{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,4,29]],"date-time":"2026-04-29T23:32:03Z","timestamp":1777505523177,"version":"3.51.4"},"reference-count":41,"publisher":"Oxford University Press (OUP)","license":[{"start":{"date-parts":[[2024,6,12]],"date-time":"2024-06-12T00:00:00Z","timestamp":1718150400000},"content-version":"vor","delay-in-days":163,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100002383","name":"King Saud University","doi-asserted-by":"publisher","award":["Distinguished Scientist Fellowship Programme"],"award-info":[{"award-number":["Distinguished Scientist Fellowship Programme"]}],"id":[{"id":"10.13039\/501100002383","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100008530","name":"European Regional Development Fund","doi-asserted-by":"publisher","award":["MOBERC66 MOBTP198"],"award-info":[{"award-number":["MOBERC66 MOBTP198"]}],"id":[{"id":"10.13039\/501100008530","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100003072","name":"LOEWE Zentrum AdRIA","doi-asserted-by":"publisher","id":[{"id":"10.13039\/501100003072","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100002383","name":"King Saud University","doi-asserted-by":"publisher","award":["Distinguished Scientist Fellowship Programme"],"award-info":[{"award-number":["Distinguished Scientist Fellowship Programme"]}],"id":[{"id":"10.13039\/501100002383","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100008530","name":"European Regional Development Fund","doi-asserted-by":"publisher","award":["MOBERC66 MOBTP198"],"award-info":[{"award-number":["MOBERC66 MOBTP198"]}],"id":[{"id":"10.13039\/501100008530","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100003072","name":"LOEWE Zentrum AdRIA","doi-asserted-by":"publisher","id":[{"id":"10.13039\/501100003072","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2024,6,12]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Molecular identification of micro- and macroorganisms based on nuclear markers has revolutionized our understanding of their taxonomy, phylogeny and ecology. Today, research on the diversity of eukaryotes in global ecosystems heavily relies on nuclear ribosomal RNA (rRNA) markers. Here, we present the research community-curated reference database EUKARYOME for nuclear ribosomal 18S rRNA, internal transcribed spacer (ITS) and 28S rRNA markers for all eukaryotes, including metazoans (animals), protists, fungi and plants. It is particularly useful for the identification of arbuscular mycorrhizal fungi as it bridges the four commonly used molecular markers\u2014ITS1, ITS2, 18S V4\u2013V5 and 28S D1\u2013D2 subregions. The key benefits of this database over other annotated reference sequence databases are that it is not restricted to certain taxonomic groups and it includes all rRNA markers. EUKARYOME also offers a number of reference long-read sequences that are derived from (meta)genomic and (meta)barcoding\u2014a unique feature that can be used for taxonomic identification and chimera control of third-generation, long-read, high-throughput sequencing data. Taxonomic assignments of rRNA genes in the database are verified based on phylogenetic approaches. The reference datasets are available in multiple formats from the project homepage, http:\/\/www.eukaryome.org.<\/jats:p>","DOI":"10.1093\/database\/baae043","type":"journal-article","created":{"date-parts":[[2024,6,12]],"date-time":"2024-06-12T16:09:08Z","timestamp":1718208548000},"source":"Crossref","is-referenced-by-count":62,"title":["EUKARYOME: the rRNA gene reference database for identification of all eukaryotes"],"prefix":"10.1093","volume":"2024","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-1635-1249","authenticated-orcid":false,"given":"Leho","family":"Tedersoo","sequence":"first","affiliation":[{"name":"Mycology and Microbiology Center, University of Tartu , Liivi 2, Tartu 50400, Estonia"},{"name":"Institute of Ecology and Earth Sciences, University of Tartu , Liivi 2, Tartu 50400, Estonia"},{"name":"Department of Zoology, College of Science, King Saud University , PO Box 2455, Riyadh 11451, Saudi Arabia"}]},{"given":"Mahdieh S","family":"Hosseyni Moghaddam","sequence":"additional","affiliation":[{"name":"Institute of Ecology and Earth Sciences, University of Tartu , Liivi 2, Tartu 50400, Estonia"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-2786-2690","authenticated-orcid":false,"given":"Vladimir","family":"Mikryukov","sequence":"additional","affiliation":[{"name":"Mycology and Microbiology Center, University of Tartu , Liivi 2, Tartu 50400, Estonia"},{"name":"Institute of Ecology and Earth Sciences, University of Tartu , Liivi 2, Tartu 50400, Estonia"}]},{"given":"Ali","family":"Hakimzadeh","sequence":"additional","affiliation":[{"name":"Institute of Ecology and Earth Sciences, University of Tartu , Liivi 2, Tartu 50400, Estonia"}]},{"given":"Mohammad","family":"Bahram","sequence":"additional","affiliation":[{"name":"Institute of Ecology and Earth Sciences, University of Tartu , Liivi 2, Tartu 50400, Estonia"},{"name":"Department of Ecology, Swedish University of Agricultural Sciences , Ulls v\u00e4g 16, Uppsala 75651, Sweden"}]},{"given":"R Henrik","family":"Nilsson","sequence":"additional","affiliation":[{"name":"Department of Biological and Environmental Sciences, Gothenburg Global Biodiversity Centre, University of Gothenburg , Box 461, G\u00f6teborg 40530, Sweden"}]},{"given":"Iryna","family":"Yatsiuk","sequence":"additional","affiliation":[{"name":"Institute of Ecology and Earth Sciences, University of Tartu , Liivi 2, Tartu 50400, Estonia"}]},{"given":"Stefan","family":"Geisen","sequence":"additional","affiliation":[{"name":"Laboratory of Nematology, Wageningen University , Droevendaalsesteeg 1, Wageningen 6708PB, The Netherlands"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-7164-5365","authenticated-orcid":false,"given":"Arne","family":"Schwelm","sequence":"additional","affiliation":[{"name":"Laboratory of Nematology, Wageningen University , Droevendaalsesteeg 1, Wageningen 6708PB, The Netherlands"},{"name":"Department of Environment, Soils and Land-Use , Teagasc, Oak Park House, Wexford R93 XE12, Ireland"}]},{"given":"Kasia","family":"Piwosz","sequence":"additional","affiliation":[{"name":"National Marine Fisheries Research Institute , Ko\u0142\u0142\u0105taja 1, Gdynia 81332, Poland"}]},{"given":"Marko","family":"Prous","sequence":"additional","affiliation":[{"name":"Institute of Ecology and Earth Sciences, University of Tartu , Liivi 2, Tartu 50400, Estonia"},{"name":"Ecology and Genetics Research Unit, University of Oulu , Box 8000, Oulu 90014, Finland"}]},{"given":"Sirje","family":"Sildever","sequence":"additional","affiliation":[{"name":"Department of Marine Systems, Tallinn University of Technology , M\u00e4ealuse 14a, Tallinn 12618, Estonia"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-2156-4791","authenticated-orcid":false,"given":"Dominika","family":"Chmolowska","sequence":"additional","affiliation":[{"name":"Institute of Systematics and Evolution of Animals, Polish Academy of Sciences , S\u0142awkowska 17, Krak\u00f3w 31016, Poland"}]},{"given":"Sonja","family":"Rueckert","sequence":"additional","affiliation":[{"name":"Eukaryotic Microbiology, Faculty of Biology, University of Duisburg-Essen , Universit\u00e4tsstra\u00dfe 1, Essen, Nordrhein-Westfalen 45141, Germany"}]},{"given":"Pavel","family":"Skaloud","sequence":"additional","affiliation":[{"name":"Department of Botany, Faculty of Science, Charles University , Benatska 2, Praha 12800, Czech Republic"}]},{"given":"Peeter","family":"Laas","sequence":"additional","affiliation":[{"name":"Department of Marine Systems, Tallinn University of Technology , M\u00e4ealuse 14a, Tallinn 12618, Estonia"},{"name":"Institute of Technology, University of Tartu , Nooruse 1, Tartu 50400, Estonia"}]},{"given":"Marco","family":"Tines","sequence":"additional","affiliation":[{"name":"Department for Biological Sciences, Institute for Ecology, Evolution, and Diversity, Goethe University Frankfurt am Main , Max-von-Laue-Str. 13, Frankfurt am Main 60438, Germany"},{"name":"Senckenberg Biodiversity and Climate Research Centre , Georg-Voigt-Stra\u00dfe 14-16, Frankfurt am Main 60325, Germany"}]},{"given":"Jae-Ho","family":"Jung","sequence":"additional","affiliation":[{"name":"Department of Biology, Gangneung-Wonju National University , Jukheon-gil 7, Gangneung 25457, South Korea"}]},{"given":"Ji Hye","family":"Choi","sequence":"additional","affiliation":[{"name":"Department of Biology, Gangneung-Wonju National University , Jukheon-gil 7, Gangneung 25457, South Korea"}]},{"given":"Saad","family":"Alkahtani","sequence":"additional","affiliation":[{"name":"Department of Zoology, College of Science, King Saud University , PO Box 2455, Riyadh 11451, Saudi Arabia"}]},{"given":"Sten","family":"Anslan","sequence":"additional","affiliation":[{"name":"Institute of Ecology and Earth Sciences, University of Tartu , Liivi 2, Tartu 50400, Estonia"}]}],"member":"286","published-online":{"date-parts":[[2024,6,12]]},"reference":[{"key":"2024062912241879900_R1","volume-title":"Topics in the Philosophy of Biology","author":"Grene","year":"2012"},{"key":"2024062912241879900_R2","doi-asserted-by":"crossref","first-page":"96","DOI":"10.1016\/j.ejop.2011.11.004","article-title":"Concepts in protistology: species definitions and boundaries","volume":"48","author":"Boenigk","year":"2012","journal-title":"Eur. 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