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Exhaustive reanalysis of barcode sequences from public repositories highlights ongoing misidentifications and impacts taxa diversity and distribution.

Authors
  • Fort, Antoine1
  • McHale, Marcus1
  • Cascella, Kevin2
  • Potin, Philippe2
  • Perrineau, Marie-Mathilde3
  • Kerrison, Philip D3
  • da Costa, Elisabete4
  • Calado, Ricardo5
  • Domingues, Maria do Rosário4
  • Costa Azevedo, Isabel6
  • Sousa-Pinto, Isabel6, 7
  • Gachon, Claire3, 8
  • van der Werf, Adrie9
  • de Visser, Willem9
  • Beniers, Johanna E9
  • Jansen, Henrice9
  • Guiry, Michael D10
  • Sulpice, Ronan1
  • 1 National University of Ireland - Galway, Plant Systems Biology Laboratory, Ryan Institute & MaREI Centre for Marine, Climate and Energy, School of Natural Sciences, Galway, Ireland. , (Ireland)
  • 2 CNRS, Sorbonne Université Sciences, UMR 8227, Integrative Biology of Marine Models, Station Biologique de Roscoff, Roscoff, France. , (France)
  • 3 Scottish Association for Marine Science (SAMS), Scottish Marine Institute, Oban, UK.
  • 4 CESAM & LAQV-REQUIMTE, Department of Chemistry, University of Aveiro, Campus Universitário de Santiago, Aveiro, Portugal. , (Portugal)
  • 5 ECOMARE & CESAM, Departamento de Biologia & Universidade de Aveiro, Campus Universitário de Santiago, Aveiro, Portugal. , (Portugal)
  • 6 CIIMAR/CIMAR, Interdisciplinary Centre of Marine and Environmental Research, Novo Edifício do Terminal de Cruzeiros do Porto de Leixões, Matosinhos, Portugal. , (Portugal)
  • 7 Department of Biology, Faculty of Sciences, University of Porto, Matosinhos, Portugal. , (Portugal)
  • 8 UMR 7245 - Molécules de Communication et Adaptation des Micro-organismes, Muséum National d'Histoire Naturelle, CNRS, Paris, France. , (France)
  • 9 Wageningen University & Research, Wageningen, The Netherlands. , (Netherlands)
  • 10 AlgaeBase, Ryan Institute, National University of Ireland, Galway, Ireland. , (Ireland)
Type
Published Article
Journal
Molecular Ecology Resources
Publisher
Wiley (Blackwell Publishing)
Publication Date
Jan 01, 2022
Volume
22
Issue
1
Pages
86–101
Identifiers
DOI: 10.1111/1755-0998.13453
PMID: 34153167
Source
Medline
Keywords
Language
English
License
Unknown

Abstract

Accurate species identification often relies on public repositories to compare the barcode sequences of the investigated individual(s) with taxonomically assigned sequences. However, the accuracy of identifications in public repositories is often questionable, and the names originally given are rarely updated. For instance, species of the Sea Lettuce (Ulva spp.; Ulvophyceae, Ulvales, Ulvaceae) are frequently misidentified in public repositories, including herbaria and gene banks, making species identification based on traditional barcoding unreliable. We DNA barcoded 295 individual distromatic foliose strains of Ulva from the North-East Atlantic for three loci (rbcL, tufA, ITS1). Seven distinct species were found, and we compared our results with all worldwide Ulva spp. sequences present in the NCBI database for the three barcodes rbcL, tufA and the ITS1. Our results demonstrate a large degree of species misidentification, where we estimate that 24%-32% of the entries pertaining to foliose species are misannotated and provide an exhaustive list of NCBI sequences reannotations. An analysis of the global distribution of registered samples from foliose species also indicates possible geographical isolation for some species, and the absence of U. lactuca from Northern Europe. We extended our analytical framework to three other genera, Fucus, Porphyra and Pyropia and also identified erroneously labelled accessions and possibly new synonymies, albeit less than for Ulva spp. Altogether, exhaustive taxonomic clarification by aggregation of a library of barcode sequences highlights misannotations and delivers an improved representation of species diversity and distribution. © 2021 The Authors. Molecular Ecology Resources published by John Wiley & Sons Ltd.

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