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The curse of the uncultured fungus

Abarenkov, Kessy and Kristiansson, Erik and Ryberg, Martin and Nogal-Prata, Sandra and Kristiansson, Erik and Gomez-Martinez, Daniela and Stueer-Patowsky, Katrin and Jansson, Tobias and Polme, Sergei and Corcoll, Natalia and Scharn, Ruud and Sanchez-Garcia, Marisol and Wurzbacher, Christian and Khomich, Maryia and Nilsson, R. Henrik (2022). The curse of the uncultured fungus. MycoKeys :86 , 177-194
[Research article]

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Abstract

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.

Authors/Creators:Abarenkov, Kessy and Kristiansson, Erik and Ryberg, Martin and Nogal-Prata, Sandra and Kristiansson, Erik and Gomez-Martinez, Daniela and Stueer-Patowsky, Katrin and Jansson, Tobias and Polme, Sergei and Corcoll, Natalia and Scharn, Ruud and Sanchez-Garcia, Marisol and Wurzbacher, Christian and Khomich, Maryia and Nilsson, R. Henrik
Title:The curse of the uncultured fungus
Series Name/Journal:MycoKeys
Year of publishing :2022
Number:86
Page range:177-194
Number of Pages:18
Publisher:PENSOFT PUBLISHERS
ISSN:1314-4057
Language:English
Publication Type:Research article
Article category:Scientific peer reviewed
Version:Published version
Copyright:Creative Commons: Attribution 4.0
Full Text Status:Public
Subjects:(A) Swedish standard research categories 2011 > 1 Natural sciences > 106 Biological Sciences (Medical to be 3 and Agricultural to be 4) > Biological Systematics
Keywords:Data interoperability, data mining, DNA barcoding, scientific practice, species identification, taxonomic, annotation
URN:NBN:urn:nbn:se:slu:epsilon-p-115967
Permanent URL:
http://urn.kb.se/resolve?urn=urn:nbn:se:slu:epsilon-p-115967
Additional ID:
Type of IDID
DOI10.3897/mycokeys.86.76053
Web of Science (WoS)000751832200003
ID Code:27161
Faculty:S - Faculty of Forest Sciences
Department:(NL, NJ) > Dept. of Forest Mycology and Plant Pathology
(S) > Dept. of Forest Mycology and Plant Pathology
Deposited By: SLUpub Connector
Deposited On:21 Feb 2022 13:25
Metadata Last Modified:21 Feb 2022 13:31

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