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A comprehensive, automatically updated fungal ITS sequence dataset for reference-based chimera control in environmental sequencing efforts

R. Henrik Nilsson ; Leho Tedersoo ; Martin Ryberg ; Erik Kristiansson (Institutionen för matematiska vetenskaper, matematisk statistik) ; Martin Hartmann ; Martin Unterseher ; Teresita M. Porter ; Johan Bengtsson-Palme ; Donald M. Walker ; Filipe de Sousa ; Hannes Andres Gamper ; Ellen Larsson ; Karl-Henrik Larsson ; Urmas Kõljalg ; Robert C. Edgar ; Kessy Abarenkov
Microbes and Environments (1342-6311). Vol. 30 (2015), 2, p. 145-150.
[Artikel, refereegranskad vetenskaplig]

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.

Nyckelord: fungi, chimera detection, reference dataset, molecular ecology, PCR artifacts

Denna post skapades 2015-03-23. Senast ändrad 2015-07-10.
CPL Pubid: 214176


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Institutioner (Chalmers)

Institutionen för biologi och miljövetenskap (GU)
Institutionen för matematiska vetenskaper, matematisk statistik (2005-2016)
Institutionen för biomedicin, avdelningen för infektionssjukdomar (GU)


Bioinformatik (beräkningsbiologi)
Bioinformatik och systembiologi
Terrestrisk ekologi
Biologisk systematik
Medicinsk mikrobiologi
Mikrobiologi och immunologi

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