Document of bibliographic reference 328279

BibliographicReference record

Type

Bibliographic resource

Type of document

Journal article

BibLvlCode

AS

Title

Significant taxon sampling gaps in DNA databases limit the operational use of marine macrofauna metabarcoding

Abstract

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.

WebOfScience code

https://www.webofscience.com/wos/woscc/full-record/WOS:000560432400001

Bibliographic citation

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. https://dx.doi.org/10.1007/s12526-020-01093-5

Topic

Marine

Is peer reviewed

true

Access rights

open access

Is accessible for free

true