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

被引：229

作者：

Abarenkov, Kessy ^{[1
]}

Nilsson, R. Henrik ^{[2
,3
]}

Larsson, Karl-Henrik ^{[3
,4
]}

Taylor, Andy F. S. ^{[5
,6
]}

May, Tom W. ^{[7
]}

Froslev, Tobias Guldberg ^{[8
]}

Pawlowska, Julia ^{[9
]}

Lindahl, Bjorn ^{[10
]}

Poldmaa, Kadri ^{[1
,11
]}

Truong, Camille ^{[7
]}

Duong Vu ^{[12
]}

Hosoya, Tsuyoshi ^{[13
]}

Niskanen, Tuula ^{[14
]}

Piirmann, Timo ^{[1
]}

Ivanov, Filipp ^{[1
]}

Zirk, Allan ^{[1
]}

Peterson, Marko ^{[11
]}

Cheeke, Tanya E. ^{[15
]}

Ishigami, Yui ^{[11
]}

Jansson, Arnold Tobias ^{[2
]}

Jeppesen, Thomas Stjernegaard ^{[8
]}

Kristiansson, Erik ^{[16
]}

Mikryukov, Vladimir ^{[11
]}

Miller, Joseph T. ^{[8
]}

Oono, Ryoko ^{[17
]}

Ossandon, Francisco J. ^{[18
]}

Pauperio, Joana ^{[19
]}

Saar, Irja ^{[1
,11
]}

Schigel, Dmitry ^{[8
]}

Suija, Ave ^{[1
]}

Tedersoo, Leho ^{[11
]}

Koljalg, Urmas ^{[11
]}

机构：

[1] Univ Tartu, Nat Hist Museum, Vanemuise 46, EE-51003 Tartu, Estonia

[2] Univ Gothenburg, Dept Biol & Environm Sci, Box 453, S-40530 Gothenburg, Sweden

[3] Univ Gothenburg, Gothenburg Global Biodivers Ctr, Box 453, S-40530 Gothenburg, Sweden

[4] Univ Oslo, Nat Hist Museum, Box 1172 Blindern, N-0318 Oslo, Norway

[5] James Hutton Inst, Aberdeen AB15 8QH, Scotland

[6] Univ Aberdeen, Inst Biol & Environm Sci, Cruickshank Bldg,St Machar Dr, Aberdeen AB24 3UU, Scotland

[7] Royal Bot Gardens Victoria, Birdwood Ave, Melbourne, Vic 3004, Australia

[8] Global Biodivers Informat Facil GBIF, Univ 15, DK-2100 Copenhagen O, Denmark

[9] Univ Warsaw, Inst Evolutionary Biol, Fac Biol, Ul Zwirki & Wigury 101, PL-02089 Warsaw, Poland

[10] Swedish Univ Agr Sci, Dept Soil & Environm, Box 7014, SE-75007 Uppsala, Sweden

[11] Univ Tartu, Inst Ecol & Earth Sci, J Liivi 2, EE-50409 Tartu, Estonia

[12] Westerdijk Fungal Biodivers Inst, Utrecht, Netherlands

[13] Natl Museum Nat & Sci, Tokyo, Japan

[14] Univ Helsinki, Finnish Museum Nat Hist, Bot Unit, POB 7, Helsinki 00014, Finland

[15] Washington State Univ, Sch Biol Sci, 2710 Crimson Way, Richland, WA USA

[16] Chalmers Univ Technol, Dept Math Sci, Gothenburg, Sweden

[17] Univ Calif Santa Barbara, Dept Ecol Evolut & Marine Biol, Santa Barbara, CA USA

[18] Biome Makers Inc, Davis, CA USA

[19] European Bioinformat Inst, European Mol Biol Lab, Cambridge, England

来源：

NUCLEIC ACIDS RESEARCH | 2023年 / 52卷 / D1期

关键词：

DNA; GENERATION; SEARCH;

D O I：

10.1093/nar/gkad1039

中图分类号：

Q5 [生物化学]; Q7 [分子生物学];

学科分类号：

071010 ; 081704 ;

摘要：

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 similar to 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. [GRAPHICS] .

引用

页码：D791 / D797

页数：7

共 36 条

[1]

Abarenkov K., 2023, UNITE - Unified system for the DNA based fungal species linked to the classification, DOI [10.15468/mkpcy3, DOI 10.15468/MKPCY3]

[2]

Abarenkov K., 2022, Biodivers. Inf. Sci. Stand, V6, pe93856

[3]

Abarenkov K., 2021, Biodivers. Inf. Sci. Stand, V5, DOI [DOI 10.3897/BISS.5.74249, 10.3897/biss.5.74249]

[4] PlutoF-a Web Based Workbench for Ecological and Taxonomic Research, with an Online Implementation for Fungal ITS Sequences [J].

Abarenkov, Kessy ;

Tedersoo, Leho ;

Nilsson, R. Henrik ;

Vellak, Kai ;

Saar, Irja ;

Veldre, Vilmar ;

Parmasto, Erast ;

Prous, Marko ;

Aan, Anne ;

Ots, Margus ;

Kurina, Olavi ;

Ostonen, Ivika ;

Jogeva, Janno ;

Halapuu, Siim ;

Poldmaa, Kadri ;

Toots, Maert ;

Truu, Jaak ;

Larsson, Karl-Henrik ;

Koljalg, Urmas .

EVOLUTIONARY BIOINFORMATICS, 2010, 6 :189-196

[5] Gapped BLAST and PSI-BLAST: a new generation of protein database search programs [J].

Altschul, SF ;

Madden, TL ;

Schaffer, AA ;

Zhang, JH ;

Zhang, Z ;

Miller, W ;

Lipman, DJ .

NUCLEIC ACIDS RESEARCH, 1997, 25 (17) :3389-3402

[6] The international nucleotide sequence database collaboration [J].

Arita, Masanori ;

Karsch-Mizrachi, Ilene ;

Cochrane, Guy .

NUCLEIC ACIDS RESEARCH, 2021, 49 (D1) :D121-D124

[7] Improved software detection and extraction of ITS1 and ITS2 from ribosomal ITS sequences of fungi and other eukaryotes for analysis of environmental sequencing data [J].

Bengtsson-Palme, Johan ;

Ryberg, Martin ;

Hartmann, Martin ;

Branco, Sara ;

Wang, Zheng ;

Godhe, Anna ;

De Wit, Pierre ;

Sanchez-Garcia, Marisol ;

Ebersberger, Ingo ;

de Sousa, Filipe ;

Amend, Anthony S. ;

Jumpponen, Ari ;

Unterseher, Martin ;

Kristiansson, Erik ;

Abarenkov, Kessy ;

Bertrand, Yann J. K. ;

Sanli, Kemal ;

Eriksson, K. Martin ;

Vik, Unni ;

Veldre, Vilmar ;

Nilsson, R. Henrik .

METHODS IN ECOLOGY AND EVOLUTION, 2013, 4 (10) :914-919

[8] Defining operational taxonomic units using DNA barcode data [J].

Blaxter, M ;

Mann, J ;

Chapman, T ;

Thomas, F ;

Whitton, C ;

Floyd, R ;

Abebe, E .

PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES, 2005, 360 (1462) :1935-1943

[9]

Bnki O., 2023, Catalogue Life, DOI [10.48580/dfqz, DOI 10.48580/DFQZ]

[10] Reproducible, interactive, scalable and extensible microbiome data science using QIIME 2 [J].

Bolyen, Evan ;

Rideout, Jai Ram ;

Dillon, Matthew R. ;

Bokulich, NicholasA. ;

Abnet, Christian C. ;

Al-Ghalith, Gabriel A. ;

Alexander, Harriet ;

Alm, Eric J. ;

Arumugam, Manimozhiyan ;

Asnicar, Francesco ;

Bai, Yang ;

Bisanz, Jordan E. ;

Bittinger, Kyle ;

Brejnrod, Asker ;

Brislawn, Colin J. ;

Brown, C. Titus ;

Callahan, Benjamin J. ;

Caraballo-Rodriguez, Andres Mauricio ;

Chase, John ;

Cope, Emily K. ;

Da Silva, Ricardo ;

Diener, Christian ;

Dorrestein, Pieter C. ;

Douglas, Gavin M. ;

Durall, Daniel M. ;

Duvallet, Claire ;

Edwardson, Christian F. ;

Ernst, Madeleine ;

Estaki, Mehrbod ;

Fouquier, Jennifer ;

Gauglitz, Julia M. ;

Gibbons, Sean M. ;

Gibson, Deanna L. ;

Gonzalez, Antonio ;

Gorlick, Kestrel ;

Guo, Jiarong ;

Hillmann, Benjamin ;

Holmes, Susan ;

Holste, Hannes ;

Huttenhower, Curtis ;

Huttley, Gavin A. ;

Janssen, Stefan ;

Jarmusch, Alan K. ;

Jiang, Lingjing ;

Kaehler, Benjamin D. ;

Bin Kang, Kyo ;

Keefe, Christopher R. ;

Keim, Paul ;

Kelley, Scott T. ;

Knights, Dan .

NATURE BIOTECHNOLOGY, 2019, 37 (08) :852-857

← 1 2 3 4 →