Database Commons

a catalog of biological databases

e.g., animal; RNA; Methylation; China

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

Publications

The UNITE database for molecular identification of fungi: handling dark taxa and parallel taxonomic classifications. [PMID: 30371820]
Rolf Henrik Nilsson, Karl-Henrik Larsson, Andy F S Taylor, Johan Bengtsson-Palme, Thomas S Jeppesen, Dmitry Schigel, Peter Kennedy, Kathryn Picard, Frank Oliver Glöckner, Leho Tedersoo, Irja Saar, Urmas Kõljalg, Kessy Abarenkov

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) | 15 Citations (from Europe PMC, 2019-11-01)
Taxonomic annotation of public fungal ITS sequences from the built environment - a report from an April 10-11, 2017 workshop (Aberdeen, UK). [PMID: 29559822]
R Henrik Nilsson, Andy F S Taylor, Rachel I Adams, Christiane Baschien, null Johan Bengtsson-Palme, Patrik Cangren, Claudia Coleine, null Heide-Marie Daniel, Sydney I Glassman, Yuuri Hirooka, Laszlo Irinyi, null Reda Iršėnaitė, null Pedro M Martin-Sanchez, Wieland Meyer, null Seung-Yoon Oh, null Jose Paulo Sampaio, Keith A Seifert, Frantisek Sklenář, null Dirk Stubbe, Sung-Oui Suh, Richard Summerbell, Sten Svantesson, null Martin Unterseher, null Cobus M Visagie, Michael Weiss, Joyce Hc Woudenberg, null Christian Wurzbacher, Silke Van den Wyngaert, Neriman Yilmaz, null Andrey Yurkov, Urmas Kõljalg, Kessy Abarenkov

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, 2019-11-01)
A Comprehensive, Automatically Updated Fungal ITS Sequence Dataset for Reference-Based Chimera Control in Environmental Sequencing Efforts. [PMID: 25786896]
R Henrik Nilsson, Leho Tedersoo, Martin Ryberg, Erik Kristiansson, 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,

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) | 47 Citations (from Europe PMC, 2019-11-01)
The UNITE database for molecular identification of fungi--recent updates and future perspectives. [PMID: 20409185]
Kessy Abarenkov, R Henrik Nilsson, Karl-Henrik Larsson, Ian J Alexander, Ursula Eberhardt, Susanne Erland, Klaus Høiland, Rasmus Kjøller, Ellen Larsson, Taina Pennanen, Robin Sen, Andy F S Taylor, Leho Tedersoo, Björn M Ursing, Trude Vrålstad, Kare Liimatainen, Ursula Peintner, Urmas Kõljalg

null

New Phytol. 2010:186(2) | 373 Citations (from Europe PMC, 2019-11-01)
Fungal networks made of humans: UNITE, FESIN, and frontiers in fungal ecology. [PMID: 18211473]
Thomas D Bruns, A Elizabeth Arnold, Karen W Hughes

null

New Phytol. 2008:177(3) | 10 Citations (from Europe PMC, 2019-11-01)

Ranking

All databases:
189/4531 (95.851%)
Standard ontology and nomenclature:
15/178 (92.135%)
189
Total Rank
450
Citations
40.909
z-index

Community reviews

Not Rated
Submit a review
Data quality & quantity:
Content organization & presentation
System accessibility & reliability:

Word cloud

Record metadata

Created on: 2018-01-28
Curated by:
***leem@***u.edu.pk [2019-10-28]
***d@***c.cn [2019-01-04]
***ina@***c.cn [2018-06-07]
***dra@***u.edu.pk [2018-04-24]
***dra@***u.edu.pk [2018-04-04]
***6490594@***m [2018-01-27]