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      A Comprehensive, Automatically Updated Fungal ITS Sequence Dataset for Reference-Based Chimera Control in Environmental Sequencing Efforts

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          Abstract

          The nuclear ribosomal internal transcribed spacer (ITS) region is the most commonly chosen genetic marker for the molecular identification of fungi in environmental sequencing and molecular ecology studies. Several analytical issues complicate such efforts, one of which is the formation of chimeric—artificially joined—DNA sequences during PCR amplification or sequence assembly. Several software tools are currently available for chimera detection, but rely to various degrees on the presence of a chimera-free reference dataset for optimal performance. However, no such dataset is available for use with the fungal ITS region. This study introduces a comprehensive, automatically updated reference dataset for fungal ITS sequences based on the UNITE database for the molecular identification of fungi. This dataset supports chimera detection throughout the fungal kingdom and for full-length ITS sequences as well as partial (ITS1 or ITS2 only) datasets. The performance of the dataset on a large set of artificial chimeras was above 99.5%, and we subsequently used the dataset to remove nearly 1,000 compromised fungal ITS sequences from public circulation. The dataset is available at http://unite.ut.ee/repository.php and is subject to web-based third-party curation.

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          The magnitude of fungal diversity: the 1.5 million species estimate revisited

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            Current state and perspectives of fungal DNA barcoding and rapid identification procedures.

            Fungal research is experiencing a new wave of methodological improvements that most probably will boost mycology as profoundly as molecular phylogeny has done during the last 15 years. Especially the next generation sequencing technologies can be expected to have a tremendous effect on fungal biodiversity and ecology research. In order to realise the full potential of these exciting techniques by accelerating biodiversity assessments, identification procedures of fungi need to be adapted to the emerging demands of modern large-scale ecological studies. But how should fungal species be identified in the near future? While the answer might seem trivial to most microbiologists, taxonomists working with fungi may have other views. In the present review, we will analyse the state of the art of the so-called barcoding initiatives in the light of fungi, and we will seek to evaluate emerging trends in the field. We will furthermore demonstrate that the usability of DNA barcoding as a major tool for identification of fungi largely depends on the development of high-quality sequence databases that are thoroughly curated by taxonomists and systematists.
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              Parsing ecological signal from noise in next generation amplicon sequencing.

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                Author and article information

                Journal
                Microbes Environ
                Microbes Environ
                Microbes and Environments
                the Japanese Society of Microbial Ecology (JSME)/the Japanese Society of Soil Microbiology (JSSM)/the Taiwan Society of Microbial Ecology (TSME)/the Japanese Society of Plant Microbe Interactions (JSPMI)
                1342-6311
                1347-4405
                June 2015
                19 March 2015
                : 30
                : 2
                : 145-150
                Affiliations
                [1 ]Department of Biological and Environmental Sciences, University of Gothenburg Box 461, 405 30 GothenburgSweden
                [2 ]Institute of Ecology and Earth Sciences, University of Tartu Lai 40, Tartu 51005Estonia
                [3 ]Department of Organismal Biology, Uppsala University Norbyvägen 18D, 75236 UppsalaSweden
                [4 ]Department of Mathematical Statistics, Chalmers University of Technology 412 96 GöteborgSweden
                [5 ]Forest Soils and Biogeochemistry, Swiss Federal Research Institute WSL Zuercherstrasse 111, 8903 BirmensdorfSwitzerland
                [6 ]Molecular Ecology, Institute for Sustainability Sciences Agroscope, Reckenholzstrasse 191, 8046 ZurichSwitzerland
                [7 ]Ernst-Moritz-Arndt University, Institute of Botany and Landscape Ecology Soldmannstr. 15, D-17487 GreifswaldGermany
                [8 ]Department of Biology, McMaster University Hamilton, Ontario, L8S 4K1Canada
                [9 ]Department of Infectious Diseases, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg Guldhedsgatan 10, SE-413 46 GothenburgSweden
                [10 ]Department of Natural Sciences, The University of Findlay Findlay, OHUSA
                [11 ]Group of Plant Nutrition, Institute of Agricultural Sciences, Department of Environmental Systems Science ETH Zurich, Eschikon 33, 8315 Lindau (ZH)Switzerland
                [12 ]Natural History Museum P.O. Box 1172 Blindern, 0318 OsloNorway
                [13 ]Natural History Museum, University of Tartu Vanemuise 46, Tartu 51014Estonia
                [14 ]Tiburon, CAUSA
                Author notes
                [* ]Corresponding author. E-mail: henrik.nilsson@ 123456bioenv.gu.se ; Tel: +46–31–7862623; Fax: +46-31-786 2560.
                Article
                30_145
                10.1264/jsme2.ME14121
                4462924
                25786896
                005ea735-8bc9-4d00-aeaa-627421717ee0
                Copyright 2015 by Japanese Society of Microbial Ecology / Japanese Society of Soil Microbiology / Taiwan Society of Microbial Ecology / Japanese Society of Plant Microbe Interactions

                This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.

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