The curse of the uncultured fungus
Journal article, 2022
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.
Scientific practice
Data mining
Data interoperability
Species identification
DNA barcoding
Taxonomic annotation
Author
Kessy Abarenkov
University of Tartu
Erik Kristiansson
Chalmers, Mathematical Sciences, Applied Mathematics and Statistics
University of Gothenburg
M. Ryberg
Uppsala University
Sandra Nogal-Prata
Real Jardín Botanico
Daniela Gómez-Martínez
University of Gothenburg
Katrin Stüer-Patowsky
Technical University of Munich
Tobias Jansson
University of Gothenburg
Sergei Põlme
University of Tartu
Masoomeh Ghobad-Nejhad
Iranian Research Organization for Science and Technology
Natàlia Corcoll
University of Gothenburg
Ruud Scharn
University of Gothenburg
Marisol Sánchez-García
Swedish University of Agricultural Sciences (SLU)
Maryia Khomich
University of Bergen
Christian Wurzbacher
Technical University of Munich
R. Henrik Nilsson
University of Gothenburg
MycoKeys
1314-4057 (ISSN) 1314-4049 (eISSN)
Vol. 86 177-194Subject Categories (SSIF 2011)
Biological Systematics
Bioinformatics and Systems Biology
Genetics
DOI
10.3897/MYCOKEYS.86.76053