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Berney C, Ciuprina A, Bender S, Brodie J, Edgcomb V, Kim E, Rajan J, Parfrey LW, Adl S, Audic S, Bass D, Caron DA, Cochrane G, Czech L, Dunthorn M, Geisen S, Glöckner FO, Mahé F, Quast C, Kaye JZ, Simpson AGB, Stamatakis A, Del Campo J, Yilmaz P, de Vargas C. UniEuk: Time to Speak a Common Language in Protistology! J Eukaryot Microbiol 2017; 64:407-411. [PMID: 28337822 PMCID: PMC5435949 DOI: 10.1111/jeu.12414] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2017] [Accepted: 03/13/2017] [Indexed: 12/19/2022]
Abstract
Universal taxonomic frameworks have been critical tools to structure the fields of botany, zoology, mycology, and bacteriology as well as their large research communities. Animals, plants, and fungi have relatively solid, stable morpho‐taxonomies built over the last three centuries, while bacteria have been classified for the last three decades under a coherent molecular taxonomic framework. By contrast, no such common language exists for microbial eukaryotes, even though environmental ‘‐omics’ surveys suggest that protists make up most of the organismal and genetic complexity of our planet's ecosystems! With the current deluge of eukaryotic meta‐omics data, we urgently need to build up a universal eukaryotic taxonomy bridging the protist ‐omics age to the fragile, centuries‐old body of classical knowledge that has effectively linked protist taxa to morphological, physiological, and ecological information. UniEuk is an open, inclusive, community‐based and expert‐driven international initiative to build a flexible, adaptive universal taxonomic framework for eukaryotes. It unites three complementary modules, EukRef, EukBank, and EukMap, which use phylogenetic markers, environmental metabarcoding surveys, and expert knowledge to inform the taxonomic framework. The UniEuk taxonomy is directly implemented in the European Nucleotide Archive at EMBL‐EBI, ensuring its broad use and long‐term preservation as a reference taxonomy for eukaryotes.
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Affiliation(s)
- Cédric Berney
- Sorbonne Universités UPMC Université Paris 06 & CNRS, UMR7144, Station Biologique de Roscoff, Place Georges Teissier, Roscoff, 29680, France
| | - Andreea Ciuprina
- Department of Life Sciences and Chemistry, Jacobs University gGmbH, Bremen, D-28759, Germany
| | - Sara Bender
- Gordon and Betty Moore Foundation, 1661 Page Mill Road, Palo Alto, California, 94304, USA
| | - Juliet Brodie
- Department of Life Sciences, Natural History Museum, Cromwell Road, London, SW7 5BD, United Kingdom
| | - Virginia Edgcomb
- Geology and Geophysics Department, Woods Hole Oceanographic Institution, Woods Hole, Massachusetts, 02543, USA
| | - Eunsoo Kim
- Division of Invertebrate Zoology & Sackler Institute for Comparative Genomics, American Museum of Natural History, New York, New York, 10024, USA
| | - Jeena Rajan
- European Nucleotide Archive, EMBL-EBI, Wellcome Genome Campus, Cambridge, CB10 1SD, United Kingdom
| | - Laura Wegener Parfrey
- Department of Botany and Zoology, University of British Columbia, 109-2212 Main Mall, Vancouver, BC, V6T 1Z4, Canada
| | - Sina Adl
- Department of Soil Sciences, College of Agriculture and Bioresources, University of Saskatchewan, Saskatoon, SK, S7N 5C5, Canada
| | - Stéphane Audic
- Sorbonne Universités UPMC Université Paris 06 & CNRS, UMR7144, Station Biologique de Roscoff, Place Georges Teissier, Roscoff, 29680, France
| | - David Bass
- Department of Life Sciences, Natural History Museum, Cromwell Road, London, SW7 5BD, United Kingdom.,Centre for Environment, Fisheries and Aquaculture Science, Barrack Road, Weymouth, DT4 8UB, United Kingdom
| | - David A Caron
- Department of Biological Sciences, University of Southern California, 3616 Trousdale Parkway, Los Angeles, California, 90089-0371, USA
| | - Guy Cochrane
- European Nucleotide Archive, EMBL-EBI, Wellcome Genome Campus, Cambridge, CB10 1SD, United Kingdom
| | - Lucas Czech
- Scientific Computing Group, Heidelberg Institute for Theoretical Studies, Schloss-Wolfsbrunnenweg 35, Heidelberg, D-69118, Germany
| | - Micah Dunthorn
- Department of Ecology, University of Kaiserslautern, Kaiserslautern, D-67663, Germany
| | - Stefan Geisen
- Department of Terrestrial Ecology, Netherlands Institute of Ecology (NIOO-KNAW) & Laboratory of Nematology, Wageningen University, Droevendaalsesteeg 10, Wageningen, 6708 PB, The Netherlands
| | - Frank Oliver Glöckner
- Department of Life Sciences and Chemistry, Jacobs University gGmbH, Bremen, D-28759, Germany.,Microbial Genomics and Bioinformatics Research Group, Max Planck Institute for Marine Microbiology, Celsiusstrasse 1, Bremen, D-28359, Germany
| | | | - Christian Quast
- Microbial Genomics and Bioinformatics Research Group, Max Planck Institute for Marine Microbiology, Celsiusstrasse 1, Bremen, D-28359, Germany
| | - Jonathan Z Kaye
- Gordon and Betty Moore Foundation, 1661 Page Mill Road, Palo Alto, California, 94304, USA
| | - Alastair G B Simpson
- Department of Biology, Dalhousie University, 1355 Oxford Street, Halifax, NS, B3H 4R2, Canada
| | - Alexandros Stamatakis
- Scientific Computing Group, Heidelberg Institute for Theoretical Studies, Schloss-Wolfsbrunnenweg 35, Heidelberg, D-69118, Germany.,Karlsruhe Institute of Technology, Institute for Theoretical Informatics, Postfach 6980, Karlsruhe, 76128, Germany
| | - Javier Del Campo
- Department of Botany and Zoology, University of British Columbia, 109-2212 Main Mall, Vancouver, BC, V6T 1Z4, Canada
| | - Pelin Yilmaz
- Microbial Genomics and Bioinformatics Research Group, Max Planck Institute for Marine Microbiology, Celsiusstrasse 1, Bremen, D-28359, Germany
| | - Colomban de Vargas
- Sorbonne Universités UPMC Université Paris 06 & CNRS, UMR7144, Station Biologique de Roscoff, Place Georges Teissier, Roscoff, 29680, France
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