Towards genomic criteria for delineating fungal species

Gostinčar, Cene (author)

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.

• Language: English
• Keywords: fungi, species delineation, species concept, genomic distance, species similarity, mash, dashing
• Work type: Article
• Typology: 1.01 - Original Scientific Article
• Organization: BF - Biotechnical Faculty
• Publication status: Published
• Publication version: Version of Record
• Year: 2020
• Number of pages: 18 str.
• Numbering: Vol. 6, iss. 4, art. 246
• PID: 20.500.12556/RUL-121868
• DOI: 10.3390/jof6040246
• COBISS.SI-ID: 34257923
• Publication date in RUL: 04.11.2020

Record is a part of a journal

• Title: Journal of Fungi
• Shortened title: J. Fungi
• Publisher: MDPI
• ISSN: 2309-608X
• COBISS.SI-ID: 525300761

Licences

• License: CC BY 4.0, Creative Commons Attribution 4.0 International
• Link: http://creativecommons.org/licenses/by/4.0/
• Description: This is the standard Creative Commons license that gives others maximum freedom to do what they want with the work as long as they credit the author.
• Licensing start date: 01.12.2020

Secondary language

• Language: Slovenian
• Keywords: koncept vrste, glive, genomska razdalja, podobnost vrst