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.

Highlights

  • How to define a species is a perennial question of biology

  • Pairwise genomic distances were calculated between 1544 assembled fungal genomes deposited in GenBank at different taxonomic levels using Mash and Dashing

  • A total of 5867 genomic distances were calculated at the species level, 19,849 at the genus level, 13,152 at the family, 58,097 at the order, 68,175 at the class, and 566,436 at the phylum levels

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Summary

Introduction

How to define a species is a perennial question of biology. The biological species concept of ErnstMayr [1] for example, while seminal in practice, turned out to be poorly applicable to major parts of the tree of life. The clones are not distributed over an unstructured continuous spectrum, but mimic biological species by forming cohesive clusters, which maintain their within-cluster similarity over time. This phenomenon can be explained by the formation of ecotypes driven by periodic selection or genetic drift or both [3]. These periodically compress the diversity to near zero, unless the accumulating mutations or recombinations place the organism into a new ecological niche, which forms a new (in most cases monophyletic) ecotype with a different set of selection pressures [3]. This process results in discontinuities in the spectrum of possible diversity, leaving more or less well-separated

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