Research and Publications - Department of Biological Sciences

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Browsing Research and Publications - Department of Biological Sciences by Author "AgroSup Dijon"

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    Finding needles in haystacks: linking scientific names, reference specimens and molecular data for Fungi
    (Oxford University Press, 2014) Schoch, Conrad L.; Robbertse, Barbara; Robert, Vincent; Duong Vu; Cardinali, Gianluigi; Irinyi, Laszlo; Meyer, Wieland; Nilsson, R. Henrik; Hughes, Karen; Miller, Andrew N.; Kirk, Paul M.; Abarenkov, Kessy; Aime, M. Catherine; Ariyawansa, Hiran A.; Bidartondo, Martin; Boekhout, Teun; Buyck, Bart; Cai, Qing; Chen, Jie; Crespo, Ana; Crous, Pedro W.; Damm, Ulrike; De Beer, Z. Wilhelm; Dentinger, Bryn T. M.; Divakar, Pradeep K.; Duenas, Margarita; Feau, Nicolas; Fliegerova, Katerina; Garcia, Miguel A.; Ge, Zai-Wei; Griffith, GarethW.; Groenewald, Johannes Z.; Groenewald, Marizeth; Grube, Martin; Gryzenhout, Marieka; Gueidan, Cecile; Guo, Liangdong; Hambleton, Sarah; Hamelin, Richard; Hansen, Karen; Hofstetter, Valerie; Hong, Seung-Beom; Houbraken, Jos; Hyde, Kevin D.; Inderbitzin, Patrik; Johnston, Peter R.; Karunarathna, Samantha C.; Koljalg, Urmas; Kovacs, Gabor M.; Kraichak, Ekaphan; Krizsan, Krisztina; Kurtzman, Cletus P.; Larsson, Karl-Henrik; Leavitt, Steven; Letcher, Peter M.; Liimatainen, Kare; Liu, Jian-Kui; Lodge, D. Jean; Luangsa-ard, Janet Jennifer; Lumbsch, H. Thorsten; Maharachchikumbura, Sajeewa S. N.; Manamgoda, Dimuthu; Martin, Maria P.; Minnis, Andrew M.; Moncalvo, Jean-Marc; Mule, Giuseppina; Nakasone, Karen K.; Niskanen, Tuula; Olariaga, Ibai; Papp, Tamas; Petkovits, Tamas; Pino-Bodas, Raquel; Powell, Martha J.; Raja, Huzefa A.; Redecker, Dirk; Sarmiento-Ramirez, J. M.; Seifert, Keith A.; Shrestha, Bhushan; Stenroos, Soili; Stielow, Benjamin; Suh, Sung-Oui; Tanaka, Kazuaki; Tedersoo, Leho; Teresa Telleria, M.; Udayanga, Dhanushka; Untereiner, Wendy A.; Dieguez Uribeondo, Javier; Subbarao, Krishna V.; Vagvoelgyi, Csaba; Visagie, Cobus; Voigt, Kerstin; Walker, Donald M.; Weir, Bevan S.; Weiss, Michael; Wijayawardene, Nalin N.; Wingfield, Michael J.; Xu, J. P.; Yang, Zhu L.; Zhang, Ning; Zhuang, Wen-Ying; Federhen, Scott; National Institutes of Health (NIH) - USA; NIH National Library of Medicine (NLM); Royal Netherlands Academy of Arts & Sciences; Westerdijk Fungal Biodiversity Institute (KNAW); University of Perugia; University of Sydney; Westmead Institute for Medical Research; University of Gothenburg; University of Tennessee Knoxville; Illinois Natural History Survey; University of Illinois Urbana-Champaign; Royal Botanic Gardens, Kew; University of Tartu; Purdue University West Lafayette Campus; Purdue University; Mae Fah Luang University; Imperial College London; UDICE-French Research Universities; Sorbonne Universite; Centre National de la Recherche Scientifique (CNRS); CNRS - Institute of Ecology & Environment (INEE); Museum National d'Histoire Naturelle (MNHN); Chinese Academy of Sciences; Kunming Institute of Botany, CAS; Complutense University of Madrid; Senckenberg Gesellschaft fur Naturforschung (SGN); University of Pretoria; Consejo Superior de Investigaciones Cientificas (CSIC); CSIC - Real Jardin Botanico de Madrid; University of British Columbia; Czech Academy of Sciences; Institute of Animal Physiology & Genetics of the Czech Academy of Sciences; University of Toronto; University Toronto Mississauga; Aberystwyth University; UK Research & Innovation (UKRI); Biotechnology and Biological Sciences Research Council (BBSRC); Institute of Biological, Environmental, Rural & Sciences (IBERS); University of Graz; University of the Free State; Commonwealth Scientific & Industrial Research Organisation (CSIRO); Institute of Microbiology, CAS; Agriculture & Agri Food Canada; Swedish Museum of Natural History; Swiss Federal Research Station Agroscope; Rural Development Administration (RDA), Republic of Korea; University of California Davis; Landcare Research - New Zealand; Eotvos Lorand University; Eotvos Lorand Research Network; Hungarian Academy of Sciences; Hungarian Centre for Agricultural Research; Field Museum of Natural History (Chicago); Szeged University; United States Department of Agriculture (USDA); University of Alabama Tuscaloosa; University of Helsinki; United States Forest Service; National Science & Technology Development Agency - Thailand; National Center Genetic Engineering & Biotechnology (BIOTEC); University of Wisconsin Madison; Royal Ontario Museum; Consiglio Nazionale delle Ricerche (CNR); Istituto Scienze delle Produzioni Alimentari (ISPA-CNR); University of North Carolina; University of North Carolina Greensboro; Universite de Bourgogne; Institut Agro; AgroSup Dijon; Sungkyunkwan University (SKKU); Hirosaki University; Brandon University; Hans Knoll Institute (HKI); Friedrich Schiller University of Jena; University of Findlay; Eberhard Karls University of Tubingen; McMaster University; Rutgers State University New Brunswick
    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.