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Article Dans Une Revue Database - The journal of Biological Databases and Curation Année : 2014

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

Conrad L. Schoch (1, 2, 3) , Barbara Robbertse (1, 2, 3) , Vincent Robert (4) , Duong Vu (4) , Gianluigi Cardinali (5) , Laszlo Irinyi (6, 7, 8) , Wieland Meyer (6, 7, 8) , R. Henrik Nilsson (9) , Karen Hughes (10) , Andrew N. Miller (11) , Paul M. Kirk (12) , Kessy Abarenkov (13) , M. Catherine Aime (14) , Hiran A. Ariyawansa (15) , Martin Bidartondo (16, 17) , Teun Boekhout (4) , Bart Buyck (18) , Qing Cai (19) , Jie Chen (20, 21) , Ana Crespo (22) , Pedro W. Crous (4) , Ulrike Damm (23) , Z. Wilhelm de Beer (24, 25) , Bryn T. M. Dentinger (12) , Pradeep K. Divakar (22) , Margarita Duenas (26) , Nicolas Feau (27) , Katerina Fliegerova (28) , Miguel A. Garcia (29) , Zai-Wei Ge (19) , Gareth W. Griffith (30) , Johannes Z. Groenewald (4) , Marizeth Groenewald (4) , Martin Grube (31) , Marieka Gryzenhout (32) , Cecile Gueidan (33) , Liangdong Guo (34) , Sarah Hambleton (35) , Richard Hamelin (27) , Karen Hansen (36) , Valérie Hofstetter (37) , Seung-Beom Hong (38) , Jos Houbraken (4) , Kevin D. Hyde (15) , Patrik Inderbitzin (39) , Peter R. Johnston (40) , Samantha C. Karunarathna (15) , Urmas Koljalg (13) , Gabor M. Kovacs (41, 42) , Ekaphan Kraichak (43) , Krisztina Krizsan (44) , Cletus P. Kurtzman (45) , Karl-Henrik Larsson (46) , Steven Leavitt (43) , Peter M. Letcher (47) , Kare Liimatainen (48) , Jian-Kui Liu (15) , D. Jean Lodge (49) , Janet Jennifer Luangsa-Ard (50) , H. Thorsten Lumbsch (43) , Sajeewa S. N. Maharachchikumbura (15) , Dimuthu Manamgoda (15) , Maria P. Martin (26) , Andrew M. Minnis (51) , Jean-Marc Moncalvo (52, 53) , Giuseppina Mule (54) , Karen K. Nakasone (55) , Tuula Niskanen (48) , Ibai Olariaga (36) , Tamas Papp (44) , Tamas Petkovits (44) , Raquel Pino-Bodas (56) , Martha J. Powell (47) , Huzefa A. Raja (57) , Dirk Redecker (58) , J. M. Sarmiento-Ramirez (26) , Keith A. Seifert (35) , Bhushan Shrestha (59) , Soili Stenroos (56) , Benjamin Stielow (4) , Sung-Oui Suh (60) , Kazuaki Tanaka (61) , Leho Tedersoo (62) , M. Teresa Telleria (26) , Dhanushka Udayanga (15) , Wendy A. Untereiner (29) , Javier Dieguez Uribeondo (26) , Krishna V. Subbarao (63) , Csaba Vagvolgyi (44) , Cobus Visagie (4) , Kerstin Voigt (64, 65) , Donald M. Walker (66) , Bevan S. Weir (40) , Michael Weiss (67) , Nalin N. Wijayawardene (15) , Michael J. Wingfield (24, 25) , J. P. Xu (68) , Zhu L. Yang (69) , Ning Zhang (70) , Wen-Ying Zhuang (34) , Scott Federhen (1)
1 NCBI - National Center for Biotechnology Information
2 NLM
3 NIH - National Institutes of Health [Bethesda, MD, USA]
4 CBS-KNAW Fungal Biodiversity Centre
5 Department of Pharmaceutical Sciences – Microbiology
6 Molecular Mycology Research Laboratory
7 Marie Bashir Institute for Infectious Diseases and Biosecurity, Sydney Medical School-Westmead Hospital
8 The Westmead Institute for Medical Research
9 Faculty of Biological and Environmental Sciences [Helsinki]
10 Ecology and Evolutionary Biology
11 Illinois Natural History Survey
12 Mycology Section, Jodrell Laboratory
13 University of Tartu
14 Department of Botany and Plant Pathology
15 Institute of Excellence in Fungal Research and School of Science
16 Imperial College London
17 Royal Botanic Gardens
18 ISYEB - Institut de Systématique, Evolution, Biodiversité
19 CAS - Chinese Academy of Sciences [Beijing]
20 MFU - Mae Fah Luang University [Thaïlande]
21 School of Science
22 Departamento de Biologia Vegetal II, Facultad de Farmacia
23 Museum of Natural History Görlitz
24 Department of Microbiology and Plant Pathology
25 University of Pretoria [South Africa]
26 RJB - Real Jardin Botanico
27 Department of Forest and Conservation Sciences, Faculty of Forestry
28 CAS - Czech Academy of Sciences [Prague]
29 Department of Biology
30 Aberystwyth University
31 Institute of Plant Sciences
32 Department of Plant Sciences
33 Plant Industry
34 State Key Laboratory of Mycology, Institute of Microbiology
35 Biodiversity (Mycology and Microbiology)
36 Department of Botany
37 Département de recherche en Protection des végétaux grandes cultures et vigne/Viticulture et oenologie
38 Korean Agricultural Culture Collection
39 Davis Department of Plant Pathology
40 Manaaki Whenua – Landcare Research [Lincoln]
41 Institute of Biology, Department of Plant Anatomy
42 ATK NOVI - Plant Protection Institute [Budapest]
43 Science and Education
44 Department of Microbiology [Szeged]
45 Bacterial Foodborne Pathogens and Mycology Research Unit, U.S. Department of Agriculture, Agricultural Research Service
46 NHM - The Natural History Museum [London]
47 Department of Biological Sciences
48 Plant Biology, Department of Biosciences
49 Forest Service
50 Biotec - National Center for Genetic Engineering and Biotechnology
51 Department of Medical Microbiology and Immunology [Göteborg]
52 Department of Natural History
53 Department of Ecology Evolutionary Biology
54 ISPA - Institute of Sciences of Food Production
55 Northern Research Station, U.S. Forest Service
56 Botany Unit, Finnish Museum of Natural History
57 Department of Chemistry and Biochemistry
58 Agroécologie [Dijon]
59 Institute of Life Science and Biotechnology
60 Mycology and Botany Program
61 Faculty of Agriculture and Life Science
62 Natural History Museum
63 Davis Department of Plant Pathology
64 Jena Microbial Resource Collection
65 Friedrich-Schiller-Universität = Friedrich Schiller University Jena [Jena, Germany]
66 Department of Natural Sciences
67 Institute of Evolution and Ecology
68 Department of Biology
69 KIB - Kunming Institute of Botany [CAS]
70 Department of Plant Biology and Pathology
Jie Chen
  • Fonction : Auteur
  • PersonId : 761941
  • IdRef : 200253832
Marizeth Groenewald
  • Fonction : Auteur
  • PersonId : 970652
Cecile Gueidan
  • Fonction : Auteur
D. Jean Lodge
  • Fonction : Auteur
J. P. Xu
  • Fonction : Auteur
Ning Zhang

Résumé

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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Dates et versions

hal-01595064 , version 1 (26-09-2017)

Identifiants

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Conrad L. Schoch, Barbara Robbertse, Vincent Robert, Duong Vu, Gianluigi Cardinali, et al.. Finding needles in haystacks: linking scientific names, reference specimens and molecular data for Fungi. Database - The journal of Biological Databases and Curation, 2014, 21p. ⟨10.1093/database/bau061⟩. ⟨hal-01595064⟩
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