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Improving ITS sequence data for identification of plant pathogenic fungi

Journal article
Authors R. Henrik Nilsson
Kevin D. Hyde
Julia Pawłowska
Martin Ryberg
Leho Tedersoo
Anders Bjørnsgard Aas
Siti A. Alias
Artur Alves
Cajsa Lisa Anderson
Alexandre Antonelli
A. Elizabeth Arnold
Barbara Bahnmann
Mohammad Bahram
Johan Bengtsson-Palme
Anna Berlin
Sara Branco
Putarak Chomnunti
Asha Dissanayake
Rein Drenkhan
Hanna Friberg
Tobias Guldberg Frøslev
Bettina Halwachs
Martin Hartmann
Beatrice Henricot
Ruvishika Jayawardena
Ari Jumpponen
Håvard Kauserud
Sonja Koskela
Tomasz Kulik
Kare Liimatainen
Björn Lindahl
Daniel Lindner
Jian-Kui Liu
Sajeewa Maharachchikumbura
Dimuthu Manamgoda
Svante Martinsson
Maria Alice Neves
Tuula Niskanen
Stephan Nylinder
Olinto Liparini Pereira
Danilo Batista Pinho
Teresita M. Porter
Valentin Queloz
Taavi Riit
Marisol Sánchez-García
Filipe de Sousa
Emil Stefańczyk
Mariusz Tadych
Susumu Takamatsu
Qing Tian
Dhanushka Udayanga
Martin Unterseher
Zheng Wang
Saowanee Wikee
Jiye Yan
Ellen Larsson
Karl-Henrik Larsson
Urmas Kõljalg
Kessy Abarenkov
Published in Fungal diversity
Volume 67
Issue 1
Pages 11-19
ISSN 1560-2745
Publication year 2014
Published at Department of Biological and Environmental Sciences
Institute of Biomedicine, Department of Infectious Medicine
Pages 11-19
Language en
Links link.springer.com/article/10.1007/s...
Keywords Phytopathogenic fungi ; Molecular identification ; ITS ; Taxonomy ; Annotation
Subject categories Microbiology, Botany, Bioinformatics and Systems Biology, Terrestrial ecology, Biological Systematics, Medical microbiology, Plant and forest protection, Horticulture, Soil biology

Abstract

Plant pathogenic fungi are a large and diverse assemblage of eukaryotes with substantial impacts on natural ecosystems and human endeavours. These taxa often have complex and poorly understood life cycles, lack observable, discriminatory morphological characters, and may not be amenable to in vitro culturing. As a result, species identification is frequently difficult. Molecular (DNA sequence) data have emerged as crucial information for the taxonomic identification of plant pathogenic fungi, with the nuclear ribosomal internal transcribed spacer (ITS) region being the most popular marker. However, international nucleotide sequence databases are accumulating numerous sequences of compromised or low-resolution taxonomic annotations and substandard technical quality, making their use in the molecular identification of plant pathogenic fungi problematic. Here we report on a concerted effort to identify high-quality reference sequences for various plant pathogenic fungi and to re-annotate incorrectly or insufficiently annotated public ITS sequences from these fungal lineages. A third objective was to enrich the sequences with geographical and ecological metadata. The results – a total of 31,954 changes – are incorporated in and made available through the UNITE database for molecular identification of fungi (http://unite.ut.ee), including standalone FASTA files of sequence data for local BLAST searches, use in the next-generation sequencing analysis platforms QIIME and mothur, and related applications. The present initiative is just a beginning to cover the wide spectrum of plant pathogenic fungi, and we invite all researchers with pertinent expertise to join the annotation effort.

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