Large-scale generation and analysis of filamentous fungal DNA barcodes boosts coverage for kingdom fungi and reveals thresholds for fungal species and higher taxon delimitation

作者：Duong Vu, Marizeth Groenewald, Michèl de Vries, Thies Gehrmann, J. Benjamin Stielow, Ursula Eberhardt, Abdullah M. S. Al‐Hatmi, J.Z. Groenewald, Gianluigi Cardinali, Jos Houbraken, Teun Boekhout, P.W. Crous, Vincent Robert, G.J.M. Verkley · 发表于：Studies in Mycology · 年份：2018 · DOI：10.1016/j.simyco.2018.05.001 · 被引用次数：972 · 研究领域：Plant Pathogens and Fungal Diseases、Mycorrhizal Fungi and Plant Interactions、Yeasts and Rust Fungi Studies

Species identification lies at the heart of biodiversity studies that has in recent years favoured DNA-based approaches. Microbial Biological Resource Centres are a rich source for diverse and high-quality reference materials in microbiology, and yet the strains preserved in these biobanks have been exploited only on a limited scale to generate DNA barcodes. As part of a project funded in the Netherlands to barcode specimens of major national biobanks, sequences of two nuclear ribosomal genetic markers, the Internal Transcribed Spaces and 5.8S gene (ITS) and the D1/D2 domain of the 26S Large Subunit (LSU), were generated as DNA barcode data for ca. 100 000 fungal strains originally assigned to ca. 17 000 species in the CBS fungal biobank maintained at the Westerdijk Fungal Biodiversity Institute, Utrecht. Using more than 24 000 DNA barcode sequences of 12 000 ex-type and manually validated filamentous fungal strains of 7 300 accepted species, the optimal identity thresholds to discriminate filamentous fungal species were predicted as 99.6 % for ITS and 99.8 % for LSU. We showed that 17 % and 18 % of the species could not be discriminated by the ITS and LSU genetic markers, respectively. Among them, ∼8 % were indistinguishable using both genetic markers. ITS has been shown to outperform LSU in filamentous fungal species discrimination with a probability of correct identification of 82 % vs. 77.6 %, and a clustering quality value of 84 % vs. 77.7 %. At higher taxonomic classifi...