Towards a unified paradigm for sequence-based identification of Fungi

Urmas Kõljalg and R. Henrik Nilsson and Kessy Abarenkov and Leho Tedersoo and Andy F. S. Taylor and Mohammad Bahram and Scott T. Bates and Thomas D. Bruns and Johan Bengtsson-Palme and Tony M. Callaghan and Brian Douglas and Tiia Drenkhan and Ursula Eberhardt and Margarita Dueñas and Tine Grebenc and Gareth W. Griffith and Martin Hartmann and Paul M. Kirk and Petr Kohout and Ellen Larsson and Björn D. Lindahl and Robert Lücking and María P. Martín and P. Brandon Matheny and Nhu H. Nguyen and Tuula Niskanen and Jane Oja and Kabir G. Peay and Ursula Peintner and Marko Peterson and Kadri Põldmaa and Lauri Saag and Irja Saar and Arthur Schüßler and James A. Scott and Carolina Senés and Matthew E. Smith and Ave Suija and D. Lee Taylor and M. Teresa Telleria and Michael Weiss and Karl-Henrik Larsson (2013) Towards a unified paradigm for sequence-based identification of Fungi. Molecular Ecology, 22 (21). pp. 5271-5277. ISSN 09621083

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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.

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