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. 2019 Jan 8;47(D1):D259-D264.
doi: 10.1093/nar/gky1022.

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

Rolf Henrik Nilsson  1 , Karl-Henrik Larsson  2 , Andy F S Taylor  3 , Johan Bengtsson-Palme  4   5   6 , Thomas S Jeppesen  7 , Dmitry Schigel  7 , Peter Kennedy  8 , Kathryn Picard  9 , Frank Oliver Glöckner  10 , Leho Tedersoo  11 , Irja Saar  11 , Urmas Kõljalg  11 , Kessy Abarenkov  12
Affiliations

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

Rolf Henrik Nilsson et al. Nucleic Acids Res. .

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.

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Figures

Figure 1.
Figure 1.
A screenshot of a UNITE SH Digital Object Identifier (DOI) page for Tomentella atroarenicolor (https://plutof.ut.ee/#/datacite/10.15156%2FBIO%2FSH009889.07FU). (A) The most accurate taxon name chosen automatically (or manually, if the default was overridden by an expert user) from the available sequence identifications. (B) Short ID of the DOI. (C) Data on reference sequence chosen to represent this SH. (D) Placement of the SH in the fungal classification and identification records for individual sequences. The number after the taxon name indicates how many sequences that carry that name. (E) Select statistics on the SH. The minimum distance 3.0% is the mandatory genetic difference between sister SHs. (F) Distribution map of the individual sequences. (G) Information on ecology (interacting taxa) if associated with the individual sequences. (H) DataCite-specific data on the DOI. (I) Images of the specimen or sample from which the DNA was extracted. Only a limited number of sequences have images attached to them. (J) Graphical overview of the SH with detailed information. (K) SH inclusiveness across sequence similarity threshold values. A threshold value ( = minimum distance) of 1.5% will split these sequences into two SHs, shown here in different colours. (L) A threshold value of 2.5% will lump all sequences into a single SH. Each such SH is hyperlinked to its own unique web page. (M) Scrollable multiple sequence alignment of the SH. ‘RefSeq’ indicates that the sequence was selected manually to be the representative sequence for the SHs. RefSeqs stem from type specimens or other authentic and particularly trustworthy material. This particular SH contains both INSDC sequences (brown) and sequences that are only found in UNITE (yellow). Some 29 000 sequences are only found in UNITE at this stage, but will be submitted to the INSDC upon publication of the underlying studies. These sequences are included in the various UNITE sequence releases and download files.
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