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Protax-fungi: A web-based tool for probabilistic taxonomic placement of fungal internal transcribed spacer sequences

Journal article
Authors Kessy Abarenkov
Panu Somervuo
R. Henrik Nilsson
Paul M. Kirk
Tea Huotari
Nerea Abrego
Otso Ovaskainen
Published in New Phytologist
Volume 220
Issue 2
Pages 517-525
ISSN 0028-646X
Publication year 2018
Published at Department of Biological and Environmental Sciences
Pages 517-525
Language en
Links https://doi.org/10.1111/nph.15301
https://nph.onlinelibrary.wiley.com...
Keywords Annotation, Data quality, Environmental sequencing, Fungi, Identification tool, Internal transcribed spacer (ITS), Molecular species identification, Probabilistic taxonomic assignment
Subject categories Agricultural Science, Forest Science, Soil Science, Biological Sciences, Microbiology, Botany, Bioinformatics and Systems Biology, Statistics, computer and systems science, Databases, Bioinformatics (Computational Biology), Biostatistics

Abstract

© 2018 New Phytologist Trust. Incompleteness of reference sequence databases and unresolved taxonomic relationships complicates taxonomic placement of fungal sequences. We developed Protax-fungi, a general tool for taxonomic placement of fungal internal transcribed spacer (ITS) sequences, and implemented it into the PlutoF platform of the UNITE database for molecular identification of fungi. With empirical data on root- and wood-associated fungi, Protax-fungi reliably identified (with at least 90% identification probability) the majority of sequences to the order level but only around one-fifth of them to the species level, reflecting the current limited coverage of the databases. Protax-fungi outperformed the Sintax and Rdb classifiers in terms of increased accuracy and decreased calibration error when applied to data on mock communities representing species groups with poor sequence database coverage. We applied Protax-fungi to examine the internal consistencies of the Index Fungorum and UNITE databases. This revealed inconsistencies in the taxonomy database as well as mislabelling and sequence quality problems in the reference database. The according improvements were implemented in both databases. Protax-fungi provides a robust tool for performing statistically reliable identifications of fungi in spite of the incompleteness of extant reference sequence databases and unresolved taxonomic relationships.

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