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A Comprehensive, Automatically Updated Fungal ITS Sequence Dataset for Reference-Based Chimera Control in Environmental Sequencing Efforts
Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Systematic Biology.
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2015 (English)In: Microbes and Environments, ISSN 1342-6311, E-ISSN 1347-4405, Vol. 30, no 2, 145-150 p.Article in journal (Refereed) Published
Abstract [en]

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.

Place, publisher, year, edition, pages
2015. Vol. 30, no 2, 145-150 p.
Keyword [en]
fungi, chimera detection, reference dataset, molecular ecology, PCR artifacts
National Category
Biological Sciences
URN: urn:nbn:se:uu:diva-258332DOI: 10.1264/jsme2.ME14121ISI: 000356608500005PubMedID: 25786896OAI: oai:DiVA.org:uu-258332DiVA: diva2:841836
Swedish Research Council Formas, 215-2011-498
Available from: 2015-07-15 Created: 2015-07-13 Last updated: 2015-07-15Bibliographically approved

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Ryberg, Martin
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