Please use this identifier to cite or link to this item: http://hdl.handle.net/10773/23393
Title: Improving ITS sequence data for identification of plant pathogenic fungi
Author: Nilsson, R. Henrik
Hyde, Kevin D.
Pawłowska, Julia
Ryberg, Martin
Tedersoo, Leho
Aas, Anders Bjørnsgard
Alias, Siti A.
Alves, Artur
Anderson, Cajsa Lisa
Antonelli, Alexandre
Arnold, A. Elizabeth
Bahnmann, Barbara
Bahram, Mohammad
Bengtsson-Palme, Johan
Berlin, Anna
Branco, Sara
Chomnunti, Putarak
Dissanayake, Asha
Drenkhan, Rein
Friberg, Hanna
Frøslev, Tobias Guldberg
Halwachs, Bettina
Hartmann, Martin
Henricot, Beatrice
Jayawardena, Ruvishika
Jumpponen, Ari
Kauserud, Håvard
Koskela, Sonja
Kulik, Tomasz
Liimatainen, Kare
Lindahl, Björn D.
Lindner, Daniel
Liu, Jian Kui
Maharachchikumbura, Sajeewa
Manamgoda, Dimuthu
Martinsson, Svante
Neves, Maria Alice
Niskanen, Tuula
Nylinder, Stephan
Pereira, Olinto Liparini
Pinho, Danilo Batista
Porter, Teresita M.
Queloz, Valentin
Riit, Taavi
Sánchez-García, Marisol
de Sousa, Filipe
Stefańczyk, Emil
Tadych, Mariusz
Takamatsu, Susumu
Tian, Qing
Udayanga, Dhanushka
Unterseher, Martin
Wang, Zheng
Wikee, Saowanee
Yan, Jiye
Larsson, Ellen
Larsson, Karl-Henrik
Kõljalg, Urmas
Abarenkov, Kessy
Keywords: Annotation
ITS
Molecular identification
Phytopathogenic fungi
Taxonomy
Issue Date: 2014
Publisher: Springer
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.
Peer review: yes
URI: http://hdl.handle.net/10773/23393
DOI: 10.1007/s13225-014-0291-8
ISSN: 1560-2745
Appears in Collections:CESAM - Artigos
DBio - Artigos

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