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A comprehensive, au...
A comprehensive, automatically updated fungal ITS sequence dataset for reference-based chimera control in environmental sequencing efforts
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- Nilsson, R. Henrik, 1976 (author)
- Gothenburg University,Göteborgs universitet,Institutionen för biologi och miljövetenskap,Department of Biological and Environmental Sciences,University of Gothenburg
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- Tedersoo, Leho (author)
- Tartu Ülikool,University of Tartu
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- Ryberg, Martin, 1976 (author)
- Uppsala universitet,Systematisk biologi
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- Kristiansson, Erik, 1978 (author)
- Gothenburg University,Göteborgs universitet,Institutionen för matematiska vetenskaper, matematisk statistik,Department of Mathematical Sciences, Mathematical Statistics,Chalmers tekniska högskola,Chalmers University of Technology,University of Gothenburg
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- Hartmann, Martin (author)
- Eidgenossische Forschungsanstalt fur Wald, Schnee Und Landschaft Eth-Bereichs
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- Unterseher, Martin (author)
- Universität Greifswald,University of Greifswald
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- Porter, Teresita M. (author)
- McMaster University
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- Bengtsson-Palme, Johan, 1985 (author)
- Gothenburg University,Göteborgs universitet,Institutionen för biomedicin, avdelningen för infektionssjukdomar,Institute of Biomedicine, Department of Infectious Medicine,University of Gothenburg
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- Walker, Donald M. (author)
- University of Findlay
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- Sousa, Filipe de, 1982 (author)
- Gothenburg University,Göteborgs universitet,Institutionen för biologi och miljövetenskap,Department of Biological and Environmental Sciences,University of Gothenburg
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- Gamper, Hannes Andres (author)
- Eidgenössische Technische Hochschule Zürich (ETH),Swiss Federal Institute of Technology in Zürich (ETH)
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- Larsson, Ellen, 1961 (author)
- Gothenburg University,Göteborgs universitet,Institutionen för biologi och miljövetenskap,Department of Biological and Environmental Sciences,University of Gothenburg
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Larsson, Karl-Henrik, 1948 (author)
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- Kõljalg, Urmas (author)
- Tartu Ülikool,University of Tartu
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Edgar, Robert C. (author)
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- Abarenkov, Kessy (author)
- Tartu Ülikool,University of Tartu
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(creator_code:org_t)
- 2015
- 2015
- English.
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In: Microbes and Environments. - 1342-6311 .- 1347-4405. ; 30:2, s. 145-150
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Abstract
Subject headings
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- The nuclear ribosomal internal transcribed spacer (ITS) region is the most commonly chosen genetic marker for the molecular identification of fungi in environmental sequencing and molecular ecology studies. Several analytical issues complicate such efforts, one of which is the formation of chimeric—artificially joined—DNA sequences during PCR amplification or sequence assembly. Several software tools are currently available for chimera detection, but rely to various degrees on the presence of a chimera-free reference dataset for optimal performance. However, no such dataset is available for use with the fungal ITS region. This study introduces a comprehensive, automatically updated reference dataset for fungal ITS sequences based on the UNITE database for the molecular identification of fungi. This dataset supports chimera detection throughout the fungal kingdom and for full-length ITS sequences as well as partial (ITS1 or ITS2 only) datasets. The performance of the dataset on a large set of artificial chimeras was above 99.5%, and we subsequently used the dataset to remove nearly 1,000 compromised fungal ITS sequences from public circulation. The dataset is available at http://unite.ut.ee/repository.php and is subject to web-based third-party curation.
Subject headings
- LANTBRUKSVETENSKAPER -- Veterinärmedicin -- Patobiologi (hsv//swe)
- AGRICULTURAL SCIENCES -- Veterinary Science -- Pathobiology (hsv//eng)
- LANTBRUKSVETENSKAPER -- Lantbruksvetenskap, skogsbruk och fiske -- Markvetenskap (hsv//swe)
- AGRICULTURAL SCIENCES -- Agriculture, Forestry and Fisheries -- Soil Science (hsv//eng)
- MEDICIN OCH HÄLSOVETENSKAP -- Medicinska och farmaceutiska grundvetenskaper -- Mikrobiologi inom det medicinska området (hsv//swe)
- MEDICAL AND HEALTH SCIENCES -- Basic Medicine -- Microbiology in the medical area (hsv//eng)
- NATURVETENSKAP -- Biologi -- Ekologi (hsv//swe)
- NATURAL SCIENCES -- Biological Sciences -- Ecology (hsv//eng)
- NATURVETENSKAP -- Biologi -- Bioinformatik och systembiologi (hsv//swe)
- NATURAL SCIENCES -- Biological Sciences -- Bioinformatics and Systems Biology (hsv//eng)
- NATURVETENSKAP -- Biologi -- Mikrobiologi (hsv//swe)
- NATURAL SCIENCES -- Biological Sciences -- Microbiology (hsv//eng)
- NATURVETENSKAP -- Biologi -- Biologisk systematik (hsv//swe)
- NATURAL SCIENCES -- Biological Sciences -- Biological Systematics (hsv//eng)
- NATURVETENSKAP -- Data- och informationsvetenskap -- Bioinformatik (hsv//swe)
- NATURAL SCIENCES -- Computer and Information Sciences -- Bioinformatics (hsv//eng)
- NATURVETENSKAP -- Biologi (hsv//swe)
- NATURAL SCIENCES -- Biological Sciences (hsv//eng)
Keyword
- fungi
- chimera detection
- reference dataset
- molecular ecology
- PCR artifacts
- reference dataset
Publication and Content Type
- ref (subject category)
- art (subject category)
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To the university's database
- By the author/editor
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Nilsson, R. Henr ...
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Tedersoo, Leho
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Ryberg, Martin, ...
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Kristiansson, Er ...
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Hartmann, Martin
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Unterseher, Mart ...
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show more...
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Porter, Teresita ...
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Bengtsson-Palme, ...
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Walker, Donald M ...
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Sousa, Filipe de ...
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Gamper, Hannes A ...
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Larsson, Ellen, ...
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Larsson, Karl-He ...
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Kõljalg, Urmas
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Edgar, Robert C.
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Abarenkov, Kessy
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- About the subject
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- AGRICULTURAL SCIENCES
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AGRICULTURAL SCI ...
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and Veterinary Scien ...
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and Pathobiology
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- AGRICULTURAL SCIENCES
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AGRICULTURAL SCI ...
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and Agriculture Fore ...
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and Soil Science
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- MEDICAL AND HEALTH SCIENCES
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MEDICAL AND HEAL ...
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and Basic Medicine
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and Microbiology in ...
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- NATURAL SCIENCES
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NATURAL SCIENCES
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and Biological Scien ...
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and Ecology
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- NATURAL SCIENCES
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NATURAL SCIENCES
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and Biological Scien ...
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and Bioinformatics a ...
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- NATURAL SCIENCES
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NATURAL SCIENCES
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and Biological Scien ...
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and Microbiology
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- NATURAL SCIENCES
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NATURAL SCIENCES
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and Biological Scien ...
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and Biological Syste ...
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- NATURAL SCIENCES
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NATURAL SCIENCES
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and Computer and Inf ...
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and Bioinformatics
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- NATURAL SCIENCES
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NATURAL SCIENCES
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and Biological Scien ...
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- Articles in the publication
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Microbes and Env ...
- By the university
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University of Gothenburg
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Chalmers University of Technology
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Uppsala University