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Taxonomic reliability of DNA sequences in public sequence databases: A fungal perspective

Journal article
Authors R. Henrik Nilsson
Martin Ryberg
Erik Kristiansson
Kessy Abarenkov
Karl-Henrik Larsson
Urmas Kõljalg
Published in PLoS ONE
Volume 1
Issue 1
Pages e59
Publication year 2006
Published at Department of Plant and Environmental Sciences
Department of Mathematical Sciences, Mathematical Statistics
Pages e59
Language en
Links dx.doi.org/10.1371/journal.pone.000...
Subject categories Biological Sciences

Abstract

Background DNA sequences are increasingly seen as one of the primary information sources for species identification in many organism groups. Such approaches, popularly known as barcoding, are underpinned by the assumption that the reference databases used for comparison are sufficiently complete and feature correctly and informatively annotated entries. Methodology/Principal Findings The present study uses a large set of fungal DNA sequences from the inclusive International Nucleotide Sequence Database to show that the taxon sampling of fungi is far from complete, that about 20% of the entries may be incorrectly identified to species level, and that the majority of entries lack descriptive and up-to-date annotations. Conclusions The problems with taxonomic reliability and insufficient annotations in public DNA repositories form a tangible obstacle to sequence-based species identification, and it is manifest that the greatest challenges to biological barcoding will be of taxonomical, rather than technical, nature.

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