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Finding needles in haystacks: linking scientific names, reference specimens and molecular data for Fungi
Conrad L Schoch1, Barbara Robbertse1, Vincent Robert1
1National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, Maryland, USA, CBS-KNAW Fungal Biodiversity Centre, P.O. Box 85167, 3508 AD Utrecht, The Netherlands, Department of Pharmaceutical Sciences - Microbiology, Università degli Studi di Perugia, Perugia, Italy, Molecular Mycology Research Laboratory, Centre for Infectious Diseases and Microbiology, Marie Bashir Institute for Infectious Diseases and Biosecurity, Sydney Medical School-Westmead Hospital, The University of Sydney, Westmead Millennium Institute, Westmead, Australia, Department of Biological and Environmental Sciences, University of Gothenburg, Box 461, 405 30 Göteborg, Sweden, Ecology and Evolutionary Biology, University of Tennessee, Knoxville, TN 37920, USA, Illinois Natural History Survey, University of Illinois, 1816 South Oak Street, Champaign, IL 61820, USA, Mycology Section, Jodrell Laboratory, Royal Botanic Gardens, Kew, Richmond, Surrey, TW9 3DS, UK, Natural History Museum, University of Tartu, 46 Vanemuise, 51014 Tartu, Estonia, Purdue University, Department of Botany and Plant Pathology, 915 W. State Street, West Lafayette, IN 47907, USA, Institute of Excellence in Fungal Research, and School of Science, Mae Fah Luang University, Chiang Rai 57100, Thailand, Imperial College London, Royal Botanic Gardens, Kew TW9 3DS, England, UK, Muséum National d'Histoire Naturelle, Dépt. Systématique et Evolution CP39, UMR7205, 12 Rue Buffon, F-75005 Paris, France, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, Yunnan, P. R. China, Departamento de Biología Vegetal II, Facultad de Farmacia, Universidad Complutense de Madrid, Madrid 28040, Spain, Senckenberg Museum of Natural History Görlitz, PF 300 154, 02806 Görlitz, Germany, Department of Microbiology and Plant Pathology, Forestry Agricultural Biotechnology Institute (FABI), University of Pretoria, Pretoria 0001, South Africa, Real Jardín Botánico, RJB-CSIC,
Accurate DNA sequencing is crucial for fungal diversity. This study re-annotates fungal reference sequences, improving species identification in molecular ecology and microbiome projects.
Area of Science:
- Mycology
- Molecular Biology
- Bioinformatics
Background:
- Morphological identification often underestimates fungal diversity.
- Accurate DNA sequence data with correct taxonomic and specimen annotations is essential.
- High-throughput sequencing in molecular ecology and microbiome studies necessitates efficient species assignment methods.
Purpose of the Study:
- To select and re-annotate marker reference sequences for all accepted fungal orders.
- To improve the quality and accessibility of fungal DNA sequence data.
- To establish standards for fungal sequence data quality.
Main Methods:
- Focus on internal transcribed spacer (ITS) sequences from type specimens or ex-type cultures.
- Re-annotation and verification of sequences.
- Deposit of curated sequences in the NCBI RefSeq Targeted Loci (RTL) database.
Main Results:
- A curated set of re-annotated fungal reference sequences is now publicly available.
- Sequences are accessible via the NCBI RTL database with NR_prefixed accession numbers.
- Proposed standards and protocols aim to enhance new sequence data quality.
Conclusions:
- Improved fungal reference sequences enhance species identification accuracy.
- Standardized protocols will benefit future fungal biodiversity and microbiome research.
- Accessible, high-quality data is vital for advancing mycology.
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