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Delineating yeast species with genome average nucleotide identity: a calibration of ANI with haplontic, heterothallic Metschnikowia species

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Abstract

We determined pairwise average nucleotide identity (ANI) values for the genomes of 71 strains assigned to 36 Metschnikowia species, 28 of which were represented by multiple isolates selected to represent the range of genetic diversity of the species, and most of which were defined on the basis of reproductive isolation. Similar to what has been proposed for prokaryote species delineation, an ANI value of 95% emerged as a good guideline for the delineation of yeast species, although some overlap exists, whereby members of a reproductive community could have slightly lower values (e.g., 94.3% for M. kamakouana), and representatives of distinct sister species could give slightly higher values (e.g., 95.2% for the sister species M. drakensbergensis and M. proteae). Unlike what is observed in prokaryotes, a sizeable gap between intraspecific and interspecific ANI values was not encountered. Given the ease with which yeast draft genomes can now be obtained, ANI values are poised to become the new standard upon which yeast species may be delineated on genetic distance. As borderline cases exist, however, the delineation of yeast species will continue to require careful evaluation of all available data. We also explore the often-neglected distinction between phylogenetic relatedness and sequence identity through the analysis of a tree constructed from ANI’ (100 − ANI) values.

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Acknowledgements

Funding from the Natural Science and Engineering Research Council of Canada is gratefully acknowledged. We thank the anonymous reviewers and the Editor for their helpful, constructive comments and suggestions.

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Authors and Affiliations

  1. Department of Biology, University of Western Ontario, London, Ontario, N6A 5B7, Canada

    Marc-André Lachance & Dong Kyung Lee

  2. School of Environmental Sciences, University of Guelph, Guelph, Ontario, N1G 2W1, Canada

    Tom Hsiang

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  1. Marc-André Lachance
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  2. Dong Kyung Lee
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  3. Tom Hsiang
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All authors contributed to the study conception and design, including data collection and analysis. The first draft of the manuscript was written by M.A. Lachance and the other authors commented on previous versions of the manuscript and the revisions. All authors read and approved the final manuscript.

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Correspondence to Marc-André Lachance.

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Lachance, MA., Lee, D.K. & Hsiang, T. Delineating yeast species with genome average nucleotide identity: a calibration of ANI with haplontic, heterothallic Metschnikowia species. Antonie van Leeuwenhoek 113, 2097–2106 (2020). https://doi.org/10.1007/s10482-020-01480-9

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