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-ITS1, ITS2, 18S V4-V5 and 28S D1-D2 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-a 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.

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

Department of Biological and Environmental Sciences Gothenburg Global Biodiversity Centre University of Gothenburg Box 461 Göteborg 40530 Sweden

Department of Biology Gangneung Wonju National University Jukheon gil 7 Gangneung 25457 South Korea

Department of Botany Faculty of Science Charles University Benatska 2 Praha 12800 Czech Republic

Department of Ecology Swedish University of Agricultural Sciences Ulls väg 16 Uppsala 75651 Sweden

Department of Environment Soils and Land Use Teagasc Oak Park House Wexford R93 XE12 Ireland

Department of Marine Systems Tallinn University of Technology Mäealuse 14a Tallinn 12618 Estonia

Department of Zoology College of Science King Saud University PO Box 2455 Riyadh 11451 Saudi Arabia

Ecology and Genetics Research Unit University of Oulu Box 8000 Oulu 90014 Finland

Eukaryotic Microbiology Faculty of Biology University of Duisburg Essen Universitätsstraße 1 Essen Nordrhein Westfalen 45141 Germany

Institute of Ecology and Earth Sciences University of Tartu Liivi 2 Tartu 50400 Estonia

Institute of Systematics and Evolution of Animals Polish Academy of Sciences Sławkowska 17 Kraków 31016 Poland

Institute of Technology University of Tartu Nooruse 1 Tartu 50400 Estonia

Laboratory of Nematology Wageningen University Droevendaalsesteeg 1 Wageningen 6708PB The Netherlands

Mycology and Microbiology Center University of Tartu Liivi 2 Tartu 50400 Estonia

National Marine Fisheries Research Institute Kołłątaja 1 Gdynia 81332 Poland

Senckenberg Biodiversity and Climate Research Centre Georg Voigt Straße 14 16 Frankfurt am Main 60325 Germany

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