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

Abstract

BackgroundDNA 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 FindingsThe 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.ConclusionsThe 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.

Profundae diversitas: the uncharted genetic diversity in a newly studied group of fungal root endophytes

“…The ITS sequence identities recovered from GenBank in our study that did not cluster within the clades containing their taxonomic counterparts may not have been correctly identified when they were originally deposited. Many sequences deposited in GenBank are associated with erroneous taxon names (Nilsson et al 2006). While the quality and reliability of DNA sequences in public databases may be improving, some GenBank sequences may not be reliable, with as much as 86% of available fungal sequences not from the named organism (Ko Ko et al 2011).…”

Fungal root endophytes of tomato from Kenya and their nematode biocontrol potential

“…It is therefore important to compare sequences with ex-type strains to avoid misinterpretation and relying on the GenBank. Errors in fungal sequences in GenBank have been found to be as high as 20 % (Nilsson et al 2006). All sequences used in this study were submitted to GenBank and are available under the accession numbers listed in Table 2.…”

High-Throughput Sequencing and Metagenomics: Moving Forward in the Culture-Independent Analysis of Food Microbial Ecology

“…The use of such bioinformatic tools in HTS-based microbial ecology has been reviewed elsewhere (43,44). The accuracy and reliability of the final determined structure of the food microbiota depend very much on the quality of the reference database used to assign the taxonomy (45)(46)(47). Various databases are available for prokaryotes (47)(48)(49)(50), with all containing reliable-quality 16S rRNA gene sequences.…”

“…Various databases are available for prokaryotes (47)(48)(49)(50), with all containing reliable-quality 16S rRNA gene sequences. There is currently less in-depth coverage of fungi: although they can be identified on the basis of internal transcribed spacers (ITS) and small and large ribosomal subunits, the public databases often have poor-quality sequences and curated databases have limited coverage (45,46). In addition, in the specific case of ITS, amplicon length unevenness can promote preferential amplification of shorter sequences, making it necessary to optimize the target regions to be analyzed (51).…”