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

Show simple item record Schoch, Conrad L. Robbertse, Barbara Robert, Vincent A. Vu, Duong 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 Garcıa, Miguel A. Ge, Zai-Wei Griffith, Gareth W. 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, Jean Luangsa-ard, Janet Jennifer Lumbsch, H. Thorsten Maharachchikumbura, Sajeewa S.N. Manamgoda, Dimuthu Martın, Marıa 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 Telleria, M. Teresa Udayanga, Dhanushka Untereiner, Wendy A. Uribeondo, Javier Dieguez Subbarao, Krishna V. Vagvolgyi, 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 2014-09-23T06:00:52Z 2014-09-23T06:00:52Z 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 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.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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