Finding needles in haystacksLinking scientific names, reference specimens and molecular data for Fungi

Authors Organisations
  • Conrad L. Schoch(Author)
    National Institutes of Health
  • Barbara Robbertse(Author)
    National Institutes of Health
  • Vincent Robert(Author)
    Centralbureau voor Schimmelcultures Fungal Centre (CBS-KNAW)
  • Duong Vu(Author)
    Centralbureau voor Schimmelcultures Fungal Centre (CBS-KNAW)
  • Gianluigi Cardinali(Author)
    Università degli Studi, Perugia
  • Laszlo Irinyi(Author)
    University of Sydney
  • Wieland Meyer(Author)
    University of Sydney
  • R. Henrik Nilsson(Author)
    University of Gothenburg
  • Karen W. Hughes(Author)
    University of Tennessee, Knoxville
  • Andrew N. Miller(Author)
    University of Illinois at Urbana-Champaign
  • Paul M. Kirk(Author)
    Royal Botanic Gardens, Kew
  • Kessy Abarenkov(Author)
    University of Tartu
  • M. Catherine Aime(Author)
    Purdue University
  • Hiran A. Ariyawansa(Author)
    Mae Fah Luang University
  • Martin. Bidartondo(Author)
    Imperial College London
  • Ten Boekhout(Author)
    Centralbureau voor Schimmelcultures Fungal Centre (CBS-KNAW)
  • B Buyck(Author)
    Natural Museum of Natural History (France)
  • Qing Cai(Author)
    Chinese Academy of Sciences
  • Jie Chen(Author)
    Mae Fah Luang University
  • Ana Crespo(Author)
    Complutense University of Madrid
  • Pedro W Crous(Author)
    Centralbureau voor Schimmelcultures Fungal Centre (CBS-KNAW)
  • Ulrike Damm(Author)
    Senckenberg Museum of Natural History Görlitz
  • Z. Wilhelm de Beer(Author)
    University of Pretoria
  • Bryn Dentinger(Author)
    Royal Botanic Gardens, Kew
  • Pradeep K. Divakar(Author)
    Complutense University of Madrid
  • Margarita Duenas(Author)
    University of Pretoria
  • Nicolas Geau(Author)
    University of British Columbia
  • Katerina Fliegerova(Author)
    Czech Academy of Sciences
  • Miguel A. Garcia(Author)
    University of Toronto
  • Zai-Wei Ge(Author)
    Chinese Academy of Sciences
  • Gareth Griffith(Author)
  • Johannes Z Groenewald(Author)
    Centralbureau voor Schimmelcultures Fungal Centre (CBS-KNAW)
  • Marizeth Groenewald(Author)
    Centralbureau voor Schimmelcultures Fungal Centre (CBS-KNAW)
  • Martin Grube(Author)
    University of Graz
  • Marieka Gryzenhout(Author)
    University of the Free State
  • Cécile Gueidan(Author)
    Commonwealth Scientific and Industrial Research Organisation (CSIRO), Australia
  • Liangdong Guo(Author)
    Chinese Academy of Sciences
  • Sarah Hambleton(Author)
    Agriculture and Agri-Food Canada
  • Richard Hamelin(Author)
    University of British Columbia
  • Karen Hansen(Author)
    Swedish Museum of Natural History
  • Valérie Hofstetter(Author)
    Agroscope
  • Seung-Beom Hong(Author)
    National Academy of Agricultural Science, Korea
  • Jos Houbraken(Author)
    Centralbureau voor Schimmelcultures Fungal Centre (CBS-KNAW)
  • Kevin D. Hyde(Author)
    Mae Fah Luang University
  • Patrik Inderbitzin(Author)
    University of California, Davis
  • Peter R Johnston(Author)
    Landcare Research
  • Samantha C. Karunarathna(Author)
    Mae Fah Luang University
  • Urmas Koljalg(Author)
    University of Tartu
  • Gabor M. Kovacs(Author)
    Eötvös Loránd University
    Plant Protection Institute of the Hungarian Academy of Sciences
  • Ekaphan Kraichak(Author)
    The Field Museum of Natural History
  • Krisztina Krizsan(Author)
    University of Szeged
  • Cletus P. Kurtzman(Author)
    National Center for Agricultural Utilization Research
  • Karl-Henrik Larsson(Author)
    Natural History Museum at the University of Oslo
  • Steven Leavitt(Author)
    The Field Museum of Natural History
  • Peter M. Letcher(Author)
    University of Alabama
  • Kare Liimatainen(Author)
    University of Helsinki
  • Jian-Kui Liu(Author)
    Mae Fah Luang University
  • Jean D. Lodge(Author)
    USDA, Puerto Rico
  • Janet J. Luangsa-Ard(Author)
    Thai National Center for Genetic Engineering and Biotechnology
  • H Thorsten Lumbsch(Author)
    The Field Museum of Natural History
  • Sajeewa S. N. Maharachchikumbura(Author)
    Mae Fah Luang University
  • Dimuthu Manamgoda(Author)
    Mae Fah Luang University
  • María P. Martín(Author)
    Royal Botanical Garden of Madrid
  • Andrew M. Minnis(Author)
    USDA-Forest Service
  • Jean-Marc Moncalvo(Author)
    Royal Ontario Museum
  • Giuseppina Mulè(Author)
    Italian National Research Council
  • Karen K. Nakasone(Author)
    American Center for Forest Mycology Research
  • Tuula Niskanen(Author)
    University of Helsinki
  • Ibai Olariaga(Author)
    Swedish Museum of Natural History
  • Tamás Papp(Author)
    University of Szeged
  • Tamás Petkovits(Author)
    University of Szeged
  • Raquel Pino-Bodas(Author)
    Finnish Museum of Natural History
  • Martha J. Powell(Author)
    University of Alabama
  • Huzefa A. Raja(Author)
    University of North Carolina at Greensboro
  • Dirk Redecker(Author)
    Université de Bourgogne
  • J.M. Sarmiento-Ramirez(Author)
    Royal Botanical Garden of Madrid
  • Keith A. Seifert(Author)
    Agriculture and Agri-Food Canada
  • Bhushan Shrestha(Author)
    Sungkyunkwan University
  • Soili Stenroos(Author)
    Finnish Museum of Natural History
  • Benjamin Stielow(Author)
    Centralbureau voor Schimmelcultures Fungal Centre (CBS-KNAW)
  • Sung-Oui Suh(Author)
    American Type Culture Collection
  • Kazuaki Tanaka(Author)
    Hirosaki University
  • Leho Tedersoo(Author)
    University of Tartu
  • M. Teresa Telleria(Author)
    Royal Botanical Garden of Madrid
  • Dhanushka Udayanga(Author)
    Mae Fah Luang University
  • Wendy A. Untereiner(Author)
    Brandon University
  • Javier Dieguez-Uribeondo(Author)
    Royal Botanical Garden of Madrid
  • Krishna V. Subbarao(Author)
    University of California, Davis
  • Csaba Vágvölgyi36(Author)
    University of Szeged
  • Johann Visagie(Author)
    Centralbureau voor Schimmelcultures Fungal Centre (CBS-KNAW)
  • Kerstin Voigt(Author)
    Friedrich Schiller University
  • Donald M. Walker(Author)
    The University of Findlay
  • Bevan S. Weir(Author)
    Landcare Research
  • Michael Weiß(Author)
    University of Tübingen
  • Nalin N. Wijayawardene(Author)
    Mae Fah Luang University
  • Michael J Wingfield(Author)
    University of Pretoria
  • J. P. Xu(Author)
    McMaster University
  • Yang Zhu L.(Author)
    Chinese Academy of Sciences
  • Ning Zhang(Author)
    Rutgers University
  • Wen-Ying Zhuang(Author)
    Chinese Academy of Sciences
  • Scott Federhen(Author)
    National Institutes of Health
Type Article
Original languageEnglish
Pages (from-to)1-21
Number of pages21
JournalDatabase: The Journal of Biological Databases and Curation
Issue number2014
Early online date28 May 2014
DOI
Publication statusPublished - 28 May 2014
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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