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 Hughes, Andrew N. Miller, Paul M. Kirk, Kessy Abarenkov, M. Catherine Aime, Hiran A. Ariyawansa, Martin Bidartondo, Teun Boekhout, Bart Buyck, Qing Cai, Jie Chen, Ana CrespoPedro W. Crous, Ulrike Damm, Z. Wilhelm De Beer, Bryn T.M. Dentinger, Pradeep K. Divakar, Margarita Dueñas, Nicolas Feau, Katerina Fliegerova, Miguel A. García, Zai Wei Ge, Gareth W. 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 Kõljalg, Gábor M. Kovács, Ekaphan Kraichak, Krisztina Krizsan, Cletus P. Kurtzman, Karl Henrik Larsson, Steven Leavitt, Peter M. Letcher, Kare Liimatainen, Jian Kui Liu, D. Jean Lodge, Janet Jennifer 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 Diéguez Uribeondo, Krishna V. Subbarao, Csaba Vágvölgyi, Cobus Visagie, Kerstin Voigt, Donald M. Walker, Bevan S. Weir, Michael Weiß, Nalin N. Wijayawardene, Michael J. Wingfield, J. P. Xu, Zhu L. Yang, Ning Zhang, Wen Ying Zhuang, Scott Federhen

Research output: Contribution to journalArticle

139 Citations (Scopus)

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.

Original languageEnglish
Article numberbau061
JournalDatabase
Volume2014
DOIs
Publication statusPublished - Jan 1 2014

    Fingerprint

ASJC Scopus subject areas

  • Information Systems
  • Biochemistry, Genetics and Molecular Biology(all)
  • Agricultural and Biological Sciences(all)

Cite this

Schoch, C. L., Robbertse, B., Robert, V., Vu, D., Cardinali, G., Irinyi, L., Meyer, W., Nilsson, R. H., Hughes, K., Miller, A. N., Kirk, P. M., Abarenkov, K., Aime, M. C., Ariyawansa, H. A., Bidartondo, M., Boekhout, T., Buyck, B., Cai, Q., Chen, J., ... Federhen, S. (2014). Finding needles in haystacks: Linking scientific names, reference specimens and molecular data for Fungi. Database, 2014, [bau061]. https://doi.org/10.1093/database/bau061