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.

reference dataset

chimera detection

molecular ecology

fungi

PCR artifacts

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Published in

Microbes and Environments

1342-6311 (ISSN) 1347-4405 (eISSN)

Vol. 30 Issue 2 p. 145-150

Categorizing

Subject Categories (SSIF 2011)

Biological Systematics

Soil Science

Ecology

Pathobiology

Microbiology

Bioinformatics (Computational Biology)

Microbiology in the medical area

Bioinformatics and Systems Biology

Control Engineering

Identifiers

DOI

10.1264/jsme2.ME14121

PubMed

25786896

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Latest update

12/10/2024