Finding needles in haystacks : linking scientific names, reference specimens and molecular data for Fungi
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Date
Authors
Schoch, Conrad L.
Robbertse, Barbara
Robert, Vincent A.
Vu, Duong
Cardinali, Gianluigi
Irinyi, Laszlo
Meyer, Wieland
Nilsson, R. Henrik
Hughes, Karen
Miller, Andrew N.
Journal Title
Journal ISSN
Volume Title
Publisher
Oxford University Press
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.
Description
Keywords
Sequences, Deoxyribonucleic acid (DNA), Scientific names, Reference specimens, Molecular data, Fungi, DNA sequence data, Taxonomic names, Specimen data
Sustainable Development Goals
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.