The UNITE database for molecular identification and taxonomic communication of fungi and other eukaryotes: sequences, taxa and classifications reconsidered
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 ∼...
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| Veröffentlicht in: | Nucleic acids research 2024, Vol.52 (D1), p.D791-D797 |
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| creator | Abarenkov, Kessy Nilsson, R Henrik Larsson, Karl-Henrik Taylor, Andy F S May, Tom W Frøslev, Tobias Guldberg Pawlowska, Julia Lindahl, Björn Põldmaa, Kadri Truong, Camille Vu, Duong Hosoya, Tsuyoshi Niskanen, Tuula Piirmann, Timo Ivanov, Filipp Zirk, Allan Peterson, Marko Cheeke, Tanya E Ishigami, Yui Jansson, Arnold Tobias Jeppesen, Thomas Stjernegaard Kristiansson, Erik Mikryukov, Vladimir Miller, Joseph T Oono, Ryoko Ossandon, Francisco J Paupério, Joana Saar, Irja Schigel, Dmitry Suija, Ave Tedersoo, Leho Kõljalg, Urmas |
| description | 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.
Graphical Abstract
Graphical Abstract |
| doi_str_mv | 10.1093/nar/gkad1039 |
| format | Article |
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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.
Graphical Abstract
Graphical Abstract</description><identifier>ISSN: 0305-1048</identifier><identifier>ISSN: 1362-4962</identifier><identifier>EISSN: 1362-4962</identifier><identifier>DOI: 10.1093/nar/gkad1039</identifier><identifier>PMID: 37953409</identifier><language>eng</language><publisher>England: Oxford University Press</publisher><subject>Biodiversity ; Bioinformatics and Systems Biology ; Bioinformatik och systembiologi ; Biological Systematics ; Biologisk systematik ; Cell and Molecular Biology ; Cell- och molekylärbiologi ; Databases, Nucleic Acid ; DNA, Fungal ; DNA, Ribosomal Spacer ; Fungi - genetics ; Microbiology ; Mikrobiologi ; Phylogeny</subject><ispartof>Nucleic acids research, 2024, Vol.52 (D1), p.D791-D797</ispartof><rights>The Author(s) 2023. Published by Oxford University Press on behalf of Nucleic Acids Research. 2024</rights><rights>The Author(s) 2023. Published by Oxford University Press on behalf of Nucleic Acids Research.</rights><rights>info:eu-repo/semantics/openAccess</rights><lds50>peer_reviewed</lds50><oa>free_for_read</oa><woscitedreferencessubscribed>false</woscitedreferencessubscribed><citedby>FETCH-LOGICAL-c469t-f1ef4f35e3b0304679c0dd1361d189a55ab25ef01f551860de48ae620f25215a3</citedby><cites>FETCH-LOGICAL-c469t-f1ef4f35e3b0304679c0dd1361d189a55ab25ef01f551860de48ae620f25215a3</cites><orcidid>0000-0003-2569-0768 ; 0000-0002-3384-4547 ; 0000-0001-5526-4845 ; 0000-0002-1635-1249</orcidid></display><links><openurl>$$Topenurl_article</openurl><openurlfulltext>$$Topenurlfull_article</openurlfulltext><thumbnail>$$Tsyndetics_thumb_exl</thumbnail><link.rule.ids>230,314,550,776,780,860,881,1598,4010,26544,27900,27901,27902</link.rule.ids><backlink>$$Uhttps://www.ncbi.nlm.nih.gov/pubmed/37953409$$D View this record in MEDLINE/PubMed$$Hfree_for_read</backlink><backlink>$$Uhttps://gup.ub.gu.se/publication/332843$$DView record from Swedish Publication Index$$Hfree_for_read</backlink><backlink>$$Uhttps://research.chalmers.se/publication/538860$$DView record from Swedish Publication Index$$Hfree_for_read</backlink><backlink>$$Uhttps://res.slu.se/id/publ/127269$$DView record from Swedish Publication Index$$Hfree_for_read</backlink></links><search><creatorcontrib>Abarenkov, Kessy</creatorcontrib><creatorcontrib>Nilsson, R Henrik</creatorcontrib><creatorcontrib>Larsson, Karl-Henrik</creatorcontrib><creatorcontrib>Taylor, Andy F S</creatorcontrib><creatorcontrib>May, Tom W</creatorcontrib><creatorcontrib>Frøslev, Tobias Guldberg</creatorcontrib><creatorcontrib>Pawlowska, Julia</creatorcontrib><creatorcontrib>Lindahl, Björn</creatorcontrib><creatorcontrib>Põldmaa, Kadri</creatorcontrib><creatorcontrib>Truong, Camille</creatorcontrib><creatorcontrib>Vu, Duong</creatorcontrib><creatorcontrib>Hosoya, Tsuyoshi</creatorcontrib><creatorcontrib>Niskanen, Tuula</creatorcontrib><creatorcontrib>Piirmann, Timo</creatorcontrib><creatorcontrib>Ivanov, Filipp</creatorcontrib><creatorcontrib>Zirk, Allan</creatorcontrib><creatorcontrib>Peterson, Marko</creatorcontrib><creatorcontrib>Cheeke, Tanya E</creatorcontrib><creatorcontrib>Ishigami, Yui</creatorcontrib><creatorcontrib>Jansson, Arnold Tobias</creatorcontrib><creatorcontrib>Jeppesen, Thomas Stjernegaard</creatorcontrib><creatorcontrib>Kristiansson, Erik</creatorcontrib><creatorcontrib>Mikryukov, Vladimir</creatorcontrib><creatorcontrib>Miller, Joseph T</creatorcontrib><creatorcontrib>Oono, Ryoko</creatorcontrib><creatorcontrib>Ossandon, Francisco J</creatorcontrib><creatorcontrib>Paupério, Joana</creatorcontrib><creatorcontrib>Saar, Irja</creatorcontrib><creatorcontrib>Schigel, Dmitry</creatorcontrib><creatorcontrib>Suija, Ave</creatorcontrib><creatorcontrib>Tedersoo, Leho</creatorcontrib><creatorcontrib>Kõljalg, Urmas</creatorcontrib><creatorcontrib>Sveriges lantbruksuniversitet</creatorcontrib><title>The UNITE database for molecular identification and taxonomic communication of fungi and other eukaryotes: sequences, taxa and classifications reconsidered</title><title>Nucleic acids research</title><addtitle>Nucleic Acids Res</addtitle><description>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.
Graphical Abstract
Graphical Abstract</description><subject>Biodiversity</subject><subject>Bioinformatics and Systems Biology</subject><subject>Bioinformatik och systembiologi</subject><subject>Biological Systematics</subject><subject>Biologisk systematik</subject><subject>Cell and Molecular Biology</subject><subject>Cell- och molekylärbiologi</subject><subject>Databases, Nucleic Acid</subject><subject>DNA, Fungal</subject><subject>DNA, Ribosomal Spacer</subject><subject>Fungi - genetics</subject><subject>Microbiology</subject><subject>Mikrobiologi</subject><subject>Phylogeny</subject><issn>0305-1048</issn><issn>1362-4962</issn><issn>1362-4962</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>2024</creationdate><recordtype>article</recordtype><sourceid>TOX</sourceid><sourceid>EIF</sourceid><sourceid>3HK</sourceid><sourceid>D8T</sourceid><recordid>eNp9ks9u1DAQhyMEokvhxhn5Boem9d-sza2qClSq4MD2bE2c8W5oEi92IuBdOPAsPBnObndv5eKR7G8-_2xNUbxm9JxRIy4GiBfre2gYFeZJsWCi4qU0FX9aLKigqmRU6pPiRUrfKGWSKfm8OBFLo4SkZlH8Xm2Q3H2-WV2TBkaoISHxIZI-dOimDiJpGxzG1rcOxjYMBIaGjPAzDKFvHXGh76fhcBY88dOwbndQGDcYCU73EH-FEdN7kvD7hIPDdDYb4O-fGXMdpHTUJxLR5ZIvjdi8LJ556BK-eqinxd2H69XVp_L2y8ebq8vb0snKjKVn6KUXCkWdXyyrpXG0afJHsIZpA0pBzRV6yrxSTFe0QakBK049V5wpEKfF-d6bfuB2qu02tn1ObQO0NnVTDXEuNqFlfMkrkxu-PtoQMSFEt7FuA12PMc19bk4qdWUFLLmVXGmrpWcWlNScNgb1UmVr-ah1PW1t3lrvUgjBtRSZJ3vexTaN7WCHEMEyqhXPqzG7oO_2yDaG_PlptH2bHHYdDBimZLnWRulKM57Rs4MtpBTRH-9ndNYJmyfNHiYt428ezFPdY3OED6OVgbd7IOTo_1X9A9en4Eo</recordid><startdate>2024</startdate><enddate>2024</enddate><creator>Abarenkov, Kessy</creator><creator>Nilsson, R Henrik</creator><creator>Larsson, Karl-Henrik</creator><creator>Taylor, Andy F S</creator><creator>May, Tom W</creator><creator>Frøslev, Tobias Guldberg</creator><creator>Pawlowska, Julia</creator><creator>Lindahl, Björn</creator><creator>Põldmaa, Kadri</creator><creator>Truong, Camille</creator><creator>Vu, Duong</creator><creator>Hosoya, Tsuyoshi</creator><creator>Niskanen, Tuula</creator><creator>Piirmann, Timo</creator><creator>Ivanov, Filipp</creator><creator>Zirk, Allan</creator><creator>Peterson, Marko</creator><creator>Cheeke, Tanya E</creator><creator>Ishigami, Yui</creator><creator>Jansson, Arnold Tobias</creator><creator>Jeppesen, Thomas Stjernegaard</creator><creator>Kristiansson, Erik</creator><creator>Mikryukov, Vladimir</creator><creator>Miller, Joseph T</creator><creator>Oono, Ryoko</creator><creator>Ossandon, Francisco J</creator><creator>Paupério, Joana</creator><creator>Saar, Irja</creator><creator>Schigel, Dmitry</creator><creator>Suija, Ave</creator><creator>Tedersoo, Leho</creator><creator>Kõljalg, Urmas</creator><general>Oxford University Press</general><scope>TOX</scope><scope>CGR</scope><scope>CUY</scope><scope>CVF</scope><scope>ECM</scope><scope>EIF</scope><scope>NPM</scope><scope>AAYXX</scope><scope>CITATION</scope><scope>7X8</scope><scope>3HK</scope><scope>ADTPV</scope><scope>AOWAS</scope><scope>F1U</scope><scope>ABBSD</scope><scope>D8T</scope><scope>F1S</scope><scope>ZZAVC</scope><orcidid>https://orcid.org/0000-0003-2569-0768</orcidid><orcidid>https://orcid.org/0000-0002-3384-4547</orcidid><orcidid>https://orcid.org/0000-0001-5526-4845</orcidid><orcidid>https://orcid.org/0000-0002-1635-1249</orcidid></search><sort><creationdate>2024</creationdate><title>The UNITE database for molecular identification and taxonomic communication of fungi and other eukaryotes: sequences, taxa and classifications reconsidered</title><author>Abarenkov, Kessy ; Nilsson, R Henrik ; Larsson, Karl-Henrik ; Taylor, Andy F S ; May, Tom W ; Frøslev, Tobias Guldberg ; Pawlowska, Julia ; Lindahl, Björn ; Põldmaa, Kadri ; Truong, Camille ; Vu, Duong ; Hosoya, Tsuyoshi ; Niskanen, Tuula ; Piirmann, Timo ; Ivanov, Filipp ; Zirk, Allan ; Peterson, Marko ; Cheeke, Tanya E ; Ishigami, Yui ; Jansson, Arnold Tobias ; Jeppesen, Thomas Stjernegaard ; Kristiansson, Erik ; Mikryukov, Vladimir ; Miller, Joseph T ; Oono, Ryoko ; Ossandon, Francisco J ; Paupério, Joana ; Saar, Irja ; Schigel, Dmitry ; Suija, Ave ; Tedersoo, Leho ; Kõljalg, Urmas</author></sort><facets><frbrtype>5</frbrtype><frbrgroupid>cdi_FETCH-LOGICAL-c469t-f1ef4f35e3b0304679c0dd1361d189a55ab25ef01f551860de48ae620f25215a3</frbrgroupid><rsrctype>articles</rsrctype><prefilter>articles</prefilter><language>eng</language><creationdate>2024</creationdate><topic>Biodiversity</topic><topic>Bioinformatics and Systems Biology</topic><topic>Bioinformatik och systembiologi</topic><topic>Biological Systematics</topic><topic>Biologisk systematik</topic><topic>Cell and Molecular Biology</topic><topic>Cell- och molekylärbiologi</topic><topic>Databases, Nucleic Acid</topic><topic>DNA, Fungal</topic><topic>DNA, Ribosomal Spacer</topic><topic>Fungi - 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Academic</collection><collection>NORA - Norwegian Open Research Archives</collection><collection>SwePub</collection><collection>SwePub Articles</collection><collection>SWEPUB Göteborgs universitet</collection><collection>SWEPUB Chalmers tekniska högskola full text</collection><collection>SWEPUB Freely available online</collection><collection>SWEPUB Chalmers tekniska högskola</collection><collection>SwePub Articles full text</collection><jtitle>Nucleic acids research</jtitle></facets><delivery><delcategory>Remote Search Resource</delcategory><fulltext>fulltext</fulltext></delivery><addata><au>Abarenkov, Kessy</au><au>Nilsson, R Henrik</au><au>Larsson, Karl-Henrik</au><au>Taylor, Andy F S</au><au>May, Tom W</au><au>Frøslev, Tobias Guldberg</au><au>Pawlowska, Julia</au><au>Lindahl, Björn</au><au>Põldmaa, Kadri</au><au>Truong, Camille</au><au>Vu, Duong</au><au>Hosoya, Tsuyoshi</au><au>Niskanen, Tuula</au><au>Piirmann, Timo</au><au>Ivanov, Filipp</au><au>Zirk, Allan</au><au>Peterson, Marko</au><au>Cheeke, Tanya E</au><au>Ishigami, Yui</au><au>Jansson, Arnold Tobias</au><au>Jeppesen, Thomas Stjernegaard</au><au>Kristiansson, Erik</au><au>Mikryukov, Vladimir</au><au>Miller, Joseph T</au><au>Oono, Ryoko</au><au>Ossandon, Francisco J</au><au>Paupério, Joana</au><au>Saar, Irja</au><au>Schigel, Dmitry</au><au>Suija, Ave</au><au>Tedersoo, Leho</au><au>Kõljalg, Urmas</au><aucorp>Sveriges lantbruksuniversitet</aucorp><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>The UNITE database for molecular identification and taxonomic communication of fungi and other eukaryotes: sequences, taxa and classifications reconsidered</atitle><jtitle>Nucleic acids research</jtitle><addtitle>Nucleic Acids Res</addtitle><date>2024</date><risdate>2024</risdate><volume>52</volume><issue>D1</issue><spage>D791</spage><epage>D797</epage><pages>D791-D797</pages><issn>0305-1048</issn><issn>1362-4962</issn><eissn>1362-4962</eissn><abstract>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.
Graphical Abstract
Graphical Abstract</abstract><cop>England</cop><pub>Oxford University Press</pub><pmid>37953409</pmid><doi>10.1093/nar/gkad1039</doi><orcidid>https://orcid.org/0000-0003-2569-0768</orcidid><orcidid>https://orcid.org/0000-0002-3384-4547</orcidid><orcidid>https://orcid.org/0000-0001-5526-4845</orcidid><orcidid>https://orcid.org/0000-0002-1635-1249</orcidid><oa>free_for_read</oa></addata></record> |
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| identifier | ISSN: 0305-1048 |
| ispartof | Nucleic acids research, 2024, Vol.52 (D1), p.D791-D797 |
| issn | 0305-1048 1362-4962 1362-4962 |
| language | eng |
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| source | Oxford Journals Open Access Collection; MEDLINE; NORA - Norwegian Open Research Archives; DOAJ Directory of Open Access Journals; PubMed Central; SWEPUB Freely available online; Free Full-Text Journals in Chemistry |
| subjects | Biodiversity Bioinformatics and Systems Biology Bioinformatik och systembiologi Biological Systematics Biologisk systematik Cell and Molecular Biology Cell- och molekylärbiologi Databases, Nucleic Acid DNA, Fungal DNA, Ribosomal Spacer Fungi - genetics Microbiology Mikrobiologi Phylogeny |
| title | The UNITE database for molecular identification and taxonomic communication of fungi and other eukaryotes: sequences, taxa and classifications reconsidered |
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