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Towards a unified paradigm for sequence-based identification of fungi.

Journal article
Authors Urmas Kõljalg
R. Henrik Nilsson
Kessy Abarenkov
Leho Tedersoo
Andy F S Taylor
Mohammad Bahram
Scott T Bates
Thomas D Bruns
Johan Bengtsson-Palme
Tony M Callaghan
Brian Douglas
Tiia Drenkhan
Ursula Eberhardt
Margarita Dueñas
Tine Grebenc
Gareth W Griffith
Martin Hartmann
Paul M Kirk
Petr Kohout
Ellen Larsson
Björn D Lindahl
Robert Lücking
María P Martín
P Brandon Matheny
Nhu H Nguyen
Tuula Niskanen
Jane Oja
Kabir G Peay
Ursula Peintner
Marko Peterson
Kadri Põldmaa
Lauri Saag
Irja Saar
Arthur Schüßler
James A Scott
Carolina Senés
Matthew E Smith
Ave Suija
D Lee Taylor
M Teresa Telleria
Michael Weiss
Karl-Henrik Larsson
Published in Molecular ecology
Volume 22
Issue 21
Pages 5271-7
ISSN 1365-294X
Publication year 2013
Published at Institute of Neuroscience and Physiology
Department of Biological and Environmental Sciences
Pages 5271-7
Language en
Links dx.doi.org/10.1111/mec.12481
Keywords DNA barcoding, bioinformatics, ecological genomics, fungi, microbial diversity
Subject categories Bioinformatics and Systems Biology, Ecology, Biological Systematics

Abstract

The nuclear ribosomal internal transcribed spacer (ITS) region is the formal fungal barcode and in most cases the marker of choice for the exploration of fungal diversity in environmental samples. Two problems are particularly acute in the pursuit of satisfactory taxonomic assignment of newly generated ITS sequences: (i) the lack of an inclusive, reliable public reference data set and (ii) the lack of means to refer to fungal species, for which no Latin name is available in a standardized stable way. Here, we report on progress in these regards through further development of the UNITE database (http://unite.ut.ee) for molecular identification of fungi. All fungal species represented by at least two ITS sequences in the international nucleotide sequence databases are now given a unique, stable name of the accession number type (e.g. Hymenoscyphus pseudoalbidus|GU586904|SH133781.05FU), and their taxonomic and ecological annotations were corrected as far as possible through a distributed, third-party annotation effort. We introduce the term 'species hypothesis' (SH) for the taxa discovered in clustering on different similarity thresholds (97-99%). An automatically or manually designated sequence is chosen to represent each such SH. These reference sequences are released (http://unite.ut.ee/repository.php) for use by the scientific community in, for example, local sequence similarity searches and in the QIIME pipeline. The system and the data will be updated automatically as the number of public fungal ITS sequences grows. We invite everybody in the position to improve the annotation or metadata associated with their particular fungal lineages of expertise to do so through the new Web-based sequence management system in UNITE.

Page Manager: Webmaster|Last update: 9/11/2012
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