A comprehensive, automatically updated fungal ITS sequence dataset for reference-based chimera control in environmental sequencing efforts
Artikel i vetenskaplig tidskrift, 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.
reference dataset
chimera detection
molecular ecology
fungi
PCR artifacts
Författare
R. Henrik Nilsson
Göteborgs universitet
Leho Tedersoo
Tartu Ülikool
Martin Ryberg
Uppsala universitet
Erik Kristiansson
Göteborgs universitet
Chalmers, Matematiska vetenskaper, Matematisk statistik
Martin Hartmann
Eidgenossische Forschungsanstalt fur Wald, Schnee Und Landschaft Eth-Bereichs
Institute for Sustainability Sciences
Martin Unterseher
Universität Greifswald
Teresita M. Porter
McMaster University
Johan Bengtsson Palme
Göteborgs universitet
Donald M. Walker
University of Findlay
Filipe de Sousa
Göteborgs universitet
Hannes Andres Gamper
Eidgenössische Technische Hochschule Zürich (ETH)
Ellen Larsson
Göteborgs universitet
Karl-Henrik Larsson
Natural History Museum
Urmas Kõljalg
Tartu Ülikool
Robert C. Edgar
Kessy Abarenkov
Tartu Ülikool
Microbes and Environments
1342-6311 (ISSN) 1347-4405 (eISSN)
Vol. 30 2 145-150Ämneskategorier (SSIF 2011)
Biologisk systematik
Markvetenskap
Ekologi
Patobiologi
Mikrobiologi
Bioinformatik (beräkningsbiologi)
Mikrobiologi inom det medicinska området
Bioinformatik och systembiologi
Reglerteknik
DOI
10.1264/jsme2.ME14121
PubMed
25786896