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Significant taxon sampling gaps in DNA databases limit the operational use of marine macrofauna metabarcoding
Hestetun, J.T.; Bye-Ingebrigtsen, E.; Nilsson, R.H.; Glover, A.G.; Johansen, P.-O.; Dahlgren, T.G. (2020). Significant taxon sampling gaps in DNA databases limit the operational use of marine macrofauna metabarcoding. Mar. Biodiv. 50(5): 70.
In: Marine Biodiversity. Springer: Heidelberg; Berlin. ISSN 1867-1616; e-ISSN 1867-1624
Peer reviewed article  

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  • Hestetun, J.T.
  • Bye-Ingebrigtsen, E.
  • Nilsson, R.H.
  • Glover, A.G., more
  • Johansen, P.-O.
  • Dahlgren, T.G.

    Significant effort is spent on monitoring of benthic ecosystems through government funding or indirectly as a cost of business, and metabarcoding of environmental DNA samples has been suggested as a possible complement or alternative to current morphological methods to assess biodiversity. In metabarcoding, a public sequence database is typically used to match barcodes to species identity, but these databases are naturally incomplete. The North Sea oil and gas industry conducts large-scale environmental monitoring programs in one of the most heavily sampled marine areas worldwide and could therefore be considered a “best-case scenario” for macrofaunal metabarcoding. As a test case, we investigated the database coverage of two common metabarcoding markers, mitochondrial COI and the ribosomal rRNA 18S gene, for a complete list of 1802 macrofauna taxa reported from the North Sea monitoring region IV. For COI, species level barcode coverage was 50.4% in GenBank and 42.4% for public sequences in BOLD. For 18S, species level coverage was 36.4% in GenBank and 27.1% in SILVA. To see whether rare species were underrepresented, we investigated the most commonly reported species as a separate dataset but found only minor coverage increases. We conclude that compared to global figures, barcode coverage is high for this area, but that a significant effort remains to fill barcode databases to levels that would make metabarcoding operational as a taxonomic tool, including for the most common macrofaunal taxa.

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