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Comprehensive DNA barcode reference databases significantly improve environmental DNA (eDNA) metabarcoding accuracy for biodiversity assessments. Including genomic variation enhances taxonomic resolution and reduces misclassifications, revealing more species.

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Area of Science:

  • Marine Biology
  • Genomics
  • Biodiversity Science

Background:

  • Environmental DNA (eDNA) metabarcoding offers rapid biodiversity assessment but is hampered by incomplete reference databases.
  • Accuracy is further challenged by intra- and interspecific DNA sequence variation.

Purpose of the Study:

  • To evaluate the impact of comprehensive reference databases, including intragenomic and intergenomic variation, on eDNA biodiversity assessments.
  • To improve the accuracy and resolution of eDNA metabarcoding for coral reef ecosystems.

Main Methods:

  • Collected coral tissue and water samples for reference barcoding and eDNA metabarcoding.
  • Utilized genome skimming to generate 28S barcodes from coral specimens.
  • Incorporated local reference barcodes and analyzed intragenomic 28S lineages.

Main Results:

  • Incorporating local reference barcodes improved ASV (Amplicon Sequence Variant) taxonomic classification, increasing genus-level resolution and correcting misclassifications.
  • Excluding intragenomic variation led to unclassified ASVs, highlighting the importance of capturing this variation.
  • Integrating reference genome skimming and eDNA metabarcoding significantly expanded known coral family richness, especially at greater depths.
  • eDNA metabarcoding detected previously unknown coral families, demonstrating its utility for biodiversity discovery.

Conclusions:

  • Incomplete reference databases lead to unclassified ASVs, false positives, and misclassifications in eDNA studies.
  • Comprehensive reference databases that account for genomic variation are crucial for accurate eDNA-based biodiversity assessments.
  • The integration of genome skimming and eDNA metabarcoding enhances biodiversity discovery, particularly in underexplored deep-sea environments.