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Navigating the seven challenges of taxonomic reference databases in metabarcoding analyses.

François Keck1, Marjorie Couton1, Florian Altermatt1,2

  • 1Department of Aquatic Ecology, Eawag: Swiss Federal Institute of Aquatic Science and Technology, Dübendorf, Switzerland.

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Summary

Metabarcoding relies on DNA reference databases for species identification. This study identifies seven overlooked challenges with these databases, such as mislabelling and taxonomic conflicts, impacting biodiversity assessments.

Keywords:
DNA reference librarybarcodingmetabarcodingreference databasetaxonomic affiliation

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Area of Science:

  • Ecology
  • Biodiversity Sciences
  • Molecular Biology

Background:

  • Metabarcoding, utilizing bulk or environmental DNA (eDNA) sampling, is crucial for ecological and biodiversity monitoring.
  • Accurate taxonomic identification of species from DNA sequences hinges on comprehensive reference databases.
  • Existing reference databases face challenges in completeness and availability across different taxonomic groups and genetic regions.

Purpose of the Study:

  • To synthesize and categorize all inherent problems associated with DNA reference databases used in metabarcoding.
  • To identify and describe seven classes of challenges impacting taxonomic assignment accuracy.
  • To raise user awareness regarding the limitations of metabarcoding data and reference databases for reliable biodiversity assessment.

Main Methods:

  • Literature review and synthesis of known issues with DNA reference databases.
  • Identification and classification of seven distinct problem categories: mislabelling, sequencing errors, sequence conflict, taxonomic conflict, low taxonomic resolution, missing taxa, and missing intraspecific variants.
  • Illustrative examples from scientific literature and quantitative analyses of public databases (GenBank, BOLD).

Main Results:

  • Seven classes of challenges inherent to DNA reference databases were identified and described.
  • Problems include mislabelling, sequencing errors, sequence and taxonomic conflicts, low resolution, and missing taxa or variants.
  • These issues can lead to inaccurate or false taxonomic assignments in biodiversity assessments.

Conclusions:

  • Overlooked problems in DNA reference databases significantly impact the reliability of metabarcoding-based biodiversity assessments.
  • Addressing issues like mislabelling, taxonomic conflicts, and database incompleteness is vital for accurate species identification.
  • Increased user awareness of these limitations is essential for the proper interpretation of metabarcoding data in ecology and conservation.