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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.
Molecular Ecology Resources
|December 8, 2022
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.
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.
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