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Towards a unified paradigm for sequence‐based identification of fungi
Authors:Urmas Kõljalg  R. Henrik Nilsson  Kessy Abarenkov  Leho Tedersoo  Andy F. S. Taylor  Mohammad Bahram  Scott T. Bates  Thomas D. Bruns  Johan Bengtsson‐Palme  Tony M. Callaghan  Brian Douglas  Tiia Drenkhan  Ursula Eberhardt  Margarita Dueñas  Tine Grebenc  Gareth W. Griffith  Martin Hartmann  Paul M. Kirk  Petr Kohout  Ellen Larsson  Björn D. Lindahl  Robert Lücking  María P. Martín  P. Brandon Matheny  Nhu H. Nguyen  Tuula Niskanen  Jane Oja  Kabir G. Peay  Ursula Peintner  Marko Peterson  Kadri Põldmaa  Lauri Saag  Irja Saar  Arthur Schüßler  James A. Scott  Carolina Senés  Matthew E. Smith  Ave Suija  D. Lee Taylor  M. Teresa Telleria  Michael Weiss  Karl‐Henrik Larsson
Affiliation:1. Institute of Ecology and Earth Sciences, University of Tartu, , Tartu, 51005 Estonia;2. Natural History Museum, University of Tartu, , Tartu, 51014 Estonia;3. Department of Biological and Environmental Sciences, University of Gothenburg, , G?teborg, SE‐40530 Sweden;4. The James Hutton Institute, , Aberdeen, AB15 8QH UK;5. Institute of Biological and Environmental Sciences, University of Aberdeen, , Aberdeen, AB24 3UU UK;6. Cooperative Institute for Research in Environmental Sciences, University of Colorado, , Boulder, CO, 80309 USA;7. Department of Plant and Microbial Biology, University of California, , Berkeley, CA, 94720 USA;8. Department of Neuroscience and Physiology, The Sahlgrenska Academy, University of Gothenburg, , G?teborg, SE‐40530 Sweden;9. Institute of Biological, Environmental and Rural Sciences, Aberystwyth University, , Aberystwyth, SY23 3DD UK;10. Institute of Forestry and Rural Engineering, Estonian University of Life Sciences, , Tartu, 51014 Estonia;11. Staatliches Museum f. Naturkunde Stuttgart, , Stuttgart, D‐70191 Germany;12. Departmento de Micología, Real Jardín Botánico (RJB‐CSIC), , Madrid, 28014 Spain;13. Department of Forest Physiology and Genetics, Slovenian Forestry Institute, , Ljubljana, SI‐1000 Slovenia;14. Forest Soils and Biogeochemistry, Swiss Federal Research Institute WSL, , CH‐8903 Birmensdorf, Switzerland;15. Molecular Ecology, Agroscope Reckenholz‐T?nikon Research Station ART, , CH‐8046 Zurich, Switzerland;16. Mycology Section, Jodrell Laboratory, Royal Botanic Gardens Kew, , Surrey, TW9 3DS UK;17. Institute of Botany, Academy of Science of the Czech Republic, , Pr?honice, CZ‐252 43 Czech Republic;18. Department of Forest Mycology and Plant Pathology, Swedish University of Agricultural Sciences, , Uppsala, SE‐75007 Sweden;19. Science and Education, Integrative Research and Collections (Botany), The Field Museum, , Chicago, IL, 60605‐2496 USA;20. Department of Ecology and Evolutionary Biology, University of Tennessee, , Knoxville, TN, 37996‐1610 USA;21. Plant Biology, Department of Biosciences, University of Helsinki, , Helsinki, FI‐00014 Finland;22. Department of Biology, Stanford University, , Stanford, CA, USA;23. Institute of Microbiology, University Innsbruck, , Innsbruck, 6020 Austria;24. Genetics, Department Biology, Ludwig‐Maximilians‐University, , Munich, 82152 Germany;25. Dalla Lana School of Public Health, University of Toronto, , Toronto, ON, M5T 1R4 Canada;26. Department of Plant Pathology, University of Florida, , Gainesville, FL, 32611‐0680 USA;27. Department of Biology, University of New Mexico, , Albuquerque, NM, 87131‐0001 USA;28. Department of Biology, University of Tübingen, , Tübingen, D‐72076 Germany;29. Natural History Museum, University of Oslo, , Oslo, 0318 Norway
Abstract:The nuclear ribosomal internal transcribed spacer (ITS) region is the formal fungal barcode and in most cases the marker of choice for the exploration of fungal diversity in environmental samples. Two problems are particularly acute in the pursuit of satisfactory taxonomic assignment of newly generated ITS sequences: (i) the lack of an inclusive, reliable public reference data set and (ii) the lack of means to refer to fungal species, for which no Latin name is available in a standardized stable way. Here, we report on progress in these regards through further development of the UNITE database ( http://unite.ut.ee ) for molecular identification of fungi. All fungal species represented by at least two ITS sequences in the international nucleotide sequence databases are now given a unique, stable name of the accession number type (e.g. Hymenoscyphus pseudoalbidus|GU586904|SH133781.05FU), and their taxonomic and ecological annotations were corrected as far as possible through a distributed, third‐party annotation effort. We introduce the term ‘species hypothesis’ (SH) for the taxa discovered in clustering on different similarity thresholds (97–99%). An automatically or manually designated sequence is chosen to represent each such SH. These reference sequences are released ( http://unite.ut.ee/repository.php ) for use by the scientific community in, for example, local sequence similarity searches and in the QIIME pipeline. The system and the data will be updated automatically as the number of public fungal ITS sequences grows. We invite everybody in the position to improve the annotation or metadata associated with their particular fungal lineages of expertise to do so through the new Web‐based sequence management system in UNITE.
Keywords:bioinformatics  DNA barcoding  ecological genomics  fungi  microbial diversity
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