TY - JOUR

T1 - Improving ITS sequence data for identification of plant pathogenic fungi

AU - Nilsson, R. Henrik

AU - Hyde, Kevin D.

AU - Pawłowska, Julia

AU - Ryberg, Martin

AU - Tedersoo, Leho

AU - Aas, Anders Bjørnsgard

AU - Alias, Siti A.

AU - Alves, Artur

AU - Anderson, Cajsa Lisa

AU - Antonelli, Alexandre

AU - Arnold, A. Elizabeth

AU - Bahnmann, Barbara

AU - Bahram, Mohammad

AU - Bengtsson-Palme, Johan

AU - Berlin, Anna

AU - Branco, Sara

AU - Chomnunti, Putarak

AU - Dissanayake, Asha

AU - Drenkhan, Rein

AU - Friberg, Hanna

AU - Frøslev, Tobias Guldberg

AU - Halwachs, Bettina

AU - Hartmann, Martin

AU - Henricot, Beatrice

AU - Jayawardena, Ruvishika

AU - Jumpponen, Ari

AU - Kauserud, Håvard

AU - Koskela, Sonja

AU - Kulik, Tomasz

AU - Liimatainen, Kare

AU - Lindahl, Björn D.

AU - Lindner, Daniel

AU - Liu, Jian Kui

AU - Maharachchikumbura, Sajeewa

AU - Manamgoda, Dimuthu

AU - Martinsson, Svante

AU - Neves, Maria Alice

AU - Niskanen, Tuula

AU - Nylinder, Stephan

AU - Pereira, Olinto Liparini

AU - Pinho, Danilo Batista

AU - Porter, Teresita M.

AU - Queloz, Valentin

AU - Riit, Taavi

AU - Sánchez-García, Marisol

AU - de Sousa, Filipe

AU - Stefańczyk, Emil

AU - Tadych, Mariusz

AU - Takamatsu, Susumu

AU - Tian, Qing

AU - Udayanga, Dhanushka

AU - Unterseher, Martin

AU - Wang, Zheng

AU - Wikee, Saowanee

AU - Yan, Jiye

AU - Larsson, Ellen

AU - Larsson, Karl Henrik

AU - Kõljalg, Urmas

AU - Abarenkov, Kessy

PY - 2014

Y1 - 2014

N2 - 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.

AB - 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.

KW - Annotation

KW - ITS

KW - Molecular identification

KW - Phytopathogenic fungi

KW - Taxonomy

U2 - 10.1007/s13225-014-0291-8

DO - 10.1007/s13225-014-0291-8

M3 - Journal article

AN - SCOPUS:84916234886

VL - 67

SP - 11

EP - 19

JO - Fungal Diversity

JF - Fungal Diversity

SN - 1560-2745

IS - 1

ER -