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
- László Irinyi
- Wieland Meyer
- R. Henrik Nilsson
- Karen Woodbury Hughes
- Andrew Nicholas Miller
- Paul M. Kirk
- Kessy Abarenkov
- M. Catherine Aime
- Hiran Anjana Ariyawansa
- Martin I. Bidartondo
- T. Boekhout
- Bart Buyck
- Qing Cai
- Jie Chen
- Ana Crespo
- Pedro Willem Crous
- Ulrike Damm
- Z. Wilhelm de Beer
- Bryn T. M. Dentinger
- Pradeep Kumar Divakar
- Margarita Dueñas
- Nicolas Feau
- Katerina Olsa Fliegerova
- Miguel A. Garcı́a
- Zhenyu Ge
- Gareth Wyn Griffith
- J.Z. Groenewald
- Marizeth Groenewald
- M. Grube
- Marieka Gryzenhout
- C. Gueidan
- Liang‐Dong Guo
- Sarah Hambleton
- Richard C. Hamelin
- K. Hansen
- Valérie Hofstetter
- Seung‐Beom Hong
- Jos A. M. P. Houbraken
- Kevin D. Hyde
- Patrik Inderbitzin
- Peter R. Johnston
- SKSamantha C. Karunarathna
- Urmas Kõljalg
- Gábor M. Kovács
- Ekaphan Kraichak
- Krisztina Krizsán
- Cletus P. Kurtzman
- Karl‐Henrik Larsson
- S. Leavitt
- Peter M. Letcher
- Kare Liimatainen
- Jian‐Kui Liu
- D. J. Lodge
- Janet Jennifer Luangsa-ard
- Helge Thorsten Lumbsch
- Sajeewa S. N. Maharachchikumbura
- Dimuthu S. Manamgoda
- María Paz 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
- Jullie M. Sarmiento-Ramírez
- Keith A. Seifert
- Bhushan Shrestha
- Soili Stenroos
- J. Benjamin Stielow
- Sung‐Oui Suh
- Kazuaki Tanaka
- Leho Tedersoo
- M. T. Telleria
- Dhanushka Udayanga
- Wendy A. Untereiner
- Javier Diéguez‐Uribeondo
- Krishna V. Subbarao
- Csaba Vágvölgyi
- Cobus M. Visagie
- Kerstin Voigt
- D. M. Walker
- Bevan Simon Weir
- M. Weiss
- Nalin N. Wijayawardene
- Michael J. Wingfield
- J. P. Xu
- Zuoren Yang
- Ning Zhang
- Wen-Ying Zhuang
Database · 2014 · University of Oxford
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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. Database URL: http://www.ncbi.nlm.nih.gov/bioproject/PRJNA177353.