R. Henrik Nilsson 1 , * , Leho Tedersoo 2 , Martin Ryberg 3 , Erik Kristiansson 4 , Martin Hartmann 5 , 6 , Martin Unterseher 7 , Teresita M. Porter 8 , Johan Bengtsson-Palme 9 , Donald M. Walker 10 , Filipe de Sousa 1 , Hannes Andres Gamper 11 , Ellen Larsson 1 , Karl-Henrik Larsson 12 , Urmas Kõljalg 2 , 13 , Robert C. Edgar 14 , Kessy Abarenkov 13
19 March 2015
the Japanese Society of Microbial Ecology (JSME)/the Japanese Society of Soil Microbiology (JSSM)/the Taiwan Society of Microbial Ecology (TSME)/the Japanese Society of Plant Microbe Interactions (JSPMI)
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.