Patterns of Genomic Variation in the Opportunistic Pathogen Candida glabrata Suggest the Existence of Mating and a Secondary Association with Humans

Abstract

SummaryCandida glabrata is an opportunistic fungal pathogen that ranks as the second most common cause of systemic candidiasis. Despite its genus name, this yeast is more closely related to the model yeast Saccharomyces cerevisiae than to other Candida pathogens, and hence its ability to infect humans is thought to have emerged independently. Moreover, C. glabrata has all the necessary genes to undergo a sexual cycle but is considered an asexual organism due to the lack of direct evidence of sexual reproduction. To reconstruct the recent evolution of this pathogen and find footprints of sexual reproduction, we assessed genomic and phenotypic variation across 33 globally distributed C. glabrata isolates. We cataloged extensive copy-number variation, which particularly affects genes encoding cell-wall-associated proteins, including adhesins. The observed level of genetic variation in C. glabrata is significantly higher than that found in Candida albicans. This variation is structured into seven deeply divergent clades, which show recent geographical dispersion and large within-clade genomic and phenotypic differences. We show compelling evidence of recent admixture between differentiated lineages and of purifying selection on mating genes, which provides the first evidence for the existence of an active sexual cycle in this yeast. Altogether, our data point to a recent global spread of previously genetically isolated populations and suggest that humans are only a secondary niche for this yeast.

Fifty Aureobasidium pullulans genomes reveal a recombining polyextremotolerant generalist

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Genomes shed light on the secret life of Candida glabrata: not so asexual, not so commensal

“…To gain novel insight into these open questions, we recently sequenced the genomes of 33 clinical C. glabrata isolates from around the globe and reconstructed their recent evolution (Carreté et al 2018). Using this genetic information, we reconstructed a ‘family tree’ for all the strains.…”

High complexity and degree of genetic variation inBrettanomyces bruxellensispopulation

“…With the currently available sequencing technologies, it is now possible to explore the intraspecific variability of a species at the genome-wide level. Such population genomic studies have been performed on multiple yeast species, including S. cerevisiae (Peter, et al 2018;Skelly, et al 2013;Bergström, et al 2014;Strope, et al 2015;Almeida, et al 2015;Zhu, et al 2016;Gonçalves, et al 2016, Gallone, et al 2016 and Schizosaccharomyces pombe (Fawcett, et al 2014;Jeffares, et al 2015) but also non-model yeast species (Leducq, et al 2016;Carreté, et al 2018;Hirakawa, et al 2015;Ford, et al 2015;Ropars, et al 2018;Friedrich, et al 2015;Ortiz-Merino, et al 2018), granting better insights into their respective evolutionary histories as well as genotype-phenotype relationships.…”