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

Conrad L. Schoch, Barbara Robbertse, Vincent Robert, Duong Vu, Gianluigi Cardinali, Laszlo Irinyi, Wieland Meyer, R. Henrik Nilsson, Karen W. Hughes, Andrew N. Miller, Paul M. Kirk, Kessy Abarenkov, M. Catherine Aime, Hiran A. Ariyawansa, Martin. Bidartondo, Ten Boekhout, B Buyck, Qing Cai, Jie Chen, Ana CrespoPedro W Crous, Ulrike Damm, Z. Wilhelm de Beer, Bryn T. M. Dentinger, Pradeep K. Divakar, Margarita Duenas, Nicolas Geau, Katerina Fliegerova, Miguel A. Garcia, Zai-Wei Ge, Gareth Wyn Griffith, Johannes Z Groenewald, Marizeth Groenewald, Martin Grube, Marieka Gryzenhout, Cécile Gueidan, Liangdong Guo, Sarah Hambleton, Richard Hamelin, Karen Hansen, Valérie Hofstetter, Seung-Beom Hong, Jos Houbraken, Kevin D. Hyde, Patrik Inderbitzin, Peter R Johnston, Samantha C. Karunarathna, Urmas Koljalg, Gabor M. Kovacs, Ekaphan Kraichak, Krisztina Krizsan, Cletus P. Kurtzman, Karl-Henrik Larsson, Steven Leavitt, Peter M. Letcher, Kare Liimatainen, Jian-Kui Liu, Jean D. Lodge, Janet J. Luangsa-Ard, H Thorsten Lumbsch, Sajeewa S. N. Maharachchikumbura, Dimuthu Manamgoda, María P. Martín, Andrew M. Minnis, Jean-Marc Moncalvo, Giuseppina Mulè, Karen K. Nakasone, Tuula Niskanen, Ibai Olariaga, Tamás Papp, Tamás Petkovits, Raquel Pino-Bodas, Martha J. Powell, Huzefa A. Raja, Dirk Redecker, J.M. Sarmiento-Ramirez, Keith A. Seifert, Bhushan Shrestha, Soili Stenroos, Benjamin Stielow, Sung-Oui Suh, Kazuaki Tanaka, Leho Tedersoo, M. Teresa Telleria, Dhanushka Udayanga, Wendy A. Untereiner, Javier Dieguez-Uribeondo, Krishna V. Subbarao, Csaba Vágvölgyi36, Johann Visagie, Kerstin Voigt, Donald M. Walker, Bevan S. Weir, Michael Weiß, Nalin N. Wijayawardene, Michael J Wingfield, J. P. Xu, Yang Zhu L., Ning Zhang, Wen-Ying Zhuang, Scott Federhen

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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
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
DOIs
Publication statusPublished - 28 May 2014

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