DNA barcode reference libraries for the monitoring of aquatic biota in Europe: Gap-analysis and recommendations for future work

Authors: HannahWeigand a, Arne J.Beermann b, Fedor Čiampor c, Filipe O.Costa de, Zoltán Csabai f,  Sofia Duarte de,  Matthias F.Geiger g,  Michał Grabowski h,  FrédéricRimet i, BjörnRulik g,  MalinStrand j,  NikolausSzucsich k,  Alexander M.Weigand ab,  EndreWillassen l,  Sofia A.Wyler m,  Agnès Bouchez i, Angel Borja, n, Zuzana Čiamporová-Zaťovičová c,  Sónia Ferreirao Klaas-Douwe B. Dijkstra p,  Jörg Freyhof r, Piotr Gadawski h, Wolfram Graf s, Arne Haegerbaeumer t, Berry B.van der Hoorn p, Bella Japoshvili u, Lujza Keresztes v, Emre Keskin w,  Florian Leese b, Jan N. Macher p, Tomasz Mamos h, Guy Paz x, Vladimir Pešić y, Daniela Maric Pfannkuchen z, Martin Andreas Pfannkuchen z, Benjamin W. Pricea a, BukiRinkevich x, Marcos A.L.Teixeira de, GáborVárbíró ab, Torbjørn Ekrem ac

a Musée National d’Histoire Naturelle, 25 Rue Münster, 2160 Luxembourg, Luxembourg b University of Duisburg-Essen, Faculty of Biology, Aquatic Ecosystem Research, Universitaetsstr. 5, 45141 Essen, Germany c Slovak Academy of Sciences, Plant Science and Biodiversity Centre, Zoology Lab, Dúbravská cesta 9, 84523 Bratislava, Slovakia d Centre of Molecular and Environmental Biology (CBMA), University of Minho, Campus de Gualtar, 4710-057 Braga, Portugal e Institute of Science and Innovation for Bio-Sustainability (IB-S), University of Minho, Campus de Gualtar, 4710-­057 Braga, Portugal f University of Pécs, Faculty of Sciences, Department of Hydrobiology, Ifjúság útja 6, H7624 Pécs, Hungary g Zoologisches Forschungsmuseum Alexander Koenig, Leibniz Institute for Animal Biodiversity, Adenauerallee 160, 53113 Bonn, Germany h University of Lodz, Faculty of Biology and Environmental Protection, Department of Invertebrate Zoology and Hydrobiology, Banacha 12/16, 90-237 Łódź, Poland i INRA, Université Savoie Mont Blanc, UMR Carrtel, FR-74200 Thonon-les-Bains, France j Swedish University of Agricultural Sciences, Swedish Species Information Centre, Uppsala, Sweden k Natural History Museum Vienna, Burgring 7, 1010 Vienna, Austria l University of Bergen, University Museum of Bergen, NO-5007 Bergen, Norway m info fauna – Centre Suisse de Cartographie de la Faune (CSCF), Avenue de Bellevaux 51, 2000 Neuchâtel, Switzerland n AZTI – Marine Research Division, Herrera Kaia, Portualdea z/g, 20110 Pasaia, Gipuzkoa, Spain o CIBIO/InBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, Universidade do Porto, Campus Agrário de Vairão, 4485-661 Vairão, Portugal p Naturalis Biodiversity Center, PO Box 9517, 2300 RA Leiden, the Netherlands q University of Salzburg, Department of Biosciences, Hellbrunnerstraße 34, 5020 Salzburg, Austria r Leibniz-Institute of Freshwater Ecology and Inland Fisheries (IGB), 12587 Berlin, Germany s University of Natural Resources and Life Sciences, Vienna, Institute of Hydrobiology and Aquatic Ecosystem Management (IHG), Gregor-Mendel-Straße 33/DG, 1180 Vienna, Austria t Bielefeld University, Department of Animal Ecology, Konsequenz 45, 33615 Bielefeld, Germany u Ilia State University, Institute of Zoology, ⅗ Cholokashvili ave, 0179 Tbilisi, Georgia v Babeș-Bolyai University, Faculty of Biology and Geology, Center of Systems Biology, Biodiversity and Bioresources, Cliniclor 5-7, 400006 Cluj Napoca, Romania w Ankara University, Agricultural Faculty, Department of Fisheries and Aquaculture, Evolutionary Genetics Laboratory (eGL), Ankara, Turkey x Israel Oceanographic and Limnological Research, National Institute of Oceanography, Haifa 31080, Israel y University of Montenegro, Department of Biology, Cetinjski put bb., 20000 Podgorica, Montenegro z Rudjer Boskovic Institute, Center for Marine Research, G. Paliaga 5, Rovinj, Croatia aa Natural History Museum, Cromwell Road, London, UK ab MTA Centre for Ecological Research, Danube Research Institute, Department of Tisza River Research, Bem square 18/C, H4026 Debrecen, Hungary ac Norwegian University of Science and Technology, NTNU University Museum, Department of Natural History, NO-7491 Trondheim, Norway

Source: H. Weigand, A. J. Beermann, F. Čiampor, F. O. Costa, Z. Csabai, S. Duarte, M. F. Geiger, M. Grabowski, F. Rimet, B. Rulik, M. Strand, N. Szucsich, A. M. Weigand, E. Willassen, S. A. Wyler, A. Bouchez et al., 2019. – DNA barcode reference libraries for the monitoring of aquatic biota in Europe: Gap-analysis and recommendations for future work. – Science of The Total Environment. Volume 678, 15 August 2019, Pages 499-524, https://doi.org/10.1016/j.scitotenv.2019.04.247

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.