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

doi:10.1093/nar/gky1022

. 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

¹ University of Gothenburg, Department of Biological and Environmental Sciences, Gothenburg Global Biodiversity Centre, Box 461, 405 30 Gothenburg, Sweden.
² Natural History Museum, University of Oslo, P.O. Box 1172, Blindern, 0318 Oslo, Norway.
³ The James Hutton Institute and University of Aberdeen, Aberdeen, UK.
⁴ Wisconsin Institute for Discovery, University of Wisconsin-Madison, 330 North Orchard Street, Madison, WI 53715, USA.
⁵ Centre for Antibiotic Resistance research (CARe) at University of Gothenburg, Gothenburg, Sweden.
⁶ Department of Infectious Diseases, Sahlgrenska Academy, University of Gothenburg, Guldhedsgatan 10, SE-413 46 Gothenburg, Sweden.
⁷ Global Biodiversity Information Facility, Universitetsparken 15, DK-2100 Copenhagen Ø, Denmark.
⁸ Department of Plant and Microbial Biology, University of Minnesota, 1479 Gortner Avenue, St. Paul, MN 55108, USA.
⁹ Department of Botany, National Museum of Natural History, Smithsonian Institution, Washington, DC 20013, USA.
¹⁰ Jacobs University Bremen and MPI for Marine Microbiology, Celsiusstr. 1, D-28359 Bremen, Germany.
¹¹ University of Tartu, Institute of Ecology and Earth Sciences, 40 Lai Street, 51005 Tartu, Estonia.
¹² Natural History Museum and Botanical Garden, University of Tartu, 46 Vanemuise Street, 51003 Tartu, Estonia.

PMID: 30371820
PMCID: PMC6324048
DOI: 10.1093/nar/gky1022

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

Rolf Henrik Nilsson et al. Nucleic Acids Res. 2019.

. 2019 Jan 8;47(D1):D259-D264.

doi: 10.1093/nar/gky1022.

Authors

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

¹ University of Gothenburg, Department of Biological and Environmental Sciences, Gothenburg Global Biodiversity Centre, Box 461, 405 30 Gothenburg, Sweden.
² Natural History Museum, University of Oslo, P.O. Box 1172, Blindern, 0318 Oslo, Norway.
³ The James Hutton Institute and University of Aberdeen, Aberdeen, UK.
⁴ Wisconsin Institute for Discovery, University of Wisconsin-Madison, 330 North Orchard Street, Madison, WI 53715, USA.
⁵ Centre for Antibiotic Resistance research (CARe) at University of Gothenburg, Gothenburg, Sweden.
⁶ Department of Infectious Diseases, Sahlgrenska Academy, University of Gothenburg, Guldhedsgatan 10, SE-413 46 Gothenburg, Sweden.
⁷ Global Biodiversity Information Facility, Universitetsparken 15, DK-2100 Copenhagen Ø, Denmark.
⁸ Department of Plant and Microbial Biology, University of Minnesota, 1479 Gortner Avenue, St. Paul, MN 55108, USA.
⁹ Department of Botany, National Museum of Natural History, Smithsonian Institution, Washington, DC 20013, USA.
¹⁰ Jacobs University Bremen and MPI for Marine Microbiology, Celsiusstr. 1, D-28359 Bremen, Germany.
¹¹ University of Tartu, Institute of Ecology and Earth Sciences, 40 Lai Street, 51005 Tartu, Estonia.
¹² Natural History Museum and Botanical Garden, University of Tartu, 46 Vanemuise Street, 51003 Tartu, Estonia.

PMID: 30371820
PMCID: PMC6324048
DOI: 10.1093/nar/gky1022

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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References

1. Hawksworth D.L., Lücking R.. Fungal diversity revisited: 2.2 to 3.8 million species. Microbiol. Spec. 2017; 5:1–17. - PMC - PubMed
1. Schoch C.L., Seifert K.A., Huhndorf S., Robert V., Spouge J.L., Levesque C.A., Chen W.. Nuclear ribosomal internal transcribed spacer (ITS) region as a universal DNA barcode marker for Fungi. Proc. Natl. Acad. Sci. Biol. 2012; 109:6241–6246. - PMC - PubMed
1. Karsch-Mizrachi I., Takagi T., Cochrane G.. The international nucleotide sequence database collaboration. Nucleic Acids Res. 2017; 46:D48–D51. - PMC - PubMed
1. Kõljalg U., Nilsson R.H., Abarenkov K., Tedersoo L., Taylor A.F., Bahram M., Bates S.T., Bruns T.D., Bengtsson-Palme J., Callaghan T.M. et al. Towards a unified paradigm for sequence-based identification of fungi. Mol. Ecol. 2013; 22:5271–5277. - PubMed
1. Blaxter M., Mann J., Chapman T., Whitton T.F., Floyd R., Abebe E.. Defining operational taxonomic units using DNA barcode data. Philos. Trans. R. Soc. B. 2005; 360:1935–1943. - PMC - PubMed

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[1] Hawksworth D.L., Lücking R.. Fungal diversity revisited: 2.2 to 3.8 million species. Microbiol. Spec. 2017; 5:1–17. - PMC - PubMed

[2] Hawksworth D.L., Lücking R.. Fungal diversity revisited: 2.2 to 3.8 million species. Microbiol. Spec. 2017; 5:1–17. - PMC - PubMed

[3] Schoch C.L., Seifert K.A., Huhndorf S., Robert V., Spouge J.L., Levesque C.A., Chen W.. Nuclear ribosomal internal transcribed spacer (ITS) region as a universal DNA barcode marker for Fungi. Proc. Natl. Acad. Sci. Biol. 2012; 109:6241–6246. - PMC - PubMed

[4] Schoch C.L., Seifert K.A., Huhndorf S., Robert V., Spouge J.L., Levesque C.A., Chen W.. Nuclear ribosomal internal transcribed spacer (ITS) region as a universal DNA barcode marker for Fungi. Proc. Natl. Acad. Sci. Biol. 2012; 109:6241–6246. - PMC - PubMed

[5] Karsch-Mizrachi I., Takagi T., Cochrane G.. The international nucleotide sequence database collaboration. Nucleic Acids Res. 2017; 46:D48–D51. - PMC - PubMed

[6] Karsch-Mizrachi I., Takagi T., Cochrane G.. The international nucleotide sequence database collaboration. Nucleic Acids Res. 2017; 46:D48–D51. - PMC - PubMed

[7] Kõljalg U., Nilsson R.H., Abarenkov K., Tedersoo L., Taylor A.F., Bahram M., Bates S.T., Bruns T.D., Bengtsson-Palme J., Callaghan T.M. et al. Towards a unified paradigm for sequence-based identification of fungi. Mol. Ecol. 2013; 22:5271–5277. - PubMed

[8] Kõljalg U., Nilsson R.H., Abarenkov K., Tedersoo L., Taylor A.F., Bahram M., Bates S.T., Bruns T.D., Bengtsson-Palme J., Callaghan T.M. et al. Towards a unified paradigm for sequence-based identification of fungi. Mol. Ecol. 2013; 22:5271–5277. - PubMed

[9] Blaxter M., Mann J., Chapman T., Whitton T.F., Floyd R., Abebe E.. Defining operational taxonomic units using DNA barcode data. Philos. Trans. R. Soc. B. 2005; 360:1935–1943. - PMC - PubMed

[10] Blaxter M., Mann J., Chapman T., Whitton T.F., Floyd R., Abebe E.. Defining operational taxonomic units using DNA barcode data. Philos. Trans. R. Soc. B. 2005; 360:1935–1943. - PMC - PubMed

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

Affiliations

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

Authors

Affiliations

Abstract

Figures

References

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LinkOut - more resources

Full Text Sources

Other Literature Sources

Medical

Miscellaneous