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Database information

UNITE (UNITE database)

General information

Description: The development of UNITE is a Northern European initiative presently involving 10 core institutions. The project links experts in fungal taxonomy, ecology and bioinformatics.
Year founded: 2003
Last update: 2017-12-01
Version: 7.2
Accessibility:
Manual:
Accessible
Real time : Checking...
Country/Region: Estonia
Data type:
DNA
Data object:
Database category:
Major organism:
Keywords:

Contact information

University/Institution: University of Tartu
Address: Department of Botany, Institute of Ecology and Earth Sciences, University of Tartu, 40 Lai St, 51005 Tartu, Estonia
City: Tartu
Province/State:
Country/Region: Estonia
Contact name (PI/Team): Urmas Kõljalg
Contact email (PI/Helpdesk): urmas.koljalg@ut.ee

Record metadata

Created on: 2018-01-28
Curated by:
Shoaib Saleem [2019-10-28]
Dong Zou [2019-01-04]
Lina Ma [2018-06-07]
Sidra Younas [2018-04-24]
Sidra Younas [2018-04-04]
姜 美叶 [2018-01-27]

Ranking

All databases:
185/4549 (95.955%)
Standard ontology and nomenclature:
15/182 (92.308%)
185
Total Rank
477
Citations
39.75
z-index

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Word cloud

Publications

30371820
The UNITE database for molecular identification of fungi: handling dark taxa and parallel taxonomic classifications. [PMID: 30371820]
Nilsson RH, Larsson KH, Taylor AFS, Bengtsson-Palme J, Jeppesen TS, Schigel D, Kennedy P, Picard K, Glöckner FO, Tedersoo L, Saar I, Kõljalg U, Abarenkov K.

UNITE (https://unite.ut.ee/) is a web-based database and sequence management environment for the molecular identification of fungi. It targets the formal fungal barcode-the nuclear ribosomal internal transcribed spacer (ITS) region-and offers all ?1 000 000 public fungal ITS sequences for reference. These are clustered into ?459 000 species hypotheses and assigned digital object identifiers (DOIs) to promote unambiguous reference across studies. In-house and web-based third-party sequence curation and annotation have resulted in more than 275 000 improvements to the data over the past 15 years. UNITE serves as a data provider for a range of metabarcoding software pipelines and regularly exchanges data with all major fungal sequence databases and other community resources. Recent improvements include redesigned handling of unclassifiable species hypotheses, integration with the taxonomic backbone of the Global Biodiversity Information Facility, and support for an unlimited number of parallel taxonomic classification systems.

Nucleic Acids Res. 2019:47(D1) | 26 Citations (from Europe PMC, 2020-05-23)
29559822
Taxonomic annotation of public fungal ITS sequences from the built environment - a report from an April 10-11, 2017 workshop (Aberdeen, UK). [PMID: 29559822]
Nilsson RH, Taylor AFS, Adams RI, Baschien C, Johan Bengtsson-Palme, Cangren P, Coleine C, Heide-Marie Daniel, Glassman SI, Hirooka Y, Irinyi L, Reda Iršėnaitė, Pedro M Martin-Sanchez, Meyer W, Seung-Yoon Oh, Jose Paulo Sampaio, Seifert KA, Sklenář F, Dirk Stubbe, Suh SO, Summerbell R, Svantesson S, Martin Unterseher, Cobus M Visagie, Weiss M, Woudenberg JH, Christian Wurzbacher, den Wyngaert SV, Yilmaz N, Andrey Yurkov, Kõljalg U, Abarenkov K.

Recent DNA-based studies have shown that the built environment is surprisingly rich in fungi. These indoor fungi - whether transient visitors or more persistent residents - may hold clues to the rising levels of human allergies and other medical and building-related health problems observed globally. The taxonomic identity of these fungi is crucial in such pursuits. Molecular identification of the built mycobiome is no trivial undertaking, however, given the large number of unidentified, misidentified, and technically compromised fungal sequences in public sequence databases. In addition, the sequence metadata required to make informed taxonomic decisions - such as country and host/substrate of collection - are often lacking even from reference and ex-type sequences. Here we report on a taxonomic annotation workshop (April 10-11, 2017) organized at the James Hutton Institute/University of Aberdeen (UK) to facilitate reproducible studies of the built mycobiome. The 32 participants went through public fungal ITS barcode sequences related to the built mycobiome for taxonomic and nomenclatural correctness, technical quality, and metadata availability. A total of 19,508 changes - including 4,783 name changes, 14,121 metadata annotations, and the removal of 99 technically compromised sequences - were implemented in the UNITE database for molecular identification of fungi (https://unite.ut.ee/) and shared with a range of other databases and downstream resources. Among the genera that saw the largest number of changes were , , , and , all of them of significant importance in both culture-based and culture-independent surveys of the built environment.

MycoKeys. 2018:(28) | 5 Citations (from Europe PMC, 2020-05-23)
25786896
A Comprehensive, Automatically Updated Fungal ITS Sequence Dataset for Reference-Based Chimera Control in Environmental Sequencing Efforts. [PMID: 25786896]
Nilsson RH, Tedersoo L, Ryberg M, Kristiansson E, Hartmann M, Unterseher M, Porter TM, Bengtsson-Palme J, Walker DM, de Sousa F, Gamper HA, Larsson E, Larsson KH, Kõljalg U, Edgar RC, Abarenkov K.

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.

Microbes Environ. 2015:30(2) | 50 Citations (from Europe PMC, 2020-05-23)
20409185
The UNITE database for molecular identification of fungi--recent updates and future perspectives. [PMID: 20409185]
Abarenkov K, Henrik Nilsson R, Larsson KH, Alexander IJ, Eberhardt U, Erland S, Høiland K, Kjøller R, Larsson E, Pennanen T, Sen R, Taylor AF, Tedersoo L, Ursing BM, Vrålstad T, Liimatainen K, Peintner U, Kõljalg U.

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New Phytol. 2010:186(2) | 386 Citations (from Europe PMC, 2020-05-23)
18211473
Fungal networks made of humans: UNITE, FESIN, and frontiers in fungal ecology. [PMID: 18211473]
Bruns TD, Arnold AE, Hughes KW.

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New Phytol. 2008:177(3) | 10 Citations (from Europe PMC, 2020-05-23)