The curse of the uncultured fungus
Artikel i vetenskaplig tidskrift, 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
Författare
Kessy Abarenkov
Tartu Ülikool
Erik Kristiansson
Chalmers, Matematiska vetenskaper, Tillämpad matematik och statistik
Göteborgs universitet
M. Ryberg
Uppsala universitet
Sandra Nogal-Prata
Real Jardín Botanico
Daniela Gómez-Martínez
Göteborgs universitet
Katrin Stüer-Patowsky
Technische Universität München
Tobias Jansson
Göteborgs universitet
Sergei Põlme
Tartu Ülikool
Masoomeh Ghobad-Nejhad
Iranian Research Organization for Science and Technology
Natàlia Corcoll
Göteborgs universitet
Ruud Scharn
Göteborgs universitet
Marisol Sánchez-García
Sveriges lantbruksuniversitet (SLU)
Maryia Khomich
Universitetet i Bergen
Christian Wurzbacher
Technische Universität München
R. Henrik Nilsson
Göteborgs universitet
MycoKeys
1314-4057 (ISSN) 1314-4049 (eISSN)
Vol. 86 177-194Ämneskategorier (SSIF 2011)
Biologisk systematik
Bioinformatik och systembiologi
Genetik
DOI
10.3897/MYCOKEYS.86.76053