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The curse of the un...
The curse of the uncultured fungus
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- Abarenkov, Kessy (författare)
- Univ Tartu, Nat Hist Museum, Vanemuise 46, EE-51014 Tartu, Estonia.
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- Kristiansson, Erik (författare)
- Chalmers Univ Technol, Dept Math Sci, Gothenburg, Sweden.;Univ Gothenburg, Gothenburg, Sweden.
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- Ryberg, Martin (författare)
- Uppsala universitet,Systematisk biologi
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- Nogal-Prata, Sandra (författare)
- Real Jardin Bot CSIC, Dept Mycol, Madrid, Spain.
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- Gomez-Martinez, Daniela (författare)
- Univ Gothenburg, Dept Biol & Environm Sci, Box 461, S-40530 Gothenburg, Sweden.
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- Stueer-Patowsky, Katrin (författare)
- Tech Univ Munich, Chair Urban Water Syst Engn, Coulombwall 3, D-85748 Garching, Germany.
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- Jansson, Tobias (författare)
- Univ Gothenburg, Dept Biol & Environm Sci, Box 461, S-40530 Gothenburg, Sweden.
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- Polme, Sergei (författare)
- Univ Tartu, Nat Hist Museum, Vanemuise 46, EE-51014 Tartu, Estonia.
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- Ghobad-Nejhad, Masoomeh (författare)
- Iranian Res Org Sci & Technol, Dept Biotechnol, POB 3353-5111, Tehran 3353136846, Iran.
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- Corcoll, Natalia (författare)
- Univ Gothenburg, Gothenburg Global Biodivers Ctr, Dept Biol & Environm Sci, Box 461, S-40530 Gothenburg, Sweden.
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- Scharn, Ruud (författare)
- Univ Gothenburg, Dept Earth Sci, Box 460, S-40530 Gothenburg, Sweden.
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- Sanchez-Garcia, Marisol (författare)
- Swedish University of Agricultural Sciences,Sveriges lantbruksuniversitet,Department of Forest Mycology and Plant Pathology,Swedish Univ Agr Sci, Dept Forest Mycol & Plant Pathol, Uppsala, Sweden.
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- Khomich, Maryia (författare)
- Univ Bergen, Dept Clin Sci, Box 7804, N-5020 Bergen, Norway.
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- Wurzbacher, Christian (författare)
- Tech Univ Munich, Chair Urban Water Syst Engn, Coulombwall 3, D-85748 Garching, Germany.
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- Nilsson, R. Henrik (författare)
- Univ Gothenburg, Gothenburg Global Biodivers Ctr, Dept Biol & Environm Sci, Box 461, S-40530 Gothenburg, Sweden.
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Univ Tartu, Nat Hist Museum, Vanemuise 46, EE-51014 Tartu, Estonia Chalmers Univ Technol, Dept Math Sci, Gothenburg, Sweden.;Univ Gothenburg, Gothenburg, Sweden. (creator_code:org_t)
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- 2022-02-02
- 2022
- Engelska.
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Ingår i: MycoKeys. - : Pensoft Publishers. - 1314-4057 .- 1314-4049. ; :86, s. 177-194
- Relaterad länk:
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https://doi.org/10.3...
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https://uu.diva-port... (primary) (Raw object)
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https://mycokeys.pen...
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https://pub.epsilon.... (primary) (Raw object) (free)
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https://urn.kb.se/re...
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https://doi.org/10.3...
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https://res.slu.se/i...
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Abstract
Ämnesord
Stäng
- 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 lowresolution 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 that represent truly unidentifiable fungal taxa - and what proportion of them that would have 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.
Ämnesord
- NATURVETENSKAP -- Biologi -- Biologisk systematik (hsv//swe)
- NATURAL SCIENCES -- Biological Sciences -- Biological Systematics (hsv//eng)
Nyckelord
- Data interoperability
- data mining
- DNA barcoding
- scientific practice
- species identification
- taxonomic
- annotation
Publikations- och innehållstyp
- ref (ämneskategori)
- art (ämneskategori)
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- Av författaren/redakt...
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Abarenkov, Kessy
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Kristiansson, Er ...
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Ryberg, Martin
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Nogal-Prata, San ...
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Gomez-Martinez, ...
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Stueer-Patowsky, ...
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visa fler...
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Jansson, Tobias
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Polme, Sergei
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Ghobad-Nejhad, M ...
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Corcoll, Natalia
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Scharn, Ruud
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Sanchez-Garcia, ...
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Khomich, Maryia
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Wurzbacher, Chri ...
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Nilsson, R. Henr ...
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visa färre...
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