ArticleJournal of fungi (Basel, Switzerland)2020
Towards Genomic Criteria for Delineating Fungal Species.
Article in Journal of fungi (Basel, Switzerland), 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 26 papers.
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Who cites it
26 citing papers in PubMed.
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- Two novel entomopathogenic fungal species of Lecanicillium isolated from soil in China.BMC microbiology · 2025Article
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- An integrative taxonomy approach reveals Saccharomyces chiloensis sp. nov. as a newly discovered species from Coastal Patagonia.PLoS genetics · 2024Article
- Isolation, genome analysis and tissue localization of Ceratobasidium theobromae, a new encounter pathogen of cassava in Southeast Asia.Scientific reports · 2024Article
- Molecular Diagnostics for Invasive Fungal Diseases: Current and Future Approaches.Journal of fungi (Basel, Switzerland) · 2024Review
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- Genomic sketching with multiplicities and locality-sensitive hashing using Dashing 2.Genome research · 2023Article
- Characterization of metagenome-assembled genomes from the International Space Station.Microbiome · 2023Article
- Genome sequencing and annotation of3 Biotech · 2023Article
- The challenges of the genome-based identification of antifungal resistance in the clinical routine.Frontiers in microbiology · 2023Article
- A Mineral-Doped Micromodel Platform Demonstrates Fungal Bridging of Carbon Hot Spots and Hyphal Transport of Mineral-Derived Nutrients.mSystems · 2022Article
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Abstract
The discussion of fungal species delineation has yet to reach a consensus, despite the advancements in technology, which helped modernise traditional approaches. In particular, the phylogenetic species concept was one of the tools that has been used with considerable success across the fungal kingdom. The fast rise of fungal genomics provides an unprecedented opportunity to expand measuring the relatedness of fungal strains to the level of whole genomes. However, the use of genomic information in taxonomy has only just begun, and few methodological guidelines have been suggested so far. Here, a simple approach of computationally measuring genomic distances and their use as a standard for species delineation is investigated. A fixed threshold genomic distance calculated by the quick and easy-to-use tools Mash and Dashing proved to be an unexpectedly widely applicable and robust criterion for determining whether two genomes belong to the same or to different species. The accuracy of species delineation in an uncurated dataset of GenBank fungal genomes was close to 90%-and exceeded 90% with minimal curation. As expected, the discriminative power of this approach was lower at higher taxonomic ranks, but still significantly larger than zero. Simple instructions for calculation of a genomic distance between two genomes and species similarity thresholds at different k-mer sizes are suggested. The calculation of genomic distance is identified as a powerful approach for delineating fungal species and is proposed-not as the only criterion-but as an additional tool in the versatile toolbox of fungal taxonomy.
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