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

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Abarenkov , K , Somervuo , P , Nilsson , R H , Kirk , P M , Huotari , T , Abrego , N & Ovaskainen , O 2018 , ' Protax-fungi : a web-based tool for probabilistic taxonomic placement of fungal internal transcribed spacer sequences ' , New Phytologist , vol. 220 , no. 2 , pp. 517-525 . https://doi.org/10.1111/nph.15301

Title: Protax-fungi : a web-based tool for probabilistic taxonomic placement of fungal internal transcribed spacer sequences
Author: Abarenkov, Kessy; Somervuo, Panu; Nilsson, R. Henrik; Kirk, Paul M.; Huotari, Tea; Abrego, Nerea; Ovaskainen, Otso
Contributor: University of Helsinki, Organismal and Evolutionary Biology Research Programme
University of Helsinki, Department of Agricultural Sciences
University of Helsinki, Department of Agricultural Sciences
University of Helsinki, Research Centre for Ecological Change
Date: 2018-10
Language: eng
Number of pages: 9
Belongs to series: New Phytologist
ISSN: 0028-646X
URI: http://hdl.handle.net/10138/307605
Abstract: 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.
Subject: 1183 Plant biology, microbiology, virology
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