Статья

Towards a unified paradigm for sequence‐based identification of fungi

Urmas KõljalgInstitute of Ecology and Earth Sciences University of Tartu Lai 40 Tartu 51005 EstoniaR. Henrik NilssonDepartment of Biological and Environmental Sciences University of Gothenburg Box 461 Göteborg SE‐40530 SwedenKessy AbarenkovNatural History Museum University of Tartu Vanemuise 46 Tartu 51014 EstoniaLeho TedersooNatural History Museum University of Tartu Vanemuise 46 Tartu 51014 EstoniaAndy F. S. TaylorInstitute of Biological and Environmental Sciences University of Aberdeen Cruickshank Building, St Machar Drive Aberdeen AB24 3UU UKMohammad BahramInstitute of Ecology and Earth Sciences University of Tartu Lai 40 Tartu 51005 EstoniaScott T. BatesCooperative Institute for Research in Environmental Sciences University of Colorado Boulder CO 80309 USAThomas D. BrunsDepartment of Plant and Microbial Biology University of California Berkeley CA 94720 USAJohan Bengtsson‐PalmeDepartment of Neuroscience and Physiology The Sahlgrenska Academy University of Gothenburg Box 434 Göteborg SE‐40530 SwedenTony M. CallaghanInstitute of Biological, Environmental and Rural Sciences Aberystwyth University Cledwyn Building Aberystwyth SY23 3DD UKBrian DouglasInstitute of Biological, Environmental and Rural Sciences Aberystwyth University Cledwyn Building Aberystwyth SY23 3DD UKTiia DrenkhanInstitute of Forestry and Rural Engineering Estonian University of Life Sciences Fr. R. Kreutzwaldi 5 Tartu 51014 EstoniaUrsula EberhardtStaatliches Museum f. Naturkunde Stuttgart Abt. Botanik, Rosenstein 1 Stuttgart D‐70191 GermanyMargarita DueñasDepartmento de Micología Real Jardín Botánico (RJB‐CSIC) Plaza de Murillo 1 Madrid 28014 SpainTine GrebencDepartment of Forest Physiology and Genetics Slovenian Forestry Institute Vecna pot 2 Ljubljana SI‐1000 SloveniaGareth GriffithInstitute of Biological, Environmental and Rural Sciences Aberystwyth University Cledwyn Building Aberystwyth SY23 3DD UKMartin HartmannForest Soils and Biogeochemistry Swiss Federal Research Institute WSL CH‐8903 Birmensdorf SwitzerlandPaul M. KirkMycology Section Jodrell Laboratory Royal Botanic Gardens Kew Surrey TW9 3DS UKPetr KohoutInstitute of Botany Academy of Science of the Czech Republic Průhonice CZ‐252 43 Czech RepublicEllen LarssonDepartment of Biological and Environmental Sciences University of Gothenburg Box 461 Göteborg SE‐40530 SwedenBjörn D. LindahlDepartment of Forest Mycology and Plant Pathology Swedish University of Agricultural Sciences Box 7026 Uppsala SE‐75007 SwedenRobert LückingScience and Education Integrative Research and Collections (Botany) The Field Museum 1400 South Lake Shore Drive Chicago IL 60605‐2496 USAMaría P. MartínDepartmento de Micología Real Jardín Botánico (RJB‐CSIC) Plaza de Murillo 1 Madrid 28014 SpainP. Brandon MathenyDepartment of Ecology and Evolutionary Biology University of Tennessee Hesler Biology Building 332 Knoxville TN 37996‐1610 USANhu NguyenDepartment of Plant and Microbial Biology University of California Berkeley CA 94720 USATuula NiskanenPlant Biology Department of Biosciences University of Helsinki P.O. Box 56 Helsinki FI‐00014 FinlandJane OjaInstitute of Ecology and Earth Sciences University of Tartu Lai 40 Tartu 51005 EstoniaKabir PeayDepartment of Biology Stanford University Stanford CA 94305 USAUrsula PeintnerInstitute of Microbiology University Innsbruck Technikerstr. 25 Innsbruck 6020 AustriaMarko PetersonInstitute of Ecology and Earth Sciences University of Tartu Lai 40 Tartu 51005 EstoniaKadri PõldmaaInstitute of Ecology and Earth Sciences University of Tartu Lai 40 Tartu 51005 EstoniaLauri SaagInstitute of Ecology and Earth Sciences University of Tartu Lai 40 Tartu 51005 EstoniaIrja SaarInstitute of Ecology and Earth Sciences University of Tartu Lai 40 Tartu 51005 EstoniaArthur SchüßlerGenetics Department Biology Ludwig‐Maximilians‐University Grosshaderner Str. 4, Martinsried Munich 82152 GermanyJames A. ScottDalla Lana School of Public Health University of Toronto 223 College Street Toronto ON M5T 1R4 CanadaCarolina Senés‐GuerreroGenetics Department Biology Ludwig‐Maximilians‐University Grosshaderner Str. 4, Martinsried Munich 82152 GermanyMatthew E. SmithDepartment of Plant Pathology University of Florida Gainesville FL 32611‐0680 USAAve SuijaInstitute of Ecology and Earth Sciences University of Tartu Lai 40 Tartu 51005 EstoniaD. Lee TaylorDepartment of Biology University of New Mexico MSC03 2020 Albuquerque NM 87131‐0001 USAM. Teresa TelleríaDepartmento de Micología Real Jardín Botánico (RJB‐CSIC) Plaza de Murillo 1 Madrid 28014 SpainMichael WeißDepartment of Biology University of Tübingen Auf der Morgenstelle 5 Tübingen D‐72076 GermanyKarl‐Henrik LarssonNatural History Museum University of Oslo P.O. Box 1172 Blindern Oslo 0318 Norway

2013en

ABI

Аннотация

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.

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Идентификаторы

DOI: 10.1111/mec.12481

Цитирования и источники

Цитирований: 4Использованных источников: 0

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