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Article Dans Une Revue (Article De Synthèse) Science of the Total Environment Année : 2019

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

Malin Strand
  • Fonction : Auteur
Nikolaus Szucsich
  • Fonction : Auteur
Alexander M. Weigand
  • Fonction : Auteur
Endre Willassen
  • Fonction : Auteur
Sofia A. Wyler
  • Fonction : Auteur
Angel Borja
  • Fonction : Auteur
Sónia Ferreira
Klaas-Douwe B. Dijkstra
  • Fonction : Auteur
Ursula Eisendle
  • Fonction : Auteur
Jörg Freyhof
Piotr Gadawski
  • Fonction : Auteur
Wolfram Graf
  • Fonction : Auteur
Arne Haegerbaeumer
  • Fonction : Auteur
Berry B. van Der Hoorn
  • Fonction : Auteur
Bella Japoshvili
  • Fonction : Auteur
Lujza Keresztes
  • Fonction : Auteur
Emre Keskin
  • Fonction : Auteur
Florian Leese
Jan N. Macher
  • Fonction : Auteur
Tomasz Mamos
  • Fonction : Auteur
Guy Paz
  • Fonction : Auteur
Vladimir Pešić
  • Fonction : Auteur
Daniela Maric Pfannkuchen
  • Fonction : Auteur
Martin Andreas Pfannkuchen
  • Fonction : Auteur
Benjamin W. Price
  • Fonction : Auteur
Buki Rinkevich
  • Fonction : Auteur
Marcos A.L. Teixeira
  • Fonction : Auteur
Gábor Várbíró
  • Fonction : Auteur
Torbjørn Ekrem
  • Fonction : Auteur

Résumé

Effective identification of species using short DNA fragments (DNA barcoding and DNA metabarcoding) requiresreliable sequence reference libraries of known taxa. Both taxonomically comprehensive coverage and contentquality are important for sufficient accuracy. For aquatic ecosystems in Europe, reliable barcode reference librar-ies are particularly important if molecular identification tools are to be implemented in biomonitoring and re-ports in the context of the EU Water Framework Directive (WFD) and the Marine Strategy FrameworkDirective (MSFD). Weanalysed gaps in the two mostimportant reference databases, Barcode of LifeDataSystems(BOLD) and NCBI GenBank, with a focus on the taxa most frequently used in WFD and MSFD. Our analyses showthat coverage varies strongly among taxonomic groups, and among geographic regions. In general, groups thatwere actively targeted in barcode projects (e.g.fish, true bugs, caddisflies and vascular plants) are well repre-sented in the barcode libraries, while others have fewer records (e.g. marine molluscs, ascidians, and freshwaterdiatoms). We also found that species monitored in several countries often are represented by barcodes in refer-ence libraries, while species monitored in a single country frequently lack sequence records. A large proportion ofspecies (up to 50%) in several taxonomic groups are only represented by private data in BOLD. Our results haveimplications for the future strategy tofill existing gaps in barcode libraries, especially if DNA metabarcoding is tobe used in the monitoring of European aquatic biota under the WFD and MSFD. For example, missing species rel-evant to monitoring in multiplecountries should be prioritizedfor future collaborative programs. Wealso discusswhy a strategy for quality control and quality assurance of barcode reference libraries is needed and recommendfuture steps to ensure full utilisation of metabarcoding in aquatic biomonitoring.

Dates et versions

hal-02626077 , version 1 (26-05-2020)

Identifiants

Citer

Hannah Weigand, Arne J. Beermann, Filipe O. Costa, Zoltán Csabai, Sofia Duarte, et al.. DNA barcode reference libraries for the monitoring of aquatic biota in Europe: Gap-analysis and recommendations for future work. Science of the Total Environment, 2019, 678, pp.499-524. ⟨10.1016/j.scitotenv.2019.04.247⟩. ⟨hal-02626077⟩
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