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      • Record: found
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      Finding needles in haystacks: linking scientific names, reference specimens and molecular data for Fungi

      research-article
      1 , * , 1 , 2 , 2 , 3 , 4 ,   4 , 5 , 6 , 7 , 8 , 9 , 10 , 11 , 12 , 2 , 13 , 14 , 11 , 15 , 2 , 16 , 17 , 8 , 15 , 18 , 19 , 20 , 21 , 14 , 22 , 2 , 2 , 23 , 24 , 25 , 26 , 27 , 19 , 28 , 29 , 30 , 2 , 11 , 31 , 32 , 11 , 9 , 33 , 34 , 35 , 36 , 37 , 38 , 35 , 39 , 40 , 11 , 41 , 42 , 35 , 11 , 11 , 18 , 43 , 44 , 45 , 46 , 40 , 28 , 36 , 36 , 47 , 39 , 48 , 49 , 18 , 27 , 50 , 47 , 2 , 51 , 52 , 9 , 18 , 11 , 53 , 18 , 31 , 36 , 2 , 54 , 55 , 32 , 56 , 11 , 17 , 57 , 14 , 58 , 26 , 1
      Database: The Journal of Biological Databases and Curation
      Oxford University Press
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          There is no author summary for this article yet. Authors can add summaries to their articles on ScienceOpen to make them more accessible to a non-specialist audience.

          Abstract

          DNA phylogenetic comparisons have shown that morphology-based species recognition often underestimates fungal diversity. Therefore, the need for accurate DNA sequence data, tied to both correct taxonomic names and clearly annotated specimen data, has never been greater. Furthermore, the growing number of molecular ecology and microbiome projects using high-throughput sequencing require fast and effective methods for en masse species assignments. In this article, we focus on selecting and re-annotating a set of marker reference sequences that represent each currently accepted order of Fungi. The particular focus is on sequences from the internal transcribed spacer region in the nuclear ribosomal cistron, derived from type specimens and/or ex-type cultures. Re-annotated and verified sequences were deposited in a curated public database at the National Center for Biotechnology Information (NCBI), namely the RefSeq Targeted Loci (RTL) database, and will be visible during routine sequence similarity searches with NR_prefixed accession numbers. A set of standards and protocols is proposed to improve the data quality of new sequences, and we suggest how type and other reference sequences can be used to improve identification of Fungi.

          Database URL: http://www.ncbi.nlm.nih.gov/bioproject/PRJNA177353

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          Most cited references44

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          Phylogenetic species recognition and species concepts in fungi.

          The operational species concept, i.e., the one used to recognize species, is contrasted to the theoretical species concept. A phylogenetic approach to recognize fungal species based on concordance of multiple gene genealogies is compared to those based on morphology and reproductive behavior. Examples where Phylogenetic Species Recognition has been applied to fungi are reviewed and concerns regarding Phylogenetic Species Recognition are discussed.
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            The online database MaarjAM reveals global and ecosystemic distribution patterns in arbuscular mycorrhizal fungi (Glomeromycota).

            • Here, we describe a new database, MaarjAM, that summarizes publicly available Glomeromycota DNA sequence data and associated metadata. The goal of the database is to facilitate the description of distribution and richness patterns in this group of fungi. • Small subunit (SSU) rRNA gene sequences and available metadata were collated from all suitable taxonomic and ecological publications. These data have been made accessible in an open-access database (http://maarjam.botany.ut.ee). • Two hundred and eighty-two SSU rRNA gene virtual taxa (VT) were described based on a comprehensive phylogenetic analysis of all collated Glomeromycota sequences. Two-thirds of VT showed limited distribution ranges, occurring in single current or historic continents or climatic zones. Those VT that associated with a taxonomically wide range of host plants also tended to have a wide geographical distribution, and vice versa. No relationships were detected between VT richness and latitude, elevation or vascular plant richness. • The collated Glomeromycota molecular diversity data suggest limited distribution ranges in most Glomeromycota taxa and a positive relationship between the width of a taxon's geographical range and its host taxonomic range. Inconsistencies between molecular and traditional taxonomy of Glomeromycota, and shortage of data from major continents and ecosystems, are highlighted.
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              • Article: not found

              Assembling the fungal tree of life: progress, classification, and evolution of subcellular traits.

              Based on an overview of progress in molecular systematics of the true fungi (Fungi/Eumycota) since 1990, little overlap was found among single-locus data matrices, which explains why no large-scale multilocus phylogenetic analysis had been undertaken to reveal deep relationships among fungi. As part of the project "Assembling the Fungal Tree of Life" (AFTOL), results of four Bayesian analyses are reported with complementary bootstrap assessment of phylogenetic confidence based on (1) a combined two-locus data set (nucSSU and nucLSU rDNA) with 558 species representing all traditionally recognized fungal phyla (Ascomycota, Basidiomycota, Chytridiomycota, Zygomycota) and the Glomeromycota, (2) a combined three-locus data set (nucSSU, nucLSU, and mitSSU rDNA) with 236 species, (3) a combined three-locus data set (nucSSU, nucLSU rDNA, and RPB2) with 157 species, and (4) a combined four-locus data set (nucSSU, nucLSU, mitSSU rDNA, and RPB2) with 103 species. Because of the lack of complementarity among single-locus data sets, the last three analyses included only members of the Ascomycota and Basidiomycota. The four-locus analysis resolved multiple deep relationships within the Ascomycota and Basidiomycota that were not revealed previously or that received only weak support in previous studies. The impact of this newly discovered phylogenetic structure on supraordinal classifications is discussed. Based on these results and reanalysis of subcellular data, current knowledge of the evolution of septal features of fungal hyphae is synthesized, and a preliminary reassessment of ascomal evolution is presented. Based on previously unpublished data and sequences from GenBank, this study provides a phylogenetic synthesis for the Fungi and a framework for future phylogenetic studies on fungi.
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                Author and article information

                Journal
                Database (Oxford)
                Database (Oxford)
                database
                databa
                Database: The Journal of Biological Databases and Curation
                Oxford University Press
                1758-0463
                2014
                28 June 2014
                28 June 2014
                : 2014
                : bau061
                Affiliations
                1National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, Maryland, USA, 2CBS-KNAW Fungal Biodiversity Centre, P.O. Box 85167, 3508 AD Utrecht, The Netherlands, 3Department of Pharmaceutical Sciences – Microbiology, Università degli Studi di Perugia, Perugia, Italy, 4Molecular Mycology Research Laboratory, Centre for Infectious Diseases and Microbiology, Marie Bashir Institute for Infectious Diseases and Biosecurity, Sydney Medical School-Westmead Hospital, The University of Sydney, Westmead Millennium Institute, Westmead, Australia, 5Department of Biological and Environmental Sciences, University of Gothenburg, Box 461, 405 30 Göteborg, Sweden, 6Ecology and Evolutionary Biology, University of Tennessee, Knoxville, TN 37920, USA, 7Illinois Natural History Survey, University of Illinois, 1816 South Oak Street, Champaign, IL 61820, USA, 8Mycology Section, Jodrell Laboratory, Royal Botanic Gardens, Kew, Richmond, Surrey, TW9 3DS, UK, 9Natural History Museum, University of Tartu, 46 Vanemuise, 51014 Tartu, Estonia, 10Purdue University, Department of Botany and Plant Pathology, 915 W. State Street, West Lafayette, IN 47907, USA, 11Institute of Excellence in Fungal Research, and School of Science, Mae Fah Luang University, Chiang Rai 57100, Thailand, 12Imperial College London, Royal Botanic Gardens, Kew TW9 3DS, England, UK, 13Muséum National d’Histoire Naturelle, Dépt. Systématique et Evolution CP39, UMR7205, 12 Rue Buffon, F-75005 Paris, France, 14Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, Yunnan, P. R. China, 15Departamento de Biología Vegetal II, Facultad de Farmacia, Universidad Complutense de Madrid, Madrid 28040, Spain, 16Senckenberg Museum of Natural History Görlitz, PF 300 154, 02806 Görlitz, Germany, 17Department of Microbiology and Plant Pathology, Forestry Agricultural Biotechnology Institute (FABI), University of Pretoria, Pretoria 0001, South Africa, 18Real Jardín Botánico, RJB-CSIC, Plaza de Murillo 2, 28014 Madrid, Spain, 19Department of Forest and Conservation Sciences, Faculty of Forestry, The University of British Columbia, 2424 Main Mall, Vancouver, BC, Canada, 20Institute of Animal Physiology and Genetics, Czech Academy of Sciences, v.v.i., Videnska 1083, Prague, Czech Republic, 21Department of Biology, University of Toronto, 3359 Mississagua Road, Mississagua, Ontario L5L 1C6, Canada, 22Institute of Biological, Environmental and Rural Sciences, Prifysgol Aberystwyth, Aberystwyth, Ceredigion Wales SY23 3DD, UK, 23Institute of Plant Sciences, Karl-Franzens-University, Holteigasse 6, 8010 Graz, Austria, 24Department of Plant Sciences, University of the Free State, P.O. Box 339, Bloemfontein 9300, South Africa, 25CSIRO-Plant Industry, CANBR, GPO Box 1600, Canberra ACT 2601, Australia, 26State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China, 27Biodiversity (Mycology and Microbiology), Agriculture and Agri-Food Canada, 960 Carling Avenue, Ottawa, Ontario, Canada, 28Department of Botany, Swedish Museum of Natural History, P.O. Box 50007, SE-104 05, Stockholm, Sweden, 29Agroscope Changins-Wädenswil Research Station ACW, Département de recherche en Protection des végétaux grandes cultures et vigne/Viticulture et oenologie, CP 1012, CH-1260 Nyon, Switzerland, 30Korean Agricultural Culture Collection, National Academy of Agricultural Science, RDA, Suwon, 441-707, Korea, 31University of California, Davis Department of Plant Pathology Davis, CA 95616, USA, 32Landcare Research, Private Bag 92170, Auckland 1142, New Zealand, 33Eötvös Loránd University, Institute of Biology, Department of Plant Anatomy, Pázmány Péter sétány 1/c, 1117 Budapest, Hungary, 34Plant Protection Institute, Centre for Agricultural Research, Hungarian Academy of Sciences, Budapest, H-1525, Hungary, 35Science and Education, The Field Museum, 1400 S. Lake Shore Drive, Chicago, IL 60605, USA, 36University of Szeged, Faculty of Science and Informatics, Department of Microbiology, Kozep fasor 52, Szeged, H-6726, Hungary, 37Bacterial Foodborne Pathogens and Mycology Research Unit, U.S. Department of Agriculture, National Center for Agricultural Utilization Research, Agricultural Research Service, 1815 North University Street, Peoria, IL 61604, USA, 38Natural History Museum, P.O. Box 1172 Blindern, 0318 Oslo, Norway, 39Department of Biological Sciences, The University of Alabama, Tuscaloosa, AL 35487, USA, 40Plant Biology, Department of Biosciences, P.O. Box 65, 00014 University of Helsinki, Finland, 41USDA Forest Service, NRS, PO Box 1377, Luquillo, Puerto Rico, 42National Center for Genetic Engineering and Biotechnology (BIOTEC), 113 Paholyothin Road, Pathum Thani 12120 Thailand, 43Department of Medical Microbiology and Immunology, University of Wisconsin-Madison, 1550 Linden Drive, Madison, WI 53706, USA, 44Department of Natural History, Royal Ontario Museum, and Department of Ecology Evolutionary Biology, University of Toronto, Toronto, Ontario, Canada, 45Institute of Sciences of Food Production, National Research Council (CNR), Via Amendola 122/O, Bari, Italy, 46Center for Forest Mycology Research, Northern Research Station, U.S. Forest Service, One Gifford Pinchot Drive, Madison, WI 53726-2398, USA, 47Botanical Museum, Finnish Museum of Natural History, FI-00014 University of Helsinki, Finland, 48The University of North Carolina at Greensboro, Department of Chemistry and Biochemistry, 457 Sullivan Science Building, P.O. Box 26170, Greensboro, NC 27402-6170, USA, 49Université de Bourgogne, UMR1347 Agroécologie, BP 86510, F-21000 Dijon, France, 50Institute of Life Science and Biotechnology, Sungkyunkwan University,Suwon 440-746, Korea, 51Mycology and Botany Program, American Type Culture Collection (ATCC), 10801 University Blvd., Manassas, VA 20110, USA, 52Faculty of Agriculture and Life Science, Hirosaki University, 3 Bunkyo-cho, Hirosaki, Aomori 036-8561, Japan, 53Department of Biology, Brandon University, Brandon, Manitoba, Canada, 54Jena Microbial Resource Collection, Leibniz Institute for Natural Product Research and Infection Biology and University of Jena, Jena, Germany, 55Department of Natural Sciences, The University of Findlay, Findlay, OH 45840, USA, 56Institute of Evolution and Ecology, University of Tübingen, Auf der Morgenstelle 1, D-72076 Tübingen, Germany, 57Department of Biology, McMaster University, Hamilton, Ontario L8S 4K1, Canada and 58Department of Plant Biology and Pathology, Rutgers University, New Brunswick, NJ 08901, USA
                Author notes
                *Corresponding author: Tel: 301-402-1502; Fax: 301-480-2918; Email: schoch2@ 123456ncbi.nlm.nih.gov

                These authors contributed equally to this work.

                Citation details: Schoch,C.L., Robbertse,B., Robert,V. et al. Finding needles in haystacks: linking scientific names, reference specimens and molecular data for Fungi. Database (2014) Vol. 2014: article ID bau061; doi:10.1093/database/bau061

                Article
                bau061
                10.1093/database/bau061
                4075928
                24980130
                3df49d1b-7232-4fcc-ae80-b25b1dcf65cf
                Published by Oxford University Press 2013. This work is written by US Government employees and is in the public domain in the US.
                History
                : 7 April 2014
                : 19 May 2014
                : 28 May 2014
                Page count
                Pages: 21
                Categories
                Original Article

                Bioinformatics & Computational biology
                Bioinformatics & Computational biology

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