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.

chimera detection

PCR artifacts

fungi

molecular ecology

reference dataset

Author

R. Henrik Nilsson

University of Gothenburg

Leho Tedersoo

University of Tartu

Martin Ryberg

Uppsala University

Erik Kristiansson

University of Gothenburg

Chalmers, Mathematical Sciences, Mathematical Statistics

Martin Hartmann

Eidgenossische Forschungsanstalt fur Wald, Schnee Und Landschaft Eth-Bereichs

Institute for Sustainability Sciences

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 2 145-150

Subject Categories

Biological Systematics

Soil Science

Ecology

Pathobiology

Microbiology

Bioinformatics (Computational Biology)

Microbiology in the medical area

Bioinformatics and Systems Biology

DOI

10.1264/jsme2.ME14121

PubMed

25786896

More information

Latest update

5/17/2018