title: A Comprehensive, Automatically Updated Fungal ITS Sequence Dataset for Reference-Based Chimera Control in Environmental Sequencing Efforts.
abstract: 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.
authors: Department of Biological and Environmental Sciences, University of Gothenburg.
authors: R Henrik
authors: RH
authors: Nilsson
authors: Leho
authors: L
authors: Tedersoo
authors: Martin
authors: M
authors: Ryberg
authors: Erik
authors: E
authors: Kristiansson
authors: Martin
authors: M
authors: Hartmann
authors: Martin
authors: M
authors: Unterseher
authors: Teresita M
authors: TM
authors: Porter
authors: Johan
authors: J
authors: Bengtsson-Palme
authors: Donald M
authors: DM
authors: Walker
authors: Filipe
authors: F
authors: de Sousa
authors: Hannes Andres
authors: HA
authors: Gamper
authors: Ellen
authors: E
authors: Larsson
authors: Karl-Henrik
authors: KH
authors: Larsson
authors: Urmas
authors: U
authors: Kõljalg
authors: Robert C
authors: RC
authors: Edgar
authors: Kessy
authors: K
authors: Abarenkov
mesh_terms: D016477:Artifacts; D004271:DNA, Fungal / Q000737:chemistry / Q000235:genetics*; D021903:DNA, Ribosomal Spacer / Q000737:chemistry / Q000235:genetics*; D004783:Environmental Microbiology; D005658:Fungi / Q000145:classification* / Q000235:genetics; D056186:Metagenomics / Q000379:methods*; D012015:Reference Standards; D017422:Sequence Analysis, DNA
chemical_list: D004271:DNA, Fungal; D021903:DNA, Ribosomal Spacer