The UNITE database for molecular identification and taxonomic communication of fungi and other eukaryotes: sequences, taxa and classifications reconsidered

Kessy Abarenkov; R Henrik Nilsson; Karl-Henrik Larsson; Andy F S Taylor; Tom W May; Tobias Guldberg Frøslev; Julia Pawlowska; Björn Lindahl; Kadri Põldmaa; Camille Truong; Duong Vu; Tsuyoshi Hosoya; Tuula Niskanen; Timo Piirmann; Filipp Ivanov; Allan Zirk; Marko Peterson; Tanya E Cheeke; Yui Ishigami; Arnold Tobias Jansson; Thomas Stjernegaard Jeppesen; Erik Kristiansson; Vladimir Mikryukov; Joseph T Miller; Ryoko Oono; Francisco J Ossandon; Joana Paupério; Irja Saar; Dmitry Schigel; Ave Suija; Leho Tedersoo; Urmas Kõljalg

doi:10.1093/nar/gkad1039

The UNITE database for molecular identification and taxonomic communication of fungi and other eukaryotes: sequences, taxa and classifications reconsidered

Kessy Abarenkov, R Henrik Nilsson, Karl-Henrik Larsson, Andy F S Taylor, Tom W May, Tobias Guldberg Frøslev, Julia Pawlowska, Björn Lindahl, Kadri Põldmaa, Camille Truong, Duong Vu, Tsuyoshi Hosoya, Tuula Niskanen, Timo Piirmann, Filipp Ivanov, Allan Zirk, Marko Peterson, Tanya E Cheeke, Yui Ishigami, Arnold Tobias JanssonThomas Stjernegaard Jeppesen, Erik Kristiansson, Vladimir Mikryukov, Joseph T Miller, Ryoko Oono, Francisco J Ossandon, Joana Paupério, Irja Saar, Dmitry Schigel, Ave Suija, Leho Tedersoo, Urmas Kõljalg

Aberdeen Centre For Environmental Sustainability

Research output: Contribution to journal › Article › peer-review

Abstract

UNITE (https://unite.ut.ee) is a web-based database and sequence management environment for molecular identification of eukaryotes. It targets the nuclear ribosomal internal transcribed spacer (ITS) region and offers nearly 10 million such sequences for reference. These are clustered into ∼2.4M species hypotheses (SHs), each assigned a unique digital object identifier (DOI) to promote unambiguous referencing across studies. UNITE users have contributed over 600 000 third-party sequence annotations, which are shared with a range of databases and other community resources. Recent improvements facilitate the detection of cross-kingdom biological associations and the integration of undescribed groups of organisms into everyday biological pursuits. Serving as a digital twin for eukaryotic biodiversity and communities worldwide, the latest release of UNITE offers improved avenues for biodiversity discovery, precise taxonomic communication and integration of biological knowledge across platforms.

Original language	English
Article number	gkad1039
Pages (from-to)	1-7
Number of pages	7
Journal	Nucleic Acids Research
Early online date	11 Nov 2023
DOIs	https://doi.org/10.1093/nar/gkad1039
Publication status	E-pub ahead of print - 11 Nov 2023

Bibliographical note

Acknowledgements
We acknowledge Marie Zirk for her work in designing the UNITE logotype and creating the visual abstract for this article.

Funding
UNITE database development is financed by the Estonian Research Council [PRG1170]; European Union's Horizon 2020 project BGE [101059492]. The PlutoF digital infrastructure is supported by the European Union's Horizon 2020 project BiCIKL [101007492]; Estonian Research Infrastructure roadmap project DiSSCo Estonia. Funding for open access charge: UNITE Community.

Conflict of interest statement. None declared.

Data Availability Statement

All sequences covered in this article are deposited in public sequence databases, INSDC and UNITE. Custom reference sequence datasets for a range of metabarcoding software pipelines are available for download on UNITE Resources page (https://unite.ut.ee/repository.php). UNITE SH datasets are published with DataCite DOIs and are accessible through UNITE (https://unite.ut.ee) and PlutoF (https://plutof.ut.ee) public homepages.

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10.1093/nar/gkad1039

Abarenkov_Etal_NAR_The_UNITE_Database_VOR
This is an Open Access article distributed under the terms of the Creative Commons Attribution License (https://creativecommons.org/licenses/by/4.0/), which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited.
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Data From: The UNITE database for molecular identification and taxonomic communication of fungi and other eukaryotes: sequences, taxa and classifications reconsidered
Abarenkov, K. (Creator), Nilsson, R. H. (Creator), Nilsson, R. H. (Creator), Way, T. (Creator), Frøslev, T. G. (Creator), Pawlowska, J. (Creator), Lindahl, B. D. (Creator), Põldmaa, K. (Creator), Truong, C. (Creator), Oono, R. (Creator), Ossandon, F. J. (Creator), Paupério, J. (Creator), Paupério, J. (Creator), Saar, I. (Creator), Schigel, D. (Creator), Suija, A. (Creator), Tedersoo, L. (Creator), Kõljalg, U. (Creator) & Taylor, A. F. S. (Creator), University of Aberdeen, Nov 2023
DOI: 10.1093/nar/gkad1039, https://oup.silverchair-cdn.com/oup/backfile/Content_public/Journal/nar/52/D1/10.1093_nar_gkad1039/1/gkad1039_supplemental_file.pdf?Expires=1715246975&Signature=3v66HmNbtImj40H~xl5eR~L5LFkt5rcBfjOHNOXuoM2m8enIlpPmHIkWA3GN~CFxt7z6Ey9VFcaAJalKXsd5iVdD6haVsLAt3WvqptitHtdfXHW3wgJjehYqKE0H9EAWmCPfbDdqS1Jn~91kW4yMWI8fHuIB6843U0tYq5stHVEZfhWNn~3mu-EylEpBi-oJMlXYxMiCLF4RgXZoFM9Rut5begbHacONvNPgb-qeJmG2T~CwNNgJ3UOaCwKbuZAuro65Acuv-8aj8i0VbLpDihF7NyqsZf9iHg9Y-r4vQp2eo3zqar25O~e92Ph4Vhd3tlyLHqRQNQAi7z1tS9K55w__&Key-Pair-Id=APKAIE5G5CRDK6RD3PGA
Dataset

Cite this

Abarenkov, K., Nilsson, R. H., Larsson, K.-H., Taylor, A. F. S., May, T. W., Frøslev, T. G., Pawlowska, J., Lindahl, B., Põldmaa, K., Truong, C., Vu, D., Hosoya, T., Niskanen, T., Piirmann, T., Ivanov, F., Zirk, A., Peterson, M., Cheeke, T. E., Ishigami, Y., ... Kõljalg, U. (2023). The UNITE database for molecular identification and taxonomic communication of fungi and other eukaryotes: sequences, taxa and classifications reconsidered. Nucleic Acids Research, 1-7. Article gkad1039. Advance online publication. https://doi.org/10.1093/nar/gkad1039

Abarenkov, K, Nilsson, RH, Larsson, K-H, Taylor, AFS, May, TW, Frøslev, TG, Pawlowska, J, Lindahl, B, Põldmaa, K, Truong, C, Vu, D, Hosoya, T, Niskanen, T, Piirmann, T, Ivanov, F, Zirk, A, Peterson, M, Cheeke, TE, Ishigami, Y, Jansson, AT, Jeppesen, TS, Kristiansson, E, Mikryukov, V, Miller, JT, Oono, R, Ossandon, FJ, Paupério, J, Saar, I, Schigel, D, Suija, A, Tedersoo, L & Kõljalg, U 2023, 'The UNITE database for molecular identification and taxonomic communication of fungi and other eukaryotes: sequences, taxa and classifications reconsidered', Nucleic Acids Research, pp. 1-7. https://doi.org/10.1093/nar/gkad1039

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abstract = "UNITE (https://unite.ut.ee) is a web-based database and sequence management environment for molecular identification of eukaryotes. It targets the nuclear ribosomal internal transcribed spacer (ITS) region and offers nearly 10 million such sequences for reference. These are clustered into ∼2.4M species hypotheses (SHs), each assigned a unique digital object identifier (DOI) to promote unambiguous referencing across studies. UNITE users have contributed over 600 000 third-party sequence annotations, which are shared with a range of databases and other community resources. Recent improvements facilitate the detection of cross-kingdom biological associations and the integration of undescribed groups of organisms into everyday biological pursuits. Serving as a digital twin for eukaryotic biodiversity and communities worldwide, the latest release of UNITE offers improved avenues for biodiversity discovery, precise taxonomic communication and integration of biological knowledge across platforms.",

author = "Kessy Abarenkov and Nilsson, {R Henrik} and Karl-Henrik Larsson and Taylor, {Andy F S} and May, {Tom W} and Fr{\o}slev, {Tobias Guldberg} and Julia Pawlowska and Bj{\"o}rn Lindahl and Kadri P{\~o}ldmaa and Camille Truong and Duong Vu and Tsuyoshi Hosoya and Tuula Niskanen and Timo Piirmann and Filipp Ivanov and Allan Zirk and Marko Peterson and Cheeke, {Tanya E} and Yui Ishigami and Jansson, {Arnold Tobias} and Jeppesen, {Thomas Stjernegaard} and Erik Kristiansson and Vladimir Mikryukov and Miller, {Joseph T} and Ryoko Oono and Ossandon, {Francisco J} and Joana Paup{\'e}rio and Irja Saar and Dmitry Schigel and Ave Suija and Leho Tedersoo and Urmas K{\~o}ljalg",

note = "Acknowledgements We acknowledge Marie Zirk for her work in designing the UNITE logotype and creating the visual abstract for this article. Funding UNITE database development is financed by the Estonian Research Council [PRG1170]; European Union's Horizon 2020 project BGE [101059492]. The PlutoF digital infrastructure is supported by the European Union's Horizon 2020 project BiCIKL [101007492]; Estonian Research Infrastructure roadmap project DiSSCo Estonia. Funding for open access charge: UNITE Community. Conflict of interest statement. None declared.",

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AU - Nilsson, R Henrik

AU - Larsson, Karl-Henrik

AU - Taylor, Andy F S

AU - May, Tom W

AU - Frøslev, Tobias Guldberg

AU - Pawlowska, Julia

AU - Lindahl, Björn

AU - Põldmaa, Kadri

AU - Truong, Camille

AU - Vu, Duong

AU - Hosoya, Tsuyoshi

AU - Niskanen, Tuula

AU - Piirmann, Timo

AU - Ivanov, Filipp

AU - Zirk, Allan

AU - Peterson, Marko

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AU - Ishigami, Yui

AU - Jansson, Arnold Tobias

AU - Jeppesen, Thomas Stjernegaard

AU - Kristiansson, Erik

AU - Mikryukov, Vladimir

AU - Miller, Joseph T

AU - Oono, Ryoko

AU - Ossandon, Francisco J

AU - Paupério, Joana

AU - Saar, Irja

AU - Schigel, Dmitry

AU - Suija, Ave

AU - Tedersoo, Leho

AU - Kõljalg, Urmas

N1 - Acknowledgements We acknowledge Marie Zirk for her work in designing the UNITE logotype and creating the visual abstract for this article. Funding UNITE database development is financed by the Estonian Research Council [PRG1170]; European Union's Horizon 2020 project BGE [101059492]. The PlutoF digital infrastructure is supported by the European Union's Horizon 2020 project BiCIKL [101007492]; Estonian Research Infrastructure roadmap project DiSSCo Estonia. Funding for open access charge: UNITE Community. Conflict of interest statement. None declared.

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The UNITE database for molecular identification and taxonomic communication of fungi and other eukaryotes: sequences, taxa and classifications reconsidered

Abstract

Bibliographical note

Data Availability Statement

Access to Document

Fingerprint

Datasets

Data From: The UNITE database for molecular identification and taxonomic communication of fungi and other eukaryotes: sequences, taxa and classifications reconsidered

Cite this