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

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.

Keywords

Affiliated Institutions

• Westmead Institute for Medical Research AU
• Institute of Plant Biology HU
• Flagstaff Medical Center US
• Agricultural Research Service US
• University of California, Los Angeles US
• Agroécologie FR
• Friedrich Schiller University Jena DE
• Plant Industry AU
• Ollscoil na Gaillimhe – University of Galway IE
• Northern Research Station US
• Czech Academy of Sciences CZ
• Applied Natural Sciences US
• Real Jardín Botánico ES
• Institute of Sciences of Food Production IT
• Science Education Solutions (United States) US
• US Forest Service US
• Senckenberg Museum für Naturkunde Görlitz DE
• National Institutes of Health US
• Chinese Academy of Sciences CN
• Kolon Life Science (South Korea) KR
• University of Pretoria ZA
• Mae Fah Luang University TH
• United States Department of Agriculture US
• National Center for Genetic Engineering and Biotechnology TH
• Kunming Institute of Botany CN
• Alberta Biodiversity Monitoring Institute CA
• Imperial College London GB
• University of Helsinki FI
• Université de Bourgogne FR
• Aberystwyth University GB
• Evolutionary Genomics (United States) US
• Institute of Microbiology CN
• Westmead Hospital AU
• University of Tartu EE
• Finnish Museum of Natural History FI
• Natural History Museum GB
• PHARM (Italy) IT
• Manaaki Whenua – Landcare Research NZ
• Institut de Systématique, Évolution, Biodiversité FR
• University of Szeged HU
• Plant (United States) US
• National Center for Biotechnology Information US
• Plant Protection Institute HU

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