The UNITE database for molecular identification of fungi: handling dark taxa and parallel taxonomic classifications

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

doi:10.1093/nar/gky1022

The UNITE database for molecular identification of fungi: handling dark taxa and parallel taxonomic classifications

Rolf Henrik Nilsson (Corresponding Author), 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

Aberdeen Centre For Environmental Sustainability

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Abstract

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.

Original language	English
Pages (from-to)	D259-264
Number of pages	6
Journal	Nucleic Acids Research
Volume	47
Issue number	D1
Early online date	29 Oct 2018
DOIs	https://doi.org/10.1093/nar/gky1022
Publication status	Published - 8 Jan 2019

Bibliographical note

Alfred P. Sloan Foundation [G-2015-14062]; Swedish Research Council of Environment, Agricultural Sciences, and Spatial Planning [FORMAS, 215-2011-498]; European Regional Development Fund (Centre of Excellence EcolChange) [TK131]; Estonian Research Council [IUT20-30]. Funding for open access charge: Swedish Research Council of Environment, Agricultural Sciences and Spatial Planning.

Keywords

DNA
MARKER
SEARCH
SEQUENCE
SOFTWARE
TOOL

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10.1093/nar/gky1022Licence: CC BY

The UNITE database for molecular identification of fungi
C The Author(s) 2018. Published by Oxford University Press on behalf of Nucleic Acids Research. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited.
Final published version, 1.47 MBLicence: CC BY

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Nilsson, R. H., Larsson, K.-H., Taylor, A. F. S., Bengtsson-Palme, J., Jeppesen, T. S., Schigel, D., Kennedy, P., Picard, K., Glöckner, F. O., Tedersoo, L., Saar, I., Kõljalg, U., & Abarenkov, K. (2019). The UNITE database for molecular identification of fungi: handling dark taxa and parallel taxonomic classifications. Nucleic Acids Research, 47(D1), D259-264. https://doi.org/10.1093/nar/gky1022

Nilsson, RH, Larsson, K-H, Taylor, AFS, Bengtsson-Palme, J, Jeppesen, TS, Schigel, D, Kennedy, P, Picard, K, Glöckner, FO, Tedersoo, L, Saar, I, Kõljalg, U & Abarenkov, K 2019, 'The UNITE database for molecular identification of fungi: handling dark taxa and parallel taxonomic classifications', Nucleic Acids Research, vol. 47, no. D1, pp. D259-264. https://doi.org/10.1093/nar/gky1022

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The UNITE database for molecular identification of fungi: handling dark taxa and parallel taxonomic classifications

Abstract

Bibliographical note

Keywords

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