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

Weigand, Hannah and Beermann, Arne J. and Ciampor, Fedor and Costa, Filipe O. and Csabai, Zoltan and Duarte, Sofia and Geiger, Matthias F. and Grabowski, Micha and Rimet, Frederic and Rulik, Bjoern and Strand, Malin and Szucsich, Nikolaus and Weigand, Alexander M. and Willassen, Endre and Wyler, Sofia A. and Bouchez, Agnes and Borja, Angel and Ciamporova-Zat'ovicova, Zuzana and Ferreira, Sonia and Dijkstra, Klaas-Douwe B. and Eisendle, Ursula and Freyhof, Joerg and Gadawski, Piotr and Graf, Wolfram and Haegerbaeumer, Arne and van der Hoorn, Berry B. and Japoshvili, Bella and Keresztes, Lujza and Keskin, Emre and Leese, Florian and Macher, Jan and Mamos, Tomasz and Paz, Guy and Pesic, Vladimir and Pfannkuchen, Daniela Maric and Pfannkuchen, Martin Andreas and Price, Benjamin W. and Rinkevich, Buki and Teixeira, Marcos A. L. and Varbiro, Gabor and Ekrem, Torbjrn (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. 678 , 499-524
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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.

Authors/Creators:Weigand, Hannah and Beermann, Arne J. and Ciampor, Fedor and Costa, Filipe O. and Csabai, Zoltan and Duarte, Sofia and Geiger, Matthias F. and Grabowski, Micha and Rimet, Frederic and Rulik, Bjoern and Strand, Malin and Szucsich, Nikolaus and Weigand, Alexander M. and Willassen, Endre and Wyler, Sofia A. and Bouchez, Agnes and Borja, Angel and Ciamporova-Zat'ovicova, Zuzana and Ferreira, Sonia and Dijkstra, Klaas-Douwe B. and Eisendle, Ursula and Freyhof, Joerg and Gadawski, Piotr and Graf, Wolfram and Haegerbaeumer, Arne and van der Hoorn, Berry B. and Japoshvili, Bella and Keresztes, Lujza and Keskin, Emre and Leese, Florian and Macher, Jan and Mamos, Tomasz and Paz, Guy and Pesic, Vladimir and Pfannkuchen, Daniela Maric and Pfannkuchen, Martin Andreas and Price, Benjamin W. and Rinkevich, Buki and Teixeira, Marcos A. L. and Varbiro, Gabor and Ekrem, Torbjrn
Title:DNA barcode reference libraries for the monitoring of aquatic biota in Europe: Gap-analysis and recommendations for future work
Series Name/Journal:Science of the Total Environment
Year of publishing :2019
Volume:678
Page range:499-524
Number of Pages:26
Publisher:ELSEVIER
ISSN:0048-9697
Language:English
Publication Type:Article Review/Survey
Article category:Scientific peer reviewed
Version:Published version
Copyright:Creative Commons: Attribution 4.0
Full Text Status:Public
Subjects:(A) Swedish standard research categories 2011 > 1 Natural sciences > 105 Earth and Related Environmental Sciences > Environmental Sciences (social aspects to be 507)
Keywords:DNA barcoding, Reference library, Biological monitoring, Freshwater, Marine, Quality assurance
URN:NBN:urn:nbn:se:slu:epsilon-p-112664
Permanent URL:
http://urn.kb.se/resolve?urn=urn:nbn:se:slu:epsilon-p-112664
Additional ID:
Type of IDID
DOI10.1016/j.scitotenv.2019.04.247
Web of Science (WoS)000468618900048
ID Code:24807
Faculty:NJ - Fakulteten för naturresurser och jordbruksvetenskap
Department:(NL, NJ) > Swedish Species Information Centre
Deposited By: SLUpub Connector
Deposited On:06 Jul 2021 07:27
Metadata Last Modified:06 Jul 2021 07:31

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