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The curse of the un...
The curse of the uncultured fungus
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Abarenkov, Kessy (author)
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- Kristiansson, Erik, 1978 (author)
- Gothenburg University,Göteborgs universitet,Institutionen för matematiska vetenskaper,Department of Mathematical Sciences
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- Ryberg, M. (author)
- Uppsala universitet,Uppsala University
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- Nogal-Prata, Sandra (author)
- Real Jardín Botanico
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- Gómez-Martínez, Daniela (author)
- Gothenburg University,Göteborgs universitet,Institutionen för biologi och miljövetenskap,Department of Biological and Environmental Sciences
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- Stüer-Patowsky, Katrin (author)
- Technische Universität München (TUM),Technical University of Munich (TUM)
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- Jansson, Tobias (author)
- Gothenburg University,Göteborgs universitet,Institutionen för biologi och miljövetenskap,Department of Biological and Environmental Sciences
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Põlme, Sergei (author)
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Ghobad-Nejhad, Masoomeh (author)
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- Corcoll, Natàlia, 1981 (author)
- Gothenburg University,Göteborgs universitet,Institutionen för biologi och miljövetenskap,Department of Biological and Environmental Sciences
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- Scharn, Ruud (author)
- Gothenburg University,Göteborgs universitet,Institutionen för biologi och miljövetenskap,Department of Biological and Environmental Sciences
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- Sánchez-García, Marisol (author)
- Sveriges lantbruksuniversitet (SLU),Swedish University of Agricultural Sciences (SLU)
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- Khomich, Maryia (author)
- Universitetet i Bergen,University of Bergen
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- Wurzbacher, Christian, 1980 (author)
- Technische Universität München (TUM),Technical University of Munich (TUM)
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- Nilsson, R. Henrik, 1976 (author)
- Gothenburg University,Göteborgs universitet,Institutionen för biologi och miljövetenskap,Department of Biological and Environmental Sciences
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(creator_code:org_t)
- 2022
- 2022
- English.
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In: MycoKeys. - 1314-4057 .- 1314-4049. ; 86, s. 177-194
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https://research.cha... (primary) (free)
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https://research.cha...
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https://doi.org/10.3...
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Abstract
Subject headings
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- The international DNA sequence databases abound in fungal sequences not annotated beyond the kingdom level, typically bearing names such as “uncultured fungus”. These sequences beget low-resolution mycological results and invite further deposition of similarly poorly annotated entries. What do these sequences represent? This study uses a 767,918-sequence corpus of public full-length fungal ITS sequences to estimate what proportion of the 95,055 “uncultured fungus” sequences that represent truly unidentifiable fungal taxa – and what proportion of them that would have been straightforward to annotate to some more meaningful taxonomic level at the time of sequence deposition. Our results suggest that more than 70% of these sequences would have been trivial to identify to at least the order/family level at the time of sequence deposition, hinting that factors other than poor availability of relevant reference sequences explain the low-resolution names. We speculate that researchers’ perceived lack of time and lack of insight into the ramifications of this problem are the main explanations for the low-resolution names. We were surprised to find that more than a fifth of these sequences seem to have been deposited by mycologists rather than researchers unfamiliar with the consequences of poorly annotated fungal sequences in molecular repositories. The proportion of these needlessly poorly annotated sequences does not decline over time, suggesting that this problem must not be left unchecked.
Subject headings
- NATURVETENSKAP -- Biologi -- Biologisk systematik (hsv//swe)
- NATURAL SCIENCES -- Biological Sciences -- Biological Systematics (hsv//eng)
- NATURVETENSKAP -- Biologi -- Bioinformatik och systembiologi (hsv//swe)
- NATURAL SCIENCES -- Biological Sciences -- Bioinformatics and Systems Biology (hsv//eng)
- NATURVETENSKAP -- Biologi -- Genetik (hsv//swe)
- NATURAL SCIENCES -- Biological Sciences -- Genetics (hsv//eng)
Keyword
- Taxonomic annotation
- Species identification
- Scientific practice
- DNA barcoding
- Data mining
- Data interoperability
Publication and Content Type
- art (subject category)
- ref (subject category)
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To the university's database
- By the author/editor
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Abarenkov, Kessy
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Kristiansson, Er ...
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Ryberg, M.
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Nogal-Prata, San ...
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Gómez-Martínez, ...
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Stüer-Patowsky, ...
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show more...
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Jansson, Tobias
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Põlme, Sergei
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Ghobad-Nejhad, M ...
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Corcoll, Natàlia ...
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Scharn, Ruud
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Sánchez-García, ...
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Khomich, Maryia
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Wurzbacher, Chri ...
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Nilsson, R. Henr ...
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show less...
- About the subject
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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 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 Genetics
- Articles in the publication
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MycoKeys
- By the university
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Chalmers University of Technology
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University of Gothenburg