UniEuk: Time to Speak a Common Language in Protistology!

Cédric Berney¹, Andreea Ciuprina², Sara Bender³, Juliet Brodie⁴, Virginia Edgcomb⁵, Eunsoo Kim⁶, Jeena Rajan⁷, Laura Wegener Parfrey⁸, Sina Adl⁹, Stéphane Audic¹, David Bass^{4

10}, David A Caron¹¹, Guy Cochrane⁷, Lucas Czech¹², Micah Dunthorn¹³, Stefan Geisen¹⁴, Frank Oliver Glöckner^{2

15}, Frédéric Mahé¹⁶, Christian Quast¹⁵, Jonathan Z Kaye³, Alastair G B Simpson¹⁷, Alexandros Stamatakis^{12

18}, Javier Del Campo⁸, Pelin Yilmaz¹⁵, Colomban de Vargas¹

Affiliations

¹ Sorbonne Universités UPMC Université Paris 06 & CNRS, UMR7144, Station Biologique de Roscoff, Place Georges Teissier, Roscoff, 29680, France.
² Department of Life Sciences and Chemistry, Jacobs University gGmbH, Bremen, D-28759, Germany.
³ Gordon and Betty Moore Foundation, 1661 Page Mill Road, Palo Alto, California, 94304, USA.
⁴ Department of Life Sciences, Natural History Museum, Cromwell Road, London, SW7 5BD, United Kingdom.
⁵ Geology and Geophysics Department, Woods Hole Oceanographic Institution, Woods Hole, Massachusetts, 02543, USA.
⁶ Division of Invertebrate Zoology & Sackler Institute for Comparative Genomics, American Museum of Natural History, New York, New York, 10024, USA.
⁷ European Nucleotide Archive, EMBL-EBI, Wellcome Genome Campus, Cambridge, CB10 1SD, United Kingdom.
⁸ Department of Botany and Zoology, University of British Columbia, 109-2212 Main Mall, Vancouver, BC, V6T 1Z4, Canada.
⁹ Department of Soil Sciences, College of Agriculture and Bioresources, University of Saskatchewan, Saskatoon, SK, S7N 5C5, Canada.
¹⁰ Centre for Environment, Fisheries and Aquaculture Science, Barrack Road, Weymouth, DT4 8UB, United Kingdom.
¹¹ Department of Biological Sciences, University of Southern California, 3616 Trousdale Parkway, Los Angeles, California, 90089-0371, USA.
¹² Scientific Computing Group, Heidelberg Institute for Theoretical Studies, Schloss-Wolfsbrunnenweg 35, Heidelberg, D-69118, Germany.
¹³ Department of Ecology, University of Kaiserslautern, Kaiserslautern, D-67663, Germany.
¹⁴ Department of Terrestrial Ecology, Netherlands Institute of Ecology (NIOO-KNAW) & Laboratory of Nematology, Wageningen University, Droevendaalsesteeg 10, Wageningen, 6708 PB, The Netherlands.
¹⁵ Microbial Genomics and Bioinformatics Research Group, Max Planck Institute for Marine Microbiology, Celsiusstrasse 1, Bremen, D-28359, Germany.
¹⁶ CIRAD, UMR LSTM, Montpellier, F-34398, France.
¹⁷ Department of Biology, Dalhousie University, 1355 Oxford Street, Halifax, NS, B3H 4R2, Canada.
¹⁸ Karlsruhe Institute of Technology, Institute for Theoretical Informatics, Postfach 6980, Karlsruhe, 76128, Germany.

PMID: 28337822
PMCID: PMC5435949
DOI: 10.1111/jeu.12414

Review

UniEuk: Time to Speak a Common Language in Protistology!

Cédric Berney et al. J Eukaryot Microbiol. 2017 May.

. 2017 May;64(3):407-411.

doi: 10.1111/jeu.12414. Epub 2017 Apr 21.

Authors

Affiliations

¹ Sorbonne Universités UPMC Université Paris 06 & CNRS, UMR7144, Station Biologique de Roscoff, Place Georges Teissier, Roscoff, 29680, France.
² Department of Life Sciences and Chemistry, Jacobs University gGmbH, Bremen, D-28759, Germany.
³ Gordon and Betty Moore Foundation, 1661 Page Mill Road, Palo Alto, California, 94304, USA.
⁴ Department of Life Sciences, Natural History Museum, Cromwell Road, London, SW7 5BD, United Kingdom.
⁵ Geology and Geophysics Department, Woods Hole Oceanographic Institution, Woods Hole, Massachusetts, 02543, USA.
⁶ Division of Invertebrate Zoology & Sackler Institute for Comparative Genomics, American Museum of Natural History, New York, New York, 10024, USA.
⁷ European Nucleotide Archive, EMBL-EBI, Wellcome Genome Campus, Cambridge, CB10 1SD, United Kingdom.
⁸ Department of Botany and Zoology, University of British Columbia, 109-2212 Main Mall, Vancouver, BC, V6T 1Z4, Canada.
⁹ Department of Soil Sciences, College of Agriculture and Bioresources, University of Saskatchewan, Saskatoon, SK, S7N 5C5, Canada.
¹⁰ Centre for Environment, Fisheries and Aquaculture Science, Barrack Road, Weymouth, DT4 8UB, United Kingdom.
¹¹ Department of Biological Sciences, University of Southern California, 3616 Trousdale Parkway, Los Angeles, California, 90089-0371, USA.
¹² Scientific Computing Group, Heidelberg Institute for Theoretical Studies, Schloss-Wolfsbrunnenweg 35, Heidelberg, D-69118, Germany.
¹³ Department of Ecology, University of Kaiserslautern, Kaiserslautern, D-67663, Germany.
¹⁴ Department of Terrestrial Ecology, Netherlands Institute of Ecology (NIOO-KNAW) & Laboratory of Nematology, Wageningen University, Droevendaalsesteeg 10, Wageningen, 6708 PB, The Netherlands.
¹⁵ Microbial Genomics and Bioinformatics Research Group, Max Planck Institute for Marine Microbiology, Celsiusstrasse 1, Bremen, D-28359, Germany.
¹⁶ CIRAD, UMR LSTM, Montpellier, F-34398, France.
¹⁷ Department of Biology, Dalhousie University, 1355 Oxford Street, Halifax, NS, B3H 4R2, Canada.
¹⁸ Karlsruhe Institute of Technology, Institute for Theoretical Informatics, Postfach 6980, Karlsruhe, 76128, Germany.

PMID: 28337822
PMCID: PMC5435949
DOI: 10.1111/jeu.12414

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.

Keywords: EukBank; EukMap; EukRef; Community expertise; diversity; eukaryotes; taxonomy.

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Figures

**Figure 1**
The *UniEuk* workflow. Bottom‐up, community‐based information on eukaryotic biodiversity from (A) classical knowledge, (B) phylogenetic diversity, and (C) environmental ‘‐omics’ surveys, converge and synergize through the *UniEuk* modules to inform the navigable and editable, consensus‐based taxonomic framework (D). Dotted and colored frames indicate input and output information, respectively. Line drawings of eukaryotes adapted with permission from https://genev.unige.ch/system/pawlowski/lab/tree.png.

See this image and copyright information in PMC

References

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UniEuk: Time to Speak a Common Language in Protistology!

Affiliations

UniEuk: Time to Speak a Common Language in Protistology!

Authors

Affiliations

Abstract

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