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Towards Genomic Criteria for Delineating Fungal Species

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 kingdo...

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Autor principal: Gostinčar, Cene
Formato: Online Artículo Texto
Lenguaje:English
Publicado: MDPI 2020
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7711752/
https://www.ncbi.nlm.nih.gov/pubmed/33114441
http://dx.doi.org/10.3390/jof6040246
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author Gostinčar, Cene
author_facet Gostinčar, Cene
author_sort Gostinčar, Cene
collection PubMed
description 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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spelling pubmed-77117522020-12-04 Towards Genomic Criteria for Delineating Fungal Species Gostinčar, Cene J Fungi (Basel) Article 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. MDPI 2020-10-24 /pmc/articles/PMC7711752/ /pubmed/33114441 http://dx.doi.org/10.3390/jof6040246 Text en © 2020 by the author. Licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY) license (http://creativecommons.org/licenses/by/4.0/).
spellingShingle Article
Gostinčar, Cene
Towards Genomic Criteria for Delineating Fungal Species
title Towards Genomic Criteria for Delineating Fungal Species
title_full Towards Genomic Criteria for Delineating Fungal Species
title_fullStr Towards Genomic Criteria for Delineating Fungal Species
title_full_unstemmed Towards Genomic Criteria for Delineating Fungal Species
title_short Towards Genomic Criteria for Delineating Fungal Species
title_sort towards genomic criteria for delineating fungal species
topic Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7711752/
https://www.ncbi.nlm.nih.gov/pubmed/33114441
http://dx.doi.org/10.3390/jof6040246
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