Improving ITS sequence data for identification of plant pathogenic fungi
Artikel i vetenskaplig tidskrift, 2014

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.

Phytopathogenic fungi

Annotation

Taxonomy

ITS

Molecular identification

Författare

R. Henrik Nilsson

Göteborgs universitet

Kevin D. Hyde

Julia Pawłowska

Martin Ryberg

Leho Tedersoo

Anders Bjørnsgard Aas

Siti A. Alias

Artur Alves

Cajsa Lisa Anderson

Göteborgs universitet

Alexandre Antonelli

Göteborgs universitet

A. Elizabeth Arnold

Barbara Bahnmann

Mohammad Bahram

Johan Bengtsson-Palme

Göteborgs universitet

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

Göteborgs universitet

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

Göteborgs universitet

Emil Stefańczyk

Mariusz Tadych

Susumu Takamatsu

Qing Tian

Dhanushka Udayanga

Martin Unterseher

Saowanee Wikee

Jiye Yan

Ellen Larsson

Göteborgs universitet

Karl-Henrik Larsson

Urmas Kõljalg

Kessy Abarenkov

Fungal Diversity

1560-2745 (ISSN)

Vol. 67 1 11-19

Ämneskategorier

Botanik

Biologisk systematik

Markvetenskap

Jordbruksvetenskap

Ekologi

Mikrobiologi

Trädgårdsvetenskap/hortikultur

Mikrobiologi inom det medicinska området

Bioinformatik och systembiologi

DOI

10.1007/s13225-014-0291-8