Missouri Botanical Garden Open Conference Systems, TDWG 2013 ANNUAL CONFERENCE

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Linking taxon names with DNA-based species
Urmas Kõljalg

Building: Main Building 1st Floor
Room: Salone degli Oceani
Last modified: 2013-10-08

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 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). 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 five different similarity thresholds (97, 97.5, 98, 98.5 and 99%). There are 44537, 52481 and  68938 SHs based on 97, 98 and 99% threshold value respectively. An automatically or manually designated sequence is chosen to represent each such SH. These reference sequences are linked to the classification (taxon names). 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 (http://qiime.org). 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 taxonomy and sequence management system provided by PlutoF (http://plutof.ut.ee). The example of the online managing system is shown in Fig. 1. The paper on this new approach linking taxon names with DNA based species is available online (doi: 10.1111/mec.12481).