Taxonomic Reliability of DNA Sequences in Public Sequence Databases: A Fungal Perspective

• Published in: PloS one Vol. 1; no. 1; p. e59
• Main Authors: Nilsson, R. Henrik, Ryberg, Martin, Kristiansson, Erik, Abarenkov, Kessy, Larsson, Karl-Henrik, Kõljalg, Urmas
• Format: Journal Article
• Language: English
• Published: United States Public Library of Science 20.12.2006; Public Library of Science (PLoS)
• Subjects: Analysis; Annotations; Bar codes; Computational Biology; Data bases; Databases, Nucleic Acid; Deoxyribonucleic acid; DNA; DNA sequencing; DNA, Fungal - genetics; DNA, Ribosomal - genetics; Ecology; Environmental science; Fungi; Fungi - classification; Fungi - genetics; Gene sequencing; Genes; Identification; Information sources; Morphology; Nucleotide sequence; Organisms; Phylogenetics; Phylogeny; Plant Biology; Reliability; Repositories; Reproducibility of Results; Species; Species Specificity; Taxonomy
• ISSN: 1932-6203; 1932-6203
• DOI: 10.1371/journal.pone.0000059

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. 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. 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.