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

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dc.contributor.author Schoch, Conrad L.
dc.contributor.author Robbertse, Barbara
dc.contributor.author Robert, Vincent A.
dc.contributor.author Vu, Duong
dc.contributor.author Cardinali, Gianluigi
dc.contributor.author Irinyi, Laszlo
dc.contributor.author Meyer, Wieland
dc.contributor.author Nilsson, R. Henrik
dc.contributor.author Hughes, Karen
dc.contributor.author Miller, Andrew N.
dc.contributor.author Kirk, Paul M.
dc.contributor.author Abarenkov, Kessy
dc.contributor.author Aime, M. Catherine
dc.contributor.author Ariyawansa, Hiran A.
dc.contributor.author Bidartondo, Martin
dc.contributor.author Boekhout, Teun
dc.contributor.author Buyck, Bart
dc.contributor.author Cai, Qing
dc.contributor.author Chen, Jie
dc.contributor.author Crespo, Ana
dc.contributor.author Crous, Pedro W.
dc.contributor.author Damm, Ulrike
dc.contributor.author De Beer, Z. Wilhelm
dc.contributor.author Dentinger, Bryn T.M.
dc.contributor.author Divakar, Pradeep K.
dc.contributor.author Duenas, Margarita
dc.contributor.author Feau, Nicolas
dc.contributor.author Fliegerova, Katerina
dc.contributor.author Garcıa, Miguel A.
dc.contributor.author Ge, Zai-Wei
dc.contributor.author Griffith, Gareth W.
dc.contributor.author Groenewald, Johannes Z.
dc.contributor.author Groenewald, Marizeth
dc.contributor.author Grube, Martin
dc.contributor.author Gryzenhout, Marieka
dc.contributor.author Gueidan, Cecile
dc.contributor.author Guo, Liangdong
dc.contributor.author Hambleton, Sarah
dc.contributor.author Hamelin, Richard
dc.contributor.author Hansen, Karen
dc.contributor.author Hofstetter, Valerie
dc.contributor.author Hong, Seung-Beom
dc.contributor.author Houbraken, Jos
dc.contributor.author Hyde, Kevin D.
dc.contributor.author Inderbitzin, Patrik
dc.contributor.author Johnston, Peter R.
dc.contributor.author Karunarathna, Samantha C.
dc.contributor.author Koljalg, Urmas
dc.contributor.author Kovacs, Gabor M.
dc.contributor.author Kraichak, Ekaphan
dc.contributor.author Krizsan, Krisztina
dc.contributor.author Kurtzman, Cletus P.
dc.contributor.author Larsson, Karl-Henrik
dc.contributor.author Leavitt, Steven
dc.contributor.author Letcher, Peter M.
dc.contributor.author Liimatainen, Kare
dc.contributor.author Liu, Jian-Kui
dc.contributor.author Lodge, Jean
dc.contributor.author Luangsa-ard, Janet Jennifer
dc.contributor.author Lumbsch, H. Thorsten
dc.contributor.author Maharachchikumbura, Sajeewa S.N.
dc.contributor.author Manamgoda, Dimuthu
dc.contributor.author Martın, Marıa P.
dc.contributor.author Minnis, Andrew M.
dc.contributor.author Moncalvo, Jean-Marc
dc.contributor.author Mule, Giuseppina
dc.contributor.author Nakasone, Karen K.
dc.contributor.author Niskanen, Tuula
dc.contributor.author Olariaga, Ibai
dc.contributor.author Papp, Tamas
dc.contributor.author Petkovits, Tamas
dc.contributor.author Pino-Bodas, Raquel
dc.contributor.author Powell, Martha J.
dc.contributor.author Raja, Huzefa A.
dc.contributor.author Redecker, Dirk
dc.contributor.author Sarmiento-Ramirez, J.M.
dc.contributor.author Seifert, Keith A.
dc.contributor.author Shrestha, Bhushan
dc.contributor.author Stenroos, Soili
dc.contributor.author Stielow, Benjamin
dc.contributor.author Suh, Sung-Oui
dc.contributor.author Tanaka, Kazuaki
dc.contributor.author Tedersoo, Leho
dc.contributor.author Telleria, M. Teresa
dc.contributor.author Udayanga, Dhanushka
dc.contributor.author Untereiner, Wendy A.
dc.contributor.author Uribeondo, Javier Dieguez
dc.contributor.author Subbarao, Krishna V.
dc.contributor.author Vagvolgyi, Csaba
dc.contributor.author Visagie, Cobus
dc.contributor.author Voigt, Kerstin
dc.contributor.author Walker, Donald M.
dc.contributor.author Weir, Bevan S.
dc.contributor.author Weiß, Michael
dc.contributor.author Wijayawardene, Nalin N.
dc.contributor.author Wingfield, Michael J.
dc.contributor.author Xu, J.P.
dc.contributor.author Yang, Zhu L.
dc.contributor.author Zhang, Ning
dc.contributor.author Zhuang, Wen-Ying
dc.contributor.author Federhen, Scott
dc.date.accessioned 2014-09-23T06:00:52Z
dc.date.available 2014-09-23T06:00:52Z
dc.date.issued 2014
dc.description.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. Reannotated 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. en_US
dc.description.librarian am2014 en_US
dc.description.sponsorship The Intramural Research Programs of the National Center for Biotechnology Information, National Library of Medicine and the National Human Genome Research Institute, both at the National Institutes of Health. en_US
dc.description.uri http://www.ncbi.nlm.nih.gov/bioproject/PRJNA177353 en_US
dc.identifier.citation 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. en_US
dc.identifier.issn 1758-0463 (print)
dc.identifier.issn 1758-0463 (online)
dc.identifier.other 10.1093/database/bau061
dc.identifier.uri http://hdl.handle.net/2263/42065
dc.language.iso en en_US
dc.publisher Oxford University Press en_US
dc.rights Published by Oxford University Press 2013 en_US
dc.subject Sequences en_US
dc.subject Deoxyribonucleic acid (DNA) en_US
dc.subject Scientific names en_US
dc.subject Reference specimens en_US
dc.subject Molecular data en_US
dc.subject Fungi en_US
dc.subject DNA sequence data en_US
dc.subject Taxonomic names en_US
dc.subject Specimen data en_US
dc.title Finding needles in haystacks : linking scientific names, reference specimens and molecular data for Fungi en_US
dc.type Article en_US


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