| Abstract Detail
Sequence-based Identification of Fungi Kőljalg, Urmas [1], Abarenkov, Kessy [1], Nilsson, R. Henrik [2], Larsson, Henrik [3]. At species crossroads. The rDNA ITS region has a long history of use as a molecular marker for species-level identification in ecological and taxonomic studies of fungi. It offers several advantages over other species-level markers in terms of high information content and ease of amplification, and it was recently designated the official barcode for fungi. To facilitate and speed up ITS-based molecular identification and discovery of fungal species, the Species Hypotheses (SH) approach has been implemented by the UNITE community (http://unite.ut.ee). UNITE was established in 2001 and two years later public web services for the molecular identification of ectomycorrhizal fungi were released. The UNITE datasets and web services have been under continuous development since then. At present, UNITE targets all fungi and geographical regions, but the founding principle - to provide reliable reference sequences for molecular identification - remains the same. UNITE includes all fungal ITS sequences in the INSD databases that have passed the quality control, as well as sequences of private datasets made available to UNITE. These sequences are subject to web-based third-party sequence annotation, and all researchers with relevant expertise are welcome to join the annotation effort. The demand for high-quality reference sequences has risen rapidly due to the increasing use of high-throughput sequencing technologies. Several software pipelines are available for overseeing more or less the entire analysis procedure, from data cleaning to sequence clustering and taxonomic assignment. Some of them, e.g. QIIME, MOTHUR, SCATA, and CREST are now utilizing the downloadable UNITE repository of SHs (http://unite.ut.ee/repository.php) as reference database for taxonomic assignment. Version six of UNITE includes a total of 354 688 SHs divided between different threshold values as follows (% is a dissimilarity gap between two SHs): 3% 42 879 SHs; 2.5% 46 470 SHs; 2% 50 643 SHs, 1.5% 56 235 SHs, 1% 66 466 SHs, 0.5% 91 995 SHs. The theoretical body of the SH approach allows the same individuals to be members of one to many SHs. For example individual sequences may belong to a single SH when a 3% gap is used but they may split between two SHs under a 2% gap, etc. In order to provide a stable communication of the SHs across datasets and studies, UNITE has implemented a set of mandatory principles: 1) all SHs are connected to the fungal classification; 2) all SHs have a unique identifier; and 3) all SHs have a globally unique URI identifier (e.g., http://unite.ut.ee/sh/SH158651.06FU).
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Related Links:
http://unite.ut.ee/repository.php
1 - University of Tartu, Natural History Museum, Vanemuise 46, Tartu 51014, Estonia
2 - University of Gothenborg, Biological and Environmental Sciences, Box 461, Göteborg SE-40530, Sweden
3 - University of OSlo, Natural History Museum, P.O. Box 1172, Blindern, Oslo 0318
Keywords:
ITS
phylogenetic species
species hypothesis.
Presentation Type: Symposium or Colloquium Presentation
Session: SY8
Location: Room 103 AB/Kellogg Hotel and Conference Center
Date: Wednesday, June 11th, 2014
Time: 2:00 PM
Number: SY8003
Abstract ID:213
Candidate for Awards:None |
