marine molluscs, ascidians, and freshwater diatoms). We also found that species monitored in several countries often are represented by barcodes in reference libraries, while species monitored in a single country frequently lack sequence records. A large proportion of species (up to 50\%) in several taxonomic groups are only represented by private data in BOLD. Our results have implications for the future strategy to fill existing gaps in barcode libraries, especially if DNA metabarcoding is to be used in the monitoring of European aquatic biota under the WFD and MSFD. For example, missing species relevant to monitoring in multiple countries should be prioritized for future collaborative programs. We also discuss why a strategy for quality control and quality assurance of barcode reference libraries is needed and recommend future steps to ensure full utilisation of metabarcoding in aquatic biomonitoring. (C) 2019 The Author(s). Published by Elsevier B.V.
Issue Date: 2019
Publisher: ELSEVIER
Type: Review
DOI: 10.1016/j.scitotenv.2019.04.247
ISSN: 0048-9697
E-ISSN: 1879-1026
Funder: Short-term Scientific Mission [ECOST-STSM-CA15219-150217-082111]
NorBOL-grant from the Research Council of Norway [226134/F50]
GBOL project
German Federal Ministry of Education and ResearchFederal Ministry of Education \& Research (BMBF) [FKZ 01LI1101, 01LI1501]
Polish National Science Centre [N N303 5794 39, 2014/15/B/NZ8/00266]
project PORBIOTA - Portuguese E-Infrastructure for Information and Research on Biodiversity [POCI-01-0145-FEDER-022127]
Operational Thematic Program for Competitiveness and Internationalization (POCI), under the PORTUGAL 2020 Partnership Agreement, through the European Regional Development Fund (FEDER)
Appears in Publication types:Artículos científicos

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