A comprehensive, automatically updated fungal ITS sequence dataset for reference-based chimera control in environmental sequencing efforts
Journal article, 2015
The nuclear ribosomal internal transcribed spacer (ITS) region is the most commonly chosen genetic marker for the molecular identification of fungi in environmental sequencing and molecular ecology studies. Several analytical issues complicate such efforts, one of which is the formation of chimeric—artificially joined—DNA sequences during PCR amplification or sequence assembly. Several software tools are currently available for chimera detection, but rely to various degrees on the presence of a chimera-free reference dataset for optimal performance. However, no such dataset is available for use with the fungal ITS region. This study introduces a comprehensive, automatically updated reference dataset for fungal ITS sequences based on the UNITE database for the molecular identification of fungi. This dataset supports chimera detection throughout the fungal kingdom and for full-length ITS sequences as well as partial (ITS1 or ITS2 only) datasets. The performance of the dataset on a large set of artificial chimeras was above 99.5%, and we subsequently used the dataset to remove nearly 1,000 compromised fungal ITS sequences from public circulation. The dataset is available at http://unite.ut.ee/repository.php and is subject to web-based third-party curation.
fungi
PCR artifacts
chimera detection
molecular ecology
reference dataset
Author
R. Henrik Nilsson
University of Gothenburg
Leho Tedersoo
University of Tartu
Martin Ryberg
Uppsala University
Erik Kristiansson
Chalmers, Mathematical Sciences, Mathematical Statistics
University of Gothenburg
Martin Hartmann
Institute for Sustainability Sciences
Eidgenossische Forschungsanstalt fur Wald, Schnee Und Landschaft Eth-Bereichs
Martin Unterseher
University of Greifswald
Teresita M. Porter
McMaster University
Johan Bengtsson-Palme
University of Gothenburg
Donald M. Walker
University of Findlay
Filipe de Sousa
University of Gothenburg
Hannes Andres Gamper
Swiss Federal Institute of Technology in Zürich (ETH)
Ellen Larsson
University of Gothenburg
Karl-Henrik Larsson
Natural History Museum
Urmas Kõljalg
University of Tartu
Robert C. Edgar
Kessy Abarenkov
University of Tartu
Microbes and Environments
1342-6311 (ISSN) 1347-4405 (eISSN)
Vol. 30 2 145-150Subject Categories
Biological Systematics
Soil Science
Ecology
Pathobiology
Microbiology
Bioinformatics (Computational Biology)
Microbiology in the medical area
Bioinformatics and Systems Biology
Control Engineering
DOI
10.1264/jsme2.ME14121
PubMed
25786896