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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 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 dataset, 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 tresholds (97-99%). An automatically or manually designated sequence is chosen to represent each such species hypothesis. These reference sequences are released (http://unite.ut.ee/repository.php) for use by the scientific community in, e.g., 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.This article is protected by copyright. All rights reserved.
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... Sequencing was performed at Macrogen Europe BV (Amsterdam, The Netherlands), using the available Standard-Seq service. The sequences along with their metadata were uploaded in PlutoF, a data management and publishing platform [21], and made available via the UNITE database [22]. The UNITE species hypotheses (SH) served as the basis for species identification by choosing an appropriate distance threshold value [23] in each case ( Table 2). ...
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... The OTUs obtained from the ITS gene were aligned on the UNITE database (version7. 2 https://unite.ut.ee/) and the lowest similarity was set to 0.8 (Koljalg et al., 2014). In order to analyze the microbial communities at the same sequencing depth, the lowest sequencing number was randomly selected per sample of which 24,477 sequences were selected for bacterial 16S rRNA gene and 27,192 sequences for fungal ITS gene. ...
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