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

By R. Henrik Nilsson, Martin Ryberg, Erik Kristiansson, Kessy Abarenkov, Karl-Henrik Larsson, Urmas Kõljalg. PLoS ONE, 2006

657 citations recorded by the source corpus.

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.

Subfields: Cell Biology, Molecular Biology, Plant Science

View Paper: https://www.semanticscholar.org/paper/91e28503efd8f533af4e748774fc94765b33c6e6

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Citations in the corpus

Ectomycorrhizal fungal diversity: seperating the wheat from the chaff (2008, background): “The phylogeny of the cantharelloid clade (Moncalvo et al., 2006) confirmed that Sistotrema is polyphyletic and showed that S. muscicola and S. alboluteum (and likely S. confluens) belong to the same clade as the ECM genera Hydnum, Cantharellus, and Craterellus – again providing strong support for ou”
Impact of DNA sequence-data on the taxonomy of anamorphic fungi (2007, background): “Nilsson et al. (2006) conducted a study based on a large set of fungal DNA sequences from the inclusive International Nucleotide Sequence Database and showed that: the taxon sampling of fungi is far from complete, about 20-30% of the entries may be incorrectly identified to species level, and the…”
A review of the trade in orchids and its implications for conservation (2018, background): “Since these identifications cannot be reliably verified, the sequences fall far short of the minimum criteria to be used as barcode reference sequences (Nilsson et al., 2006).”
Species-specific detection and quantification of environmental DNA from marine fishes in the Baltic Sea (2019, background): “The NCBI GenBank database cannot be regarded as providing complete coverage of nucleotide diversity for all organisms found in the Baltic Sea (Nilsson et al., 2006; Ojaveer et al., 2010).”
From morphology to molecular biology: can we use sequence data to identify fungal endophytes? (2011, background): “However, as already noted, the technique has serious limitations, since many sequences deposited in GenBank are associated with erroneous taxon names (Nilsson et al. 2006).”
Indirect host effect on ectomycorrhizal fungi: Leaf fall and litter quality explain changes in fungal communities on the roots of co-occurring Mediterranean oaks (2010, methodology): “This cut off level was established based on studies using the ITS region for ECM species identification that have shown that error rates generated by PCR, sequencing and interspecific variability are generally 3% (Nilsson et al., 2006).”
The Colletotrichum gloeosporioides species complex (2012, background): “Nilsson et al. (2006) summarised the frequency of inaccurately annotated data in GenBank.”
454 Pyrosequencing analyses of forest soils reveal an unexpectedly high fungal diversity. (2009, background): “In addition, these fungal taxa and several genera, including Glomeromycota, were underestimated in our survey, as poorly annotated ITS sequences from GenBank were excluded from C-DB (Vilgalys, 2003; Nilsson et al., 2008; Ryberg et al., 2009).”
The fungi: 1, 2, 3 ... 5.1 million species? (2011, background): “A physical specimen, including an inert culture, is still required as a type specimen (but see Conclusions later), and vouchers of known fungi are used for documenting DNA sequences deposited in some databases ( Nilsson et al., 2006 ).”
Initial fungal colonizer affects mass loss and fungal community development in Picea abies logs 6 yr after inoculation (2011, background): “Perhaps one of the largest drawbacks of this technique is that DNA-sequence identification is dependent on publically available databases, which often contain errors (Nilsson et al. 2006).”
Use of ITS2 Region as the Universal DNA Barcode for Plants and Animals (2010, neutral): “annotation, in addition to conducting BLAST searches of the fungal nrITS database [36].”
Metabarcoding: A powerful tool to investigate microbial communities and shape future plant protection strategies (2017, background): “The latter database, however, has a greater chance of misidentification due to the lower accuracy and reliability of the deposited sequences (Nilsson et al., 2006).”
DNA barcoding detects market substitution in North American seafood (2008, background): “Unfortunately, given the present day torrent of data generation, erroneous records have been known to make their way into public archives (Bridges, Roberts, Spooner, & Panchal, 2003; Forster, 2003; Harris, 2003; Nilsson et al., 2006; Ross & Murugan, 2006; Yao, Bravi, & Bandelt, 2004).”
ITS as an environmental DNA barcode for fungi: an in silico approach reveals potential PCR biases (2010, background): “However, these data are to some extent hampered by misidentifications or technical errors such as mixing of DNA templates or sequencing errors [12].”