The curse of the uncultured fungus

By

Abarenkov, Kessy
Kristiansson, Erik
Ryberg, Martin
Nogal-Prata, Sandra
Gómez-Martínez, Daniela
Stüer-Patowsky, Katrin
Jansson, Tobias
Põlme, Sergei
Ghobad-Nejhad, Masoomeh
Corcoll, Natàlia
Scharn, Ruud
Sánchez-García, Marisol
Khomich, Maryia
Wurzbacher, Christian
Nilsson, R. Henrik

Type

Article

Date of Publication

2022-2-2

Original Publication

MycoKeys

Volume

86

Pages

177--194

Subjects

data interoperability , Data mining , DNA barcoding , scientific practice , species identification , taxonomic annotation

Contributed by

Pensoft Publishers

Language

English

Published by

Sofia, Bulgaria Pensoft Publishers 2011-

Identifiers

DOI: https://doi.org/10.3897/mycokeys.86.76053

 

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 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.