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

Journal article
Authors 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 Crespo
Pedro 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 Luangsaard
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
Published in Database: The Journal of Biological Databases and Curation
Volume 2014
Issue bau061
Pages 1-21
ISSN 1758-0463
Publication year 2014
Published at Department of Biological and Environmental Sciences
Pages 1-21
Language en
Links dx.doi.org/10.1093/database/bau061
https://gup.ub.gu.se/file/136248
Subject categories Databases, Data processing, Information processing, Microbiology, Botany, Bioinformatics and Systems Biology, Terrestrial ecology, Biological Systematics, Medical microbiology, Soil biology

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.

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