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Improving ITS sequence data for identification of plant pathogenic fungi

Fungal Diversity 2014年第4期67卷 11-19页

作者： R.Henrik Nilsson Kevin D.Hyde Julia Pawlowska Martin Ryberg Leho Tedersoo Anders Bjornsgard Aas Siti A.Alias Artur Alves Cajsa Lisa Anderson Alexandre Antonelli A.Elizabeth Arnold Barbara Bahnmann Mohammad Bahram Johan Bengtsson-Palme Anna Berlin Sara Branco Putarak Chomnunti Asha Dissanayake Rein Drenkhan Hanna Friberg tobias guldberg froslev.bettina halwachs Martin Hartmann Beatrice Henricot Ruvishika Jayawardena Ari Jumpponen Havard Kauserud Sonja Koskela Tomasz Kulik Kare Liimatainen Bjorn D.Lindahl Daniel Lindner Jian-Kui Liu Sajeewa Maharachchikumbura Dimuthu Manamgoda Svante Martinsson Maria Alice Neves Tuula Niskanen Stephan Nylinder Olinto Liparini Pereira Danilo Batista Pinho Teresita M.Porter Valentin Queloz Taavi Riit Marisol Sánchez-García Filipe de Sousa Emil Stefańczyk Mariusz Tadych Susumu Takamatsu Qing Tian Dhanushka Udayanga Martin Unterseher Zheng Wang Saowanee Wikee Jiye Yan Ellen Larsson Karl-Henrik Larsson Urmas Koljalg Kessy Abarenkov Department of Biological and Environmental Sciences University of GothenburgBox 46140530 GothenburgSweden Institute of Excellence in Fungal Research Mae Fah Luang UniversityChiang Rai 57100Thailand School of Science Mae Fah Luang UniversityChiang Rai 57100Thailand Department of Plant Systematics and Geography Faculty of BiologyUniversity of WarsawAl.Ujazdowskie 400-478 WarsawPoland Department of Organismal Biology Uppsala UniversityNorbyvagen 18D75236 UppsalaSweden Institute of Ecology and Earth Sciences University of TartuLai 40Tartu 51005Estonia Microbial Evolution Research Group University of OsloBlindernveien 310371 OsloNorway Institute of Biological Sciences University of Malaya50603 Kuala LumpurMalaysia Department of Biology CESAMUniversity of Aveiro3810-193 AveiroPortugal School of Plant Sciences The University of Arizona1140 E South Campus DriveForbes 303TucsonAZ 85721USA Laboratory of Environmental Microbiology Institute of Microbiology ASCRVídeňská108314220 Prague 4Czech Republic Department of Infectious Diseases Institute of BiomedicineSahlgrenska AcademyUniversity of GothenburgGuldhedsgatan 1041346 GoteborgSweden Department of Forest Mycology and Plant Pathology Swedish University of Agricultural SciencesBox 702675007 UppsalaSweden University of California at Berkeley 321 Koshland Hall University of CaliforniaBerkeleyCA 94720-3102USA Agriculture and Forestry Sciences Beijing 100097China Institute of Forestry and Rural Engineering Estonian University of Life SciencesKreutzwaldi551014 TartuEstonia Natural History Museum of Denmark Øster Voldgade 5-71350 København KDenmark Institute for Genomics and Bioinformatics Graz University of Technology8010 GrazAustria Core Facility Bioinformatics Austrian Centre of Industrial Biotechnology8010 GrazAustria Forest Soils and Biogeochemistry Swiss Federal Research Institute WSLZuercherstrasse 1118903 BirmensdorfSwitzerland Molecular Ecology Institute for Sustainability SciencesAgroscopeReckenholzstrasse 191

Plant pathogenic fungi are a large and diverse assemblage of eukaryotes with substantial impacts on natural ecosystems and human *** taxa often have complex and poorly understood life cycles,lack observable,discriminatory morphological characters,and may not be amenable to in vitro *** a result,species identification is frequently ***(DNA sequence)data have emerged as crucial information for the taxonomic identification of plant pathogenic fungi,with the nuclear ribosomal internal transcribed spacer(ITS)region being the most popular ***,international nucleotide sequence databases are accumulating numerous sequences of compromised or low-resolution taxonomic annotations and substandard technical quality,making their use in the molecular identification of plant pathogenic fungi *** we report on a concerted effort to identify high-quality reference sequences for various plant pathogenic fungi and to re-annotate incorrectly or insufficiently annotated public ITS sequences from these fungal lineages.A third objective was to enrich the sequences with geographical and ecological *** results-a total of 31,954 changes-are incorporated in and made available through the UNITE database for molecular identification of fungi(http://***),including standalone FASTA files of sequence data for local BLAST searches,use in the next-generation sequencing analysis platforms QIIME and mothur,and related *** present initiative is just a beginning to cover the wide spectrum of plant pathogenic fungi,and we invite all researchers with pertinent expertise to join the annotation effort.

关键词： Phytopathogenic fungi Molecular identification ITS Taxonomy Annotation

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