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.

chimera detection

PCR artifacts

fungi

molecular ecology

reference dataset

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

Ernst-Moritz-Arndt-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. 30 145-150

Ämneskategorier

Biologisk systematik

Markvetenskap

Ekologi

Patobiologi

Mikrobiologi

Bioinformatik (beräkningsbiologi)

Mikrobiologi inom det medicinska området

Bioinformatik och systembiologi

DOI

10.1264/jsme2.ME14121

PubMed

25786896