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

Toni Gabaldón, Cécile Fairhead

<figure><img src="image_2.png" /></figure>

## To cite this version:

Toni Gabaldón, Cécile Fairhead. Genomes shed light on the secret life of Candida glabrata: not so asexual, not so commensal. Current Genetics, 2019, 65 (1), pp.93-98. 10.1007/s00294-018-0867-z. hal-02619728

HAL Id: hal-02619728

https://hal.inrae.fr/hal-02619728

Submitted on 2 Feb 2024

HAL is a multi-disciplinary open access archive for the deposit and dissemination of scientific research documents, whether they are published or not. The documents may come from teaching and research institutions in France or abroad, or from public or private research centers.

L'archive ouverte pluridisciplinaire HAL, est destinée au dépôt et à la diffusion de documents scientifiques de niveau recherche, publiés ou non, émanant des établissements d'enseignement et de recherche français ou étrangers, des laboratoires publics ou privés.

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Distributed under a Creative Commons Attribution 4.0 International License
# Genomes shed light on the secret life of Candida glabrata: not so asexual, not so commensal

Toni Gabaldón, Cécile Fairhead

<figure><img src="image_1.png" /></figure>

## To cite this version:

Toni Gabaldón, Cécile Fairhead. Genomes shed light on the secret life of Candida glabrata: not so asexual, not so commensal. Current Genetics, 2019, 65 (1), pp.93-98. 10.1007/s00294-018-0867-z. hal-02619728

HAL Id: hal-02619728

https://hal.inrae.fr/hal-02619728v1

Submitted on 2 Feb 2024

HAL is a multi-disciplinary open access
archive for the deposit and dissemination of sci-
entific research documents, whether they are pub-
lished or not. The documents may come from
teaching and research institutions in France or
abroad, or from public or private research centers.

L'archive ouverte pluridisciplinaire HAL, est
destinée au dépôt et à la diffusion de documents
scientifiques de niveau recherche, publiés ou non,
émanant des établissements d'enseignement et de
recherche français ou étrangers, des laboratoires
publics ou privés.

<figure><img src="image_2.png" /></figure>
# Genomes shed light on the secret life of *Candida glabrata*: not so asexual, not so commensal

Toni Gabaldón<fnref n="1" />,<fnref n="2" />,<fnref n="3" /> ID · Cécile Fairhead<fnref n="4" />

Received: 7 July 2018 / Revised: 15 July 2018 / Accepted: 17 July 2018 / Published online: 19 July 2018

© The Author(s) 2018

## Abstract

*Candida glabrata* is an opportunistic yeast pathogen, whose incidence has increased over the last decades. Despite its genus name, this species is actually more closely related to the budding yeast *Saccharomyces cerevisiae* than to other *Candida* pathogens, such as *Candida albicans*. Hence, *C. glabrata* and *C. albicans* must have acquired the ability to infect humans independently, which is reflected in the use of different mechanism for virulence, and survival in the host. Yet, research on *C. glabrata* suffers from assumptions carried over from the more studied *C. albicans*. Regarding the adaptation of *C. glabrata* to the human host, the prejudice was that, just as *C. albicans*, *C. glabrata* is a natural human commensal that turns deadly when immune defenses weaken. It was also considered asexual, as no one has observed mating, diploids, or spores, despite great efforts. However, the recent analysis of whole genomes from globally distributed *C. glabrata* isolates have shaken these assumptions. *C. glabrata* seems to be only secondarily associated to humans, as indicated by a lack of co-evolution with its host, and genomic footprints of recombination shows compelling evidence that this yeast is able to have sex. Here, we discuss the implications of this and other recent findings and highlight the new questions opened by this change in paradigm.

**Keywords** *Candida glabrata* · *Candida* · Fungal pathogens · Candidiasis · Genome sequencing

## Candida glabrata: the “other” Candida

*Candida* species are opportunistic yeast pathogens of increasing medical concern, as their infections can have high mortality rates, particularly when affecting immuno-compromised patients (Angoulvant et al. 2016). The list of *Candida* species reported as etiological agents in human infections comprises up to 30 different species, and keeps growing almost every year with the inclusion of new rare species (Gabaldón et al. 2016). In this infamous hall of fame, *C. albicans* and *C. glabrata* are the first two ranking

species based on their relative incidence (Angoulvant et al. 2016). *C. albicans*, accounting for over 40% of the infections, is the most studied species and has become a model for understanding *Candida* infections. As a result, knowledge acquired from the study of *C. albicans* is often taken as a framework to understand the other *Candida* species. However, *Candida* is not a true genus in the phylogenetic sense, as it comprises species that belong to different clades within the Saccharomycotina (Gabaldón et al. 2016). In particular, *C. glabrata* is only distantly related to *C. albicans*, being evolutionarily more related to the baker's yeast *Saccharomyces cerevisiae* (Gabaldón and Carreté 2016). Hence, there is an inherent risk in adopting the knowledge acquired from *C. albicans* and assume everything works the same way in *C. glabrata*. Even if *S. cerevisiae* is taken as a closer model to understand *C. glabrata* (Roetzer et al. 2011), we must not forget that these two yeasts are still as far away from each other as we are from zebrafish in terms of sequence identity between orthologous genes.

*Candida glabrata* was first identified in human stools about a century ago by Anderson, which named it *Cryptococcus glabratus* (Anderson 1917). However, it only received significant attention when it started to be identified

Communicated by M. Kupiec.

<figure><img src="image_4.png" /></figure>

<footnote>Toni Gabaldón
tgabaldon@crg.es</footnote>

<footnote n="1">¹ Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr. Aiguader 88, 08003 Barcelona, Spain</footnote>

<footnote n="2">² Universitat Pompeu Fabra (UPF), 08003 Barcelona, Spain</footnote>

<footnote n="3">³ ICREA, Pg. Lluís Companys 23, 08010 Barcelona, Spain</footnote>

<footnote n="4">⁴ GQE-Le Moulon, INRA-Université Paris-Sud-CNRS-AgroPa risTech, 91400 Orsay, France</footnote>
# Genomes shed light on the secret life of *Candida glabrata*: not so asexual, not so commensal

Toni Gabaldón<fnref n="1" />,<fnref n="2" />,<fnref n="3" /> ID • Cécile Fairhead<fnref n="4" />

Received: 7 July 2018 / Revised: 15 July 2018 / Accepted: 17 July 2018 / Published online: 19 July 2018

© The Author(s) 2018

## Abstract

*Candida glabrata* is an opportunistic yeast pathogen, whose incidence has increased over the last decades. Despite its genus name, this species is actually more closely related to the budding yeast *Saccharomyces cerevisiae* than to other *Candida* pathogens, such as *Candida albicans*. Hence, *C. glabrata* and *C. albicans* must have acquired the ability to infect humans independently, which is reflected in the use of different mechanism for virulence, and survival in the host. Yet, research on *C. glabrata* suffers from assumptions carried over from the more studied *C. albicans*. Regarding the adaptation of *C. glabrata* to the human host, the prejudice was that, just as *C. albicans*, *C. glabrata* is a natural human commensal that turns deadly when immune defenses weaken. It was also considered asexual, as no one has observed mating, diploids, or spores, despite great efforts. However, the recent analysis of whole genomes from globally distributed *C. glabrata* isolates have shaken these assumptions. *C. glabrata* seems to be only secondarily associated to humans, as indicated by a lack of co-evolution with its host, and genomic footprints of recombination shows compelling evidence that this yeast is able to have sex. Here, we discuss the implications of this and other recent findings and highlight the new questions opened by this change in paradigm.

**Keywords** *Candida glabrata* • *Candida* • Fungal pathogens • Candidiasis • Genome sequencing

## Candida glabrata: the “other” Candida

*Candida* species are opportunistic yeast pathogens of increasing medical concern, as their infections can have high mortality rates, particularly when affecting immuno-compromised patients (Angoulvant et al. 2016). The list of *Candida* species reported as etiological agents in human infections comprises up to 30 different species, and keeps growing almost every year with the inclusion of new rare species (Gabaldón et al. 2016). In this infamous hall of fame, *C. albicans* and *C. glabrata* are the first two ranking

species based on their relative incidence (Angoulvant et al. 2016). *C. albicans*, accounting for over 40% of the infections, is the most studied species and has become a model for understanding *Candida* infections. As a result, knowledge acquired from the study of *C. albicans* is often taken as a framework to understand the other *Candida* species. However, *Candida* is not a true genus in the phylogenetic sense, as it comprises species that belong to different clades within the Saccharomycotina (Gabaldón et al. 2016). In particular, *C. glabrata* is only distantly related to *C. albicans*, being evolutionarily more related to the baker's yeast *Saccharomyces cerevisiae* (Gabaldón and Carreté 2016). Hence, there is an inherent risk in adopting the knowledge acquired from *C. albicans* and assume everything works the same way in *C. glabrata*. Even if *S. cerevisiae* is taken as a closer model to understand *C. glabrata* (Roetzer et al. 2011), we must not forget that these two yeasts are still as far away from each other as we are from zebrafish in terms of sequence identity between orthologous genes.

*Candida glabrata* was first identified in human stools about a century ago by Anderson, which named it *Cryptococcus glabratus* (Anderson 1917). However, it only received significant attention when it started to be identified

Communicated by M. Kupiec.

<figure><img src="image_3.png" /></figure>

<footnote>Toni Gabaldón
tgabaldon@crg.es</footnote>

<footnote n="1">¹ Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr. Aiguader 88, 08003 Barcelona, Spain</footnote>

<footnote n="2">² Universitat Pompeu Fabra (UPF), 08003 Barcelona, Spain</footnote>

<footnote n="3">³ ICREA, Pg. Lluís Companys 23, 08010 Barcelona, Spain</footnote>

<footnote n="4">⁴ GQE-Le Moulon, INRA-Université Paris-Sud-CNRS-AgroPa risTech, 91400 Orsay, France</footnote>
as the causative agent of fungal infections in immunocom-
promised patients (Just et al. 1989). In recent years, the
incidence of *C. glabrata* has been increasing, perhaps due
to its inherent higher resistance to commonly used antifun-
gal drugs such as azoles (Angoulvant et al. 2016), and it
has been referred to as an emerging pathogen since the late
twentieth century (Hazen 1995). The first molecular stud-
ies performed on *C. glabrata* already pointed out a closer
relativeness to *S. cerevisiae* than to *C. albicans* (Kurtzman
and Robnett 2003). Soon, it was proposed to belong to the
*Nakaseomyces* clade (Kurtzman and Robnett 2003), which
comprises two additional pathogenic *Candida* species; *C.
nivarensis* and *C. bracarensis*, and three environmental spe-
cies. In 2004, the full-genomic sequence of *C. glabrata* was
obtained (Dujon et al. 2004), and almost a decade later the
sequences from all described species in the *Nakaseomyces*
were completed and compared (Gabaldón et al. 2013). These
comparisons provided unexpected insights on the emergence
of virulence within the *Nakaseomyces* clade. First of all, the
three species with virulence potential against humans were
found to be non-monophyletic; suggesting that the ability to
infect humans has emerged at least twice within this clade.
Second, most of the traits once considered to be explanatory
for the high pathogenicity (or frequent pathogenesis) of *C.
glabrata* as compared to *S. cerevisiae*; such as growth at high
temperatures or loss of the ability to synthesize nicotinic
acid, were found to be widespread in the clade pointing to
an ancient origin and, hence, disconnected from the origin
of virulence. In contrast, expansion of cell wall adhesins,
particularly those of the *EPA* family, were found to corre-
late with the virulent trait, suggesting that a potential for
higher—or more versatile—adherence has facilitated the
emergence of virulence towards humans among the *Naka-
seomyces*. These results showed that *C. glabrata*'s ability
to infect humans has evolved quite recently in evolutionary
terms. Nonetheless, many questions remain open, particu-
larly regarding the true lifestyle of this yeast.

A secret life elsewhere, or a nomadic
lifestyle?

How homogeneous is *C. glabrata* as a species? How does
the genetic diversity of *C. glabrata* relate to the diversity
of human populations? Are humans the main niche of *C.
glabrata* or are we being colonized from our close envi-
ronment? These are relevant questions for any pathogen, as
resolving them may help understanding the epidemiology
of infections and improve our chances to efficiently combat
them. Different types of associations between a pathogen (or
commensal) and its host exert different constraints on their
evolution, which can be reflected in the genome sequence of
the pathogen. For instance, the close association between the

obligate pathogen *Mycobacterium tuberculosis* and humans,
is reflected in strong parallelisms between the geographi-
cal projection of maps of genetic variation of both species
(Comas et al. 2013). Studies on natural variation across *C.
glabrata* isolates, have long been restricted to the analyses of
a few loci or the measurement of few phenotypes (Dodgson
et al. 2003, 2005; Brisse et al. 2009; Rolland et al. 2010;
Schwarzmüller et al. 2014; Klotz et al. 2016). These studies
detected the presence of several genetically distinct clades in
the population of *C. glabrata* but the number of clades var-
ied depending on the samples and markers used (de Meeûs
et al. 2002; Dodgson et al. 2003, 2005; Brisse et al. 2009).
These studies, which were based on a few loci, reported a
significant enrichment in most of the clades in a particular
geographical origin, suggesting that the distribution in *C.
glabrata* was geographically structured and their popula-
tion structure was predominantly clonal. Similarly, for *C.
albicans*, an association between clades and the geographic
origin is observed (Tavanti et al. 2005) and its mode of
reproduction is described as predominantly clonal with lim-
ited recombination (Pujol et al. 1993; Fundyga et al. 2002).
However, the low resolution imposed with the use of a lim-
ited number of loci restricted the conclusions that could be
drawn from these studies. Overall, *C. glabrata* was generally
considered a commensal of humans, although prevalence of
*C. glabrata* in different mucosa vary from study to study, and
generally increases with age and length of stays in hospitals
(Angoulvant et al. 2016).

Nevertheless, *C. glabrata* strains have also been isolated
from non-human sources, including from fermenting coffee
beans (de Melo Pereira et al. 2014), and, most commonly,
from droppings or cloaca swabs of several bird species
(Cafarchia et al. 2008; Francesca et al. 2014; Al-Yasiri et al.
2016). Furthermore, *C. glabrata* can also be commonly
found on the surface of hands or mobile phones of clinical
workers (Kordecka et al. 2016). The central question here is
whether isolation from a source supports the conclusion that
the given source is a natural niche for the isolated species.
Several lines of thought argue against this idea. First of all,
the diversity of niches from which *C. glabrata* is isolated
and the lack of common physiologically relevant character-
istics among these sources (i.e., bird cloaca, mobile phones,
and coffee beans) suggest that *C. glabrata* may just be a
passenger in at least some of these sources—if not in all.
This is consistent with the finding that *C. glabrata* is only
sporadically—i.e., not systematically—isolated from these
sources and in small amounts. Similarly, this is true for many
other yeast species, including several other *Candida* such
as *C. albicans*, that are found in the very same sources. For
instance a recent survey have isolated three diverse strains
*C. albicans* from oak trees, each one being closely related to
a different clade of clinical isolates (Bensasson et al. 2018).
Contamination from human sources could be a plausible

<figure><img src="image_5.png" /></figure>
as the causative agent of fungal infections in immunocom-
promised patients (Just et al. 1989). In recent years, the
incidence of *C. glabrata* has been increasing, perhaps due
to its inherent higher resistance to commonly used antifun-
gal drugs such as azoles (Angoulvant et al. 2016), and it
has been referred to as an emerging pathogen since the late
twentieth century (Hazen 1995). The first molecular stud-
ies performed on *C. glabrata* already pointed out a closer
relativeness to *S. cerevisiae* than to *C. albicans* (Kurtzman
and Robnett 2003). Soon, it was proposed to belong to the
*Nakaseomyces* clade (Kurtzman and Robnett 2003), which
comprises two additional pathogenic *Candida* species; *C.
nivarensis* and *C. bracarensis*, and three environmental spe-
cies. In 2004, the full-genomic sequence of *C. glabrata* was
obtained (Dujon et al. 2004), and almost a decade later the
sequences from all described species in the *Nakaseomyces*
were completed and compared (Gabaldón et al. 2013). These
comparisons provided unexpected insights on the emergence
of virulence within the *Nakaseomyces* clade. First of all, the
three species with virulence potential against humans were
found to be non-monophyletic; suggesting that the ability to
infect humans has emerged at least twice within this clade.
Second, most of the traits once considered to be explanatory
for the high pathogenicity (or frequent pathogenesis) of *C.
glabrata* as compared to *S. cerevisiae*; such as growth at high
temperatures or loss of the ability to synthesize nicotinic
acid, were found to be widespread in the clade pointing to
an ancient origin and, hence, disconnected from the origin
of virulence. In contrast, expansion of cell wall adhesins,
particularly those of the *EPA* family, were found to corre-
late with the virulent trait, suggesting that a potential for
higher—or more versatile—adherence has facilitated the
emergence of virulence towards humans among the *Naka-
seomyces*. These results showed that *C. glabrata*'s ability
to infect humans has evolved quite recently in evolutionary
terms. Nonetheless, many questions remain open, particu-
larly regarding the true lifestyle of this yeast.

A secret life elsewhere, or a nomadic
lifestyle?

How homogeneous is *C. glabrata* as a species? How does
the genetic diversity of *C. glabrata* relate to the diversity
of human populations? Are humans the main niche of *C.
glabrata* or are we being colonized from our close envi-
ronment? These are relevant questions for any pathogen, as
resolving them may help understanding the epidemiology
of infections and improve our chances to efficiently combat
them. Different types of associations between a pathogen (or
commensal) and its host exert different constraints on their
evolution, which can be reflected in the genome sequence of
the pathogen. For instance, the close association between the

obligate pathogen *Mycobacterium tuberculosis* and humans,
is reflected in strong parallelisms between the geographi-
cal projection of maps of genetic variation of both species
(Comas et al. 2013). Studies on natural variation across *C.
glabrata* isolates, have long been restricted to the analyses of
a few loci or the measurement of few phenotypes (Dodgson
et al. 2003, 2005; Brisse et al. 2009; Rolland et al. 2010;
Schwarzmüller et al. 2014; Klotz et al. 2016). These studies
detected the presence of several genetically distinct clades in
the population of *C. glabrata* but the number of clades var-
ied depending on the samples and markers used (de Meeûs
et al. 2002; Dodgson et al. 2003, 2005; Brisse et al. 2009).
These studies, which were based on a few loci, reported a
significant enrichment in most of the clades in a particular
geographical origin, suggesting that the distribution in *C.
glabrata* was geographically structured and their popula-
tion structure was predominantly clonal. Similarly, for *C.
albicans*, an association between clades and the geographic
origin is observed (Tavanti et al. 2005) and its mode of
reproduction is described as predominantly clonal with lim-
ited recombination (Pujol et al. 1993; Fundyga et al. 2002).
However, the low resolution imposed with the use of a lim-
ited number of loci restricted the conclusions that could be
drawn from these studies. Overall, *C. glabrata* was generally
considered a commensal of humans, although prevalence of
*C. glabrata* in different mucosa vary from study to study, and
generally increases with age and length of stays in hospitals
(Angoulvant et al. 2016).

Nevertheless, *C. glabrata* strains have also been isolated
from non-human sources, including from fermenting coffee
beans (de Melo Pereira et al. 2014), and, most commonly,
from droppings or cloaca swabs of several bird species
(Cafarchia et al. 2008; Francesca et al. 2014; Al-Yasiri et al.
2016). Furthermore, *C. glabrata* can also be commonly
found on the surface of hands or mobile phones of clinical
workers (Kordecka et al. 2016). The central question here is
whether isolation from a source supports the conclusion that
the given source is a natural niche for the isolated species.
Several lines of thought argue against this idea. First of all,
the diversity of niches from which *C. glabrata* is isolated
and the lack of common physiologically relevant character-
istics among these sources (i.e., bird cloaca, mobile phones,
and coffee beans) suggest that *C. glabrata* may just be a
passenger in at least some of these sources—if not in all.
This is consistent with the finding that *C. glabrata* is only
sporadically—i.e., not systematically—isolated from these
sources and in small amounts. Similarly, this is true for many
other yeast species, including several other *Candida* such
as *C. albicans*, that are found in the very same sources. For
instance a recent survey have isolated three diverse strains
*C. albicans* from oak trees, each one being closely related to
a different clade of clinical isolates (Bensasson et al. 2018).
Contamination from human sources could be a plausible

<figure><img src="image_4.png" /></figure>
explanation for the presence of such isolates or, alternatively, trees—or animals living on them—could be a natural reservoir for *C. albicans*. In any case, the example serves to illustrate the fact that isolation does not equate identification of a natural niche.

Many fungi tend to have a nearly ubiquitous presence and is difficult to identify their natural niche. Take, for instance, the well-studied *S. cerevisiae*. Although it is often purported as highly adapted to exploit fruits with high sugar content, it is only present in minute amounts on fruits and it is also commonly found—often at higher densities—in other environments such as tree barks, soils or humans. The ecological niche concept predicts that organisms should be more abundant in niches to which they are adapted to. However, alternative models in which organisms are highly versatile and able to survive across a broad spectrum of niches may better explain the ubiquitousness of certain microbes such as *S. cerevisiae* (Goddard and Greig 2015). Similarly, a “nomadic” lifestyle could explain the presence of *C. glabrata* in a diversity of niches, including humans. If this would be true, or if *C. glabrata* has a different natural niche, we should abandon the idea of *C. glabrata* as a highly specialized commensal but see it rather as an opportunistic colonizer. As we will see below, recent genomic comparisons seem to point to the idea that humans are indeed only a secondary niche of *C. glabrata*.

## No sex, or just hidden sex?

Another long-standing mystery surrounding *C. glabrata* relates to its ability to undergo a sexual cycle. Yeast species of the branch to which *C. glabrata* and *S. cerevisiae* belong, usually exhibit two mating types in haploid cells, which can fuse with each other to form diploid cells, with the potential to undergo meiosis and form spores (Muller et al. 2008). In addition, these yeasts are able to switch mating types, in a complex process that involves an endonuclease-driven cut, followed by recombination with silent loci, leading to replacement of transcription factor-encoding genes at the mating type locus (Haber 2012). Ploidy control and permanent availability to form diploid cells that can sporulate, may be the reason for the existence of such a complex phenomenon. Indeed, spores are the stage where cells can resist harsh conditions until the environment is more favorable to growth (Huang and Hull 2017). *C. glabrata*, like many other fungal pathogens of humans, is considered an asexual species and all attempts to make it mate in the laboratory have, so far, failed. However, the analysis of its genome sequence revealed the presence of homologs of all *S. cerevisiae* genes involved in the mating process (Fabre et al. 2005), and population analyses revealed the presence of cells of both mating types (Srikantha et al. 2003; Brisse et al. 2009). Moreover,

the fact that *C. glabrata* cells of opposite mating types maintain distinct cellular identities (Muller et al. 2008), and evidence for mating-type switching in populations (Brisse et al. 2009), along with possible sexual recombination (Dodgson et al. 2005), suggest that *C. glabrata* may mate in yet undiscovered conditions with a canonical (i.e., *cerevisiae*-like), but rare, sexual cycle, or with a parasexual cycle, similar to *C. albicans*.

## Resolving puzzles from genomics footprints

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. To our surprise, the genetic diversity of the species was structured in seven subpopulations (or clades) that had diverged deeply in the past (Fig. 1). For comparison, the genetic diversity found among distantly related clades was up to one order of magnitude higher than that found in worldwide sampled *C. albicans* isolates, and some of the identified clades comprised a similar level of diversity as that found between divergent *C. albicans* isolates. This means that clinical isolates of *C. glabrata* show more genetic diversity than that of *C. albicans* and, moreover, that this diversity is not homogenous but organized in a set of diverse genetic clades. Abusing of the—always conflictive in microbes—“species” concept to illustrate this, one could be talking about distinct *C. glabrata* subspecies, with some of these being as genetically diverse as the whole *C. albicans* species. This diversity was not only

<figure><img src="image_6.png" /><figcaption>**Fig. 1** Molecular phylogenies of major clades *C. glabrata* (left) and *C. albicans* (right), as reconstructed from genome-wide single-nucleotide polymorphisms in recent studies (Carreté et al. 2018; Ropars et al. 2018). For comparison, both phylogenies have been drawn to scale in terms of average substitutions per site estimated in each of the studies</figcaption></figure>
explanation for the presence of such isolates or, alternatively, trees—or animals living on them—could be a natural reservoir for *C. albicans*. In any case, the example serves to illustrate the fact that isolation does not equate identification of a natural niche.

Many fungi tend to have a nearly ubiquitous presence and is difficult to identify their natural niche. Take, for instance, the well-studied *S. cerevisiae*. Although it is often purported as highly adapted to exploit fruits with high sugar content, it is only present in minute amounts on fruits and it is also commonly found—often at higher densities—in other environments such as tree barks, soils or humans. The ecological niche concept predicts that organisms should be more abundant in niches to which they are adapted to. However, alternative models in which organisms are highly versatile and able to survive across a broad spectrum of niches may better explain the ubiquitousness of certain microbes such as *S. cerevisiae* (Goddard and Greig 2015). Similarly, a “nomadic” lifestyle could explain the presence of *C. glabrata* in a diversity of niches, including humans. If this would be true, or if *C. glabrata* has a different natural niche, we should abandon the idea of *C. glabrata* as a highly specialized commensal but see it rather as an opportunistic colonizer. As we will see below, recent genomic comparisons seem to point to the idea that humans are indeed only a secondary niche of *C. glabrata*.

## No sex, or just hidden sex?

Another long-standing mystery surrounding *C. glabrata* relates to its ability to undergo a sexual cycle. Yeast species of the branch to which *C. glabrata* and *S. cerevisiae* belong, usually exhibit two mating types in haploid cells, which can fuse with each other to form diploid cells, with the potential to undergo meiosis and form spores (Muller et al. 2008). In addition, these yeasts are able to switch mating types, in a complex process that involves an endonuclease-driven cut, followed by recombination with silent loci, leading to replacement of transcription factor-encoding genes at the mating type locus (Haber 2012). Ploidy control and permanent availability to form diploid cells that can sporulate, may be the reason for the existence of such a complex phenomenon. Indeed, spores are the stage where cells can resist harsh conditions until the environment is more favorable to growth (Huang and Hull 2017). *C. glabrata*, like many other fungal pathogens of humans, is considered an asexual species and all attempts to make it mate in the laboratory have, so far, failed. However, the analysis of its genome sequence revealed the presence of homologs of all *S. cerevisiae* genes involved in the mating process (Fabre et al. 2005), and population analyses revealed the presence of cells of both mating types (Srikantha et al. 2003; Brisse et al. 2009). Moreover,

the fact that *C. glabrata* cells of opposite mating types maintain distinct cellular identities (Muller et al. 2008), and evidence for mating-type switching in populations (Brisse et al. 2009), along with possible sexual recombination (Dodgson et al. 2005), suggest that *C. glabrata* may mate in yet undiscovered conditions with a canonical (i.e., *cerevisiae*-like), but rare, sexual cycle, or with a parasexual cycle, similar to *C. albicans*.

## Resolving puzzles from genomics footprints

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. To our surprise, the genetic diversity of the species was structured in seven subpopulations (or clades) that had diverged deeply in the past (Fig. 1). For comparison, the genetic diversity found among distantly related clades was up to one order of magnitude higher than that found in worldwide sampled *C. albicans* isolates, and some of the identified clades comprised a similar level of diversity as that found between divergent *C. albicans* isolates. This means that clinical isolates of *C. glabrata* show more genetic diversity than that of *C. albicans* and, moreover, that this diversity is not homogenous but organized in a set of diverse genetic clades. Abusing of the—always conflictive in microbes—“species” concept to illustrate this, one could be talking about distinct *C. glabrata* subspecies, with some of these being as genetically diverse as the whole *C. albicans* species. This diversity was not only

<figure><img src="image_5.png" /><figcaption>**Fig. 1** Molecular phylogenies of major clades *C. glabrata* (left) and *C. albicans* (right), as reconstructed from genome-wide single-nucleotide polymorphisms in recent studies (Carreté et al. 2018; Ropars et al. 2018). For comparison, both phylogenies have been drawn to scale in terms of average substitutions per site estimated in each of the studies</figcaption></figure>
evident by the amount of sequence divergence, but also in a
high level of variation in copy numbers resulting from gene
deletions and duplications, which were enriched in regions
coding for the abovementioned *EPA* adhesins and other cell
wall proteins. To add to the colorful genetic diversity pic-
ture, we also identified several large genomic re-arrange-
ments, including large inversions, translocations, and ane-
uploidies. Altogether, our genome comparisons revealed a
highly plastic genome. We also measured some phenotypes
of the sequenced strains and found a very high level of phe-
notypic variation, with important differences even between
strains belonging to the same clade. This puts in perspective
everything we “know” about *C. glabrata*, as most of the
experimental knowledge from this species results from the
analysis of one or two “model” lab strains.

Perhaps the most important observation, however, was
that there was no apparent geographical structure in this
genetic diversity. On the contrary, each clade seem to con-
tain strains isolated from distant locations such as Europe
and America. This is at odds with the idea of co-evolution
between humans and *C. glabrata* as it would be expected
for a tight commensal relationship. Rather, it suggests that
previously isolated populations have recently inter-mingled,
as if some new factor has favored this trend. Global spread of
species is often related to human-related phenomena, such
as global trade and climate change, and it is very likely that
human action is behind the recent global spread of these
clades. However, the long branches separating the differ-
ent clades are telltale signs of long isolation, likely in dis-
tinct geographical areas. Thus, the genetic diversity and
geographical dispersion of genetic backgrounds seem to
strengthen the idea that humans are only a secondary niche
for *C. glabrata*, and that we have facilitated its global expan-
sion. A high versatility and a possibly nomadic lifestyle has
likely favored the expansion of *C. glabrata* and would also
explain the ease with which it can colonize us, and cause
severe infections when our defenses are weakened.

The existence of clearly genetically differentiated clades
gave us another useful opportunity: find the smoking gun of
past sexual reproduction in the form of genomic recombina-
tion. Sex between cells results in genetic exchanges between
different clades—which we now know co-exist globally—
this would result in chimeric patterns of genetic diversity
along the chromosomes of the descendants, just like the
chromosomes that we transmit through our gametes consist
of stretches of genes coming from our mother and father.
This is exactly what we found in some of the sequenced
strains, suggesting the different clades have exchanged
genetic material and providing a compelling evidence for
this species’ ability to have sex. In accordance with this,
we found evidence for high levels of purifying selection
in the genetic toolkit required to have sex, indicating that

deleterious mutations in these are removed by natural selec-
tion in *C. glabrata* populations. Furthermore, our analysis
has confirmed the existence of mating-type switching, and
of illegal repair events during switching in the population.
Experimental results show that switching is lethal to many
*C. glabrata* cells in laboratory conditions (Boisnard et al.
2015). Although sex can occur in non-switching species, it
is conversely admitted that switching exists to favor sexual
reproduction. The conservation of this complex and danger-
ous mechanism in *C. glabrata* is another indication of the
existence of cryptic sex. Thus, this yeast is not asexual, we
just do not know what triggers its sexual cycle.

Future perspectives

What are the implications of these recent discoveries ena-
bled by reading the genomes of a collection of clinical
strains? We believe they are many. In the first place, they
have uncovered an astonishingly high genetic diversity in
this pathogenic yeast. In addition, the *C. glabrata* genome
seems to be very dynamic, and can be easily shaped by gene
gain, loss and large genomic re-arrangements. Thus, research
on the current single “lab strain” is of limited use, unless it
is complemented with some validation in strains from dif-
ferent clades. Second, an unexpected lifestyle seems to be
implied from this results: *C. glabrata* is probably environ-
mental and sexual, which has deep implications in how we
should understand its relationships with the human host and
its epidemiology. We may be facing a menace that is com-
ing from an unknown environment. This menace is highly
diverse and plastic, and able to have sex. This sexual ability
may favor the exchange of genetic material, thereby acceler-
ating its adaptation. A worrying hypothetical scenario is the
possibility of a drug resistance expanding through genetic
exchange across populations.

Current studies, some of which performed by us, are
expanding the breath of the genomic comparisons, focus-
ing on groups of isolates showing phenotypes of inter-
est, such as those related to virulence, drug resistance,
and adhesion. A final goal of these analyses is to uncover
genetic factors determining these traits, that is, establish-
ing links between phenotype and genotype. Moreover,
other studies may focus on the comparison of serial iso-
lates taken from the same patient at different times in the
course of an infection. The idea is to understand micro-
evolutionary processes leading to the emergence of drug
resistance—or persistence (Bojsen et al. 2017)—or a more
invasive phenotype. Last, but not least, the environment
should be tested for the presence of *C. glabrata* with mod-
ern identification techniques. Isolating a given species in
the many ecosystems that exist around humans may be like

<figure><img src="image_7.png" /></figure>
evident by the amount of sequence divergence, but also in a
high level of variation in copy numbers resulting from gene
deletions and duplications, which were enriched in regions
coding for the abovementioned *EPA* adhesins and other cell
wall proteins. To add to the colorful genetic diversity pic-
ture, we also identified several large genomic re-arrange-
ments, including large inversions, translocations, and ane-
uploidies. Altogether, our genome comparisons revealed a
highly plastic genome. We also measured some phenotypes
of the sequenced strains and found a very high level of phe-
notypic variation, with important differences even between
strains belonging to the same clade. This puts in perspective
everything we “know” about *C. glabrata*, as most of the
experimental knowledge from this species results from the
analysis of one or two “model” lab strains.

Perhaps the most important observation, however, was
that there was no apparent geographical structure in this
genetic diversity. On the contrary, each clade seem to con-
tain strains isolated from distant locations such as Europe
and America. This is at odds with the idea of co-evolution
between humans and *C. glabrata* as it would be expected
for a tight commensal relationship. Rather, it suggests that
previously isolated populations have recently inter-mingled,
as if some new factor has favored this trend. Global spread of
species is often related to human-related phenomena, such
as global trade and climate change, and it is very likely that
human action is behind the recent global spread of these
clades. However, the long branches separating the differ-
ent clades are telltale signs of long isolation, likely in dis-
tinct geographical areas. Thus, the genetic diversity and
geographical dispersion of genetic backgrounds seem to
strengthen the idea that humans are only a secondary niche
for *C. glabrata*, and that we have facilitated its global expan-
sion. A high versatility and a possibly nomadic lifestyle has
likely favored the expansion of *C. glabrata* and would also
explain the ease with which it can colonize us, and cause
severe infections when our defenses are weakened.

The existence of clearly genetically differentiated clades
gave us another useful opportunity: find the smoking gun of
past sexual reproduction in the form of genomic recombina-
tion. Sex between cells results in genetic exchanges between
different clades—which we now know co-exist globally—
this would result in chimeric patterns of genetic diversity
along the chromosomes of the descendants, just like the
chromosomes that we transmit through our gametes consist
of stretches of genes coming from our mother and father.
This is exactly what we found in some of the sequenced
strains, suggesting the different clades have exchanged
genetic material and providing a compelling evidence for
this species’ ability to have sex. In accordance with this,
we found evidence for high levels of purifying selection
in the genetic toolkit required to have sex, indicating that

deleterious mutations in these are removed by natural selec-
tion in *C. glabrata* populations. Furthermore, our analysis
has confirmed the existence of mating-type switching, and
of illegal repair events during switching in the population.
Experimental results show that switching is lethal to many
*C. glabrata* cells in laboratory conditions (Boisnard et al.
2015). Although sex can occur in non-switching species, it
is conversely admitted that switching exists to favor sexual
reproduction. The conservation of this complex and danger-
ous mechanism in *C. glabrata* is another indication of the
existence of cryptic sex. Thus, this yeast is not asexual, we
just do not know what triggers its sexual cycle.

Future perspectives

What are the implications of these recent discoveries ena-
bled by reading the genomes of a collection of clinical
strains? We believe they are many. In the first place, they
have uncovered an astonishingly high genetic diversity in
this pathogenic yeast. In addition, the *C. glabrata* genome
seems to be very dynamic, and can be easily shaped by gene
gain, loss and large genomic re-arrangements. Thus, research
on the current single “lab strain” is of limited use, unless it
is complemented with some validation in strains from dif-
ferent clades. Second, an unexpected lifestyle seems to be
implied from this results: *C. glabrata* is probably environ-
mental and sexual, which has deep implications in how we
should understand its relationships with the human host and
its epidemiology. We may be facing a menace that is com-
ing from an unknown environment. This menace is highly
diverse and plastic, and able to have sex. This sexual ability
may favor the exchange of genetic material, thereby acceler-
ating its adaptation. A worrying hypothetical scenario is the
possibility of a drug resistance expanding through genetic
exchange across populations.

Current studies, some of which performed by us, are
expanding the breath of the genomic comparisons, focus-
ing on groups of isolates showing phenotypes of inter-
est, such as those related to virulence, drug resistance,
and adhesion. A final goal of these analyses is to uncover
genetic factors determining these traits, that is, establish-
ing links between phenotype and genotype. Moreover,
other studies may focus on the comparison of serial iso-
lates taken from the same patient at different times in the
course of an infection. The idea is to understand micro-
evolutionary processes leading to the emergence of drug
resistance—or persistence (Bojsen et al. 2017)—or a more
invasive phenotype. Last, but not least, the environment
should be tested for the presence of *C. glabrata* with mod-
ern identification techniques. Isolating a given species in
the many ecosystems that exist around humans may be like

<figure><img src="image_6.png" /></figure>
finding a needle in a haystack; but, until this is done in an
extensive manner, the jury will remain out on the question
of the environmental reservoir.

**Acknowledgements** TG group acknowledges support from the Spanish Ministry of Economy, Industry, and Competitiveness (MEIC) for the EMBL partnership, and Grants ‘Centro de Excelencia Severo Ochoa 2013–2017’ SEV-2012-0208, and BFU2015-67107 cofounded by European Regional Development Fund (ERDF); from the CERCA Programme / Generalitat de Catalunya; from the Catalan Research Agency (AGAUR) SGR857, and Grant from the European Union’s Horizon 2020 research and innovation programme under the Grant Agreement ERC-2016-724173 the Marie Skłodowska-Curie Grant Agreement no. H2020-MSCA-ITN-2014-642095. CF acknowledges support from the CNRS through the GDRI iGénolevures.

**Open Access** This article is distributed under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made.

References

Al-Yasiri MH, Normand AC, L'Ollivier C et al (2016) Opportunistic fungal pathogen *Candida glabrata* circulates between humans and yellow-legged gulls. Sci Rep. https://doi.org/10.1038/srep36157

Anderson HW (1917) Yeast-like fungi of the human intestinal tract. J Infect Dis 21:341–354. https://doi.org/10.1093/infdis/21.4.341

Angoulvant A, Guitard J, Hennequin C (2016) Old and new pathogenic *Nakaseomyces* species: epidemiology, biology, identification, pathogenicity and antifungal resistance. FEMS Yeast Res 16:fov114

Bensasson D, Dicks J, Ludwig JM et al (2018) Diverse lineages of *Candida albicans* live on old oaks. bioRxiv. https://doi.org/10.1101/341032

Boisnard S, Li YZ, Arnaise S et al (2015) Efficient mating-type switching in *Candida glabrata* induces cell death. PLoS One. https://doi.org/10.1371/journal.pone.0140990

Bojsen R, Regenberg B, Folkesson A (2017) Persistence and drug tolerance in pathogenic yeast. Curr Genet 63:19–22

Brisse S, Pannier C, Angoulvant A et al (2009) Uneven distribution of mating types among genotypes of *Candida glabrata* isolates from clinical samples. Eukaryot Cell 8:287–295. https://doi.org/10.1128/EC.00215-08

Cafarchia C, Romito D, Coccioli C et al (2008) Phospholipase activity of yeasts from wild birds and possible implications for human disease. Med Mycol 46:429–434. https://doi.org/10.1080/13693780701885636

Carreté L, Ksiezopolska E, Pegueroles C et al (2018) Patterns of genomic variation in the opportunistic pathogen *Candida glabrata* suggest the existence of mating and a secondary association with humans. Curr Biol 28:15–27.e7. https://doi.org/10.1016/j.cub.2017.11.027

Comas I, Coscolla M, Luo T et al (2013) Out-of-Africa migration and Neolithic coexpansion of *Mycobacterium tuberculosis* with modern humans. Nat Genet 45:1176–1182. https://doi.org/10.1038/ng.2744

de Meeûs T, Renaud F, Mouveroux E et al (2002) Genetic structure of *Candida glabrata* populations in AIDS and non-AIDS patients. J Clin Microbiol 40:2199–2206

de Melo Pereira GV, Soccol VT, Pandey A et al (2014) Isolation, selection and evaluation of yeasts for use in fermentation of coffee beans by the wet process. Int J Food Microbiol 188:60–66. https://doi.org/10.1016/j.ijfoodmicro.2014.07.008

D Hodgson AR, Pujol C, Denning DW et al (2003) Multilocus sequence typing of *Candida glabrata* reveals geographically enriched clades. J Clin Microbiol 41:5709–5717

Dodgson AR, Pujol C, Pfaller MA et al (2005) Evidence for recombination in *Candida glabrata*. Fungal Genet Biol 42:233–243. https://doi.org/10.1016/j.fgb.2004.11.010

Dujon B et al (2004) Genome evolution in yeast. Nature 430:35–43

Fabre E, Muller H, Therizols P et al (2005) Comparative genomics in hemiascomycete yeasts: evolution of sex, silencing, and subtelomeres. Mol Biol Evol 22:856–873. https://doi.org/10.1093/molbev/msi070

Francesca N, Carvalho C, Sannino C et al (2014) Yeasts vectored by migratory birds collected in the Mediterranean island of Ustica and description of *Phaffomyces usticensis* f.a. sp. nov., a new species related to the cactus ecoclade. FEMS Yeast Res 14:910–921. https://doi.org/10.1111/1567-1364.12179

Fundyga RE, Lott TJ, Arnold J (2002) Population structure of *Candida albicans*, a member of the human flora, as determined by microsatellite loci. Infect Genet Evol 2:57–68

Gabaldón T, Carreté L (2016) The birth of a deadly yeast: tracing the evolutionary emergence of virulence traits in *Candida glabrata*. FEMS Yeast Res 16:fov110

Gabaldón T, Martin T, Marcet-Houben M et al (2013) Comparative genomics of emerging pathogens in the *Candida glabrata* clade. BMC Genom 14:623. https://doi.org/10.1186/1471-2164-14-623

Gabaldón T, Naranjo-Ortíz MA, Marcet-Houben M (2016) Evolutionary genomics of yeast pathogens in the Saccharomycotina. FEMS Yeast Res 16:fov064

Goddard MR, Greig D (2015) *Saccharomyces cerevisiae*: a nomadic yeast with no niche? FEMS Yeast Res 15:1–6. https://doi.org/10.1093/femsyr/fov009

Haber JE (2012) Mating-type genes and MAT switching in *Saccharomyces cerevisiae*. Genetics 191:33–64. https://doi.org/10.1534/genetics.111.134577

Hazen KC (1995) New and emerging yeast pathogens. Clin Microbiol Rev 8:462–478

Huang M, Hull CM (2017) Sporulation: how to survive on planet Earth (and beyond). Curr Genet 63:831–838

Just G, Steinheimer D, Schnellbach M et al (1989) Change of causative organisms under antifungal treatment in immunosuppressed patients with HIV-infections. Mycoses 32:47–51. https://doi.org/10.1111/j.1439-0507.1989.tb02310.x

Klotz U, Schmidt D, Willinger B et al (2016) Echinocandin resistance and population structure of invasive *Candida glabrata* isolates from two university hospitals in Germany and Austria. Mycoses 59:312–318. https://doi.org/10.1111/myc.12472

Kordecka A, Krajewska-Kułak E, Łukaszuk C et al (2016) Isolation frequency of Candida present on the surfaces of mobile phones and handsx. BMC Infect Dis. https://doi.org/10.1186/s12879-016-1577-0

Kurtzman CP, Robnett CJ (2003) Phylogenetic relationships among yeasts of the “Saccharomyces complex” determined from multigene sequence analyses. FEMS Yeast Res 3:417–432. https://doi.org/10.1016/S1567-1356(03)00012-6

Muller H, Hennequin C, Gallaud J et al (2008) The asexual yeast *Candida glabrata* maintains distinct a and α haploid mating types. Eukaryot Cell 7:848–858. https://doi.org/10.1128/EC.00456-07
finding a needle in a haystack; but, until this is done in an
extensive manner, the jury will remain out on the question
of the environmental reservoir.

**Acknowledgements** TG group acknowledges support from the Spanish Ministry of Economy, Industry, and Competitiveness (MEIC) for the EMBL partnership, and Grants ‘Centro de Excelencia Severo Ochoa 2013–2017’ SEV-2012-0208, and BFU2015-67107 cofounded by European Regional Development Fund (ERDF); from the CERCA Programme / Generalitat de Catalunya; from the Catalan Research Agency (AGAUR) SGR857, and Grant from the European Union’s Horizon 2020 research and innovation programme under the Grant Agreement ERC-2016-724173 the Marie Skłodowska-Curie Grant Agreement no. H2020-MSCA-ITN-2014-642095. CF acknowledges support from the CNRS through the GDRI iGénolevures.

**Open Access** This article is distributed under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made.

## References

Al-Yasiri MH, Normand AC, L'Ollivier C et al (2016) Opportunistic fungal pathogen *Candida glabrata* circulates between humans and yellow-legged gulls. Sci Rep. https://doi.org/10.1038/srep36157

Anderson HW (1917) Yeast-like fungi of the human intestinal tract. J Infect Dis 21:341–354. https://doi.org/10.1093/infdis/21.4.341

Angoulvant A, Guitard J, Hennequin C (2016) Old and new pathogenic *Nakaseomyces* species: epidemiology, biology, identification, pathogenicity and antifungal resistance. FEMS Yeast Res 16:fov114

Bensasson D, Dicks J, Ludwig JM et al (2018) Diverse lineages of *Candida albicans* live on old oaks. bioRxiv. https://doi.org/10.1101/341032

Boisnard S, Li YZ, Arnaise S et al (2015) Efficient mating-type switching in *Candida glabrata* induces cell death. PLoS One. https://doi.org/10.1371/journal.pone.0140990

Bojsen R, Regenberg B, Folkesson A (2017) Persistence and drug tolerance in pathogenic yeast. Curr Genet 63:19–22

Brisse S, Pannier C, Angoulvant A et al (2009) Uneven distribution of mating types among genotypes of *Candida glabrata* isolates from clinical samples. Eukaryot Cell 8:287–295. https://doi.org/10.1128/EC.00215-08

Cafarchia C, Romito D, Coccioli C et al (2008) Phospholipase activity of yeasts from wild birds and possible implications for human disease. Med Mycol 46:429–434. https://doi.org/10.1080/13693780701885636

Carreté L, Ksiezopolska E, Pegueroles C et al (2018) Patterns of genomic variation in the opportunistic pathogen *Candida glabrata* suggest the existence of mating and a secondary association with humans. Curr Biol 28:15–27.e7. https://doi.org/10.1016/j.cub.2017.11.027

Comas I, Coscolla M, Luo T et al (2013) Out-of-Africa migration and Neolithic coexpansion of *Mycobacterium tuberculosis* with modern humans. Nat Genet 45:1176–1182. https://doi.org/10.1038/ng.2744

de Meeûs T, Renaud F, Mouveroux E et al (2002) Genetic structure of *Candida glabrata* populations in AIDS and non-AIDS patients. J Clin Microbiol 40:2199–2206

de Melo Pereira GV, Soccol VT, Pandey A et al (2014) Isolation, selection and evaluation of yeasts for use in fermentation of coffee beans by the wet process. Int J Food Microbiol 188:60–66. https://doi.org/10.1016/j.ijfoodmicro.2014.07.008

D Hodgson AR, Pujol C, Denning DW et al (2003) Multilocus sequence typing of *Candida glabrata* reveals geographically enriched clades. J Clin Microbiol 41:5709–5717

D Hodgson AR, Pujol C, Pfaller MA et al (2005) Evidence for recombination in *Candida glabrata*. Fungal Genet Biol 42:233–243. https://doi.org/10.1016/j.fgb.2004.11.010

Dujon B et al (2004) Genome evolution in yeast. Nature 430:35–43

Fabre E, Muller H, Therizols P et al (2005) Comparative genomics in hemiascomycete yeasts: evolution of sex, silencing, and subtelomeres. Mol Biol Evol 22:856–873. https://doi.org/10.1093/molbev/msi070

Francesca N, Carvalho C, Sannino C et al (2014) Yeasts vectored by migratory birds collected in the Mediterranean island of Ustica and description of *Phaffomyces usticensis* f.a. sp. nov., a new species related to the cactus ecoclade. FEMS Yeast Res 14:910–921. https://doi.org/10.1111/1567-1364.12179

Fundyga RE, Lott TJ, Arnold J (2002) Population structure of *Candida albicans*, a member of the human flora, as determined by microsatellite loci. Infect Genet Evol 2:57–68

Gabaldón T, Carreté L (2016) The birth of a deadly yeast: tracing the evolutionary emergence of virulence traits in *Candida glabrata*. FEMS Yeast Res 16:fov110

Gabaldón T, Martin T, Marcet-Houben M et al (2013) Comparative genomics of emerging pathogens in the *Candida glabrata* clade. BMC Genom 14:623. https://doi.org/10.1186/1471-2164-14-623

Gabaldón T, Naranjo-Ortíz MA, Marcet-Houben M (2016) Evolutionary genomics of yeast pathogens in the Saccharomycotina. FEMS Yeast Res 16:fov064

Goddard MR, Greig D (2015) *Saccharomyces cerevisiae*: a nomadic yeast with no niche? FEMS Yeast Res 15:1–6. https://doi.org/10.1093/femsyr/fov009

Haber JE (2012) Mating-type genes and MAT switching in *Saccharomyces cerevisiae*. Genetics 191:33–64. https://doi.org/10.1534/genetics.111.134577

Hazen KC (1995) New and emerging yeast pathogens. Clin Microbiol Rev 8:462–478

Huang M, Hull CM (2017) Sporulation: how to survive on planet Earth (and beyond). Curr Genet 63:831–838

Just G, Steinheimer D, Schnellbach M et al (1989) Change of causative organisms under antifungal treatment in immunosuppressed patients with HIV-infections. Mycoses 32:47–51. https://doi.org/10.1111/j.1439-0507.1989.tb02310.x

Klotz U, Schmidt D, Willinger B et al (2016) Echinocandin resistance and population structure of invasive *Candida glabrata* isolates from two university hospitals in Germany and Austria. Mycoses 59:312–318. https://doi.org/10.1111/myc.12472

Kordecka A, Krajewska-Kułak E, Łukaszuk C et al (2016) Isolation frequency of Candida present on the surfaces of mobile phones and handsx. BMC Infect Dis. https://doi.org/10.1186/s12879-016-1577-0

Kurtzman CP, Robnett CJ (2003) Phylogenetic relationships among yeasts of the “Saccharomyces complex” determined from multigene sequence analyses. FEMS Yeast Res 3:417–432. https://doi.org/10.1016/S1567-1356(03)00012-6

Muller H, Hennequin C, Gallaud J et al (2008) The asexual yeast *Candida glabrata* maintains distinct a and α haploid mating types. Eukaryot Cell 7:848–858. https://doi.org/10.1128/EC.00456-07
Pujol C, Reynes J, Renaud F et al (1993) The yeast *Candida albicans* has a clonal mode of reproduction in a population of infected human immunodeficiency virus-positive patients. Proc Natl Acad Sci USA 90:9456–9459

Roetzer A, Gabaldón T, Schüller C (2011) From *Saccharomyces cerevisiae* to *Candida glabrata* in a few easy steps: important adaptations for an opportunistic pathogen. FEMS Microbiol Lett 314:1–9

Rolland T, Dujon B, Richard G-F (2010) Dynamic evolution of megasatellites in yeasts. Nucleic Acids Res 38:4731–4739. https://doi.org/10.1093/nar/gkq207

Ropars J, Maufrais C, Diogo D et al (2018) Gene flow contributes to diversification of the major fungal pathogen *Candida albicans*.

Nat Commun 9:2253. https://doi.org/10.1038/s41467-018-04787-4

Schwarzmüller T, Ma B, Hiller E et al (2014) Systematic phenotyping of a large-scale *Candida glabrata* deletion collection reveals novel antifungal tolerance genes. PLoS Pathog 10:e1004211. https://doi.org/10.1371/journal.ppat.1004211

Srikantha T, Lachke SA, Soll DR (2003) Three mating type-like loci in *Candida glabrata*. Eukaryot Cell 2:328–340. https://doi.org/10.1128/EC.2.2.328-340.2003

Tavanti A, Davidson AD, Fordyce MJ et al (2005) Population structure and properties of *Candida albicans*, as determined by multilocus sequence typing. J Clin Microbiol 43:5601–5613. https://doi.org/10.1128/JCM.43.11.5601-5613.2005
Pujol C, Reynes J, Renaud F et al (1993) The yeast *Candida albicans* has a clonal mode of reproduction in a population of infected human immunodeficiency virus-positive patients. Proc Natl Acad Sci USA 90:9456–9459

Roetzer A, Gabaldón T, Schüller C (2011) From *Saccharomyces cerevisiae* to *Candida glabrata* in a few easy steps: important adaptations for an opportunistic pathogen. FEMS Microbiol Lett 314:1–9

Rolland T, Dujon B, Richard G-F (2010) Dynamic evolution of megasatellites in yeasts. Nucleic Acids Res 38:4731–4739. https://doi.org/10.1093/nar/gkq207

Ropars J, Maufrais C, Diogo D et al (2018) Gene flow contributes to diversification of the major fungal pathogen *Candida albicans*.

Nat Commun 9:2253. https://doi.org/10.1038/s41467-018-04787-4

Schwarzmüller T, Ma B, Hiller E et al (2014) Systematic phenotyping of a large-scale *Candida glabrata* deletion collection reveals novel antifungal tolerance genes. PLoS Pathog 10:e1004211. https://doi.org/10.1371/journal.ppat.1004211

Srikantha T, Lachke SA, Soll DR (2003) Three mating type-like loci in *Candida glabrata*. Eukaryot Cell 2:328–340. https://doi.org/10.1128/EC.2.2.328-340.2003

Tavanti A, Davidson AD, Fordyce MJ et al (2005) Population structure and properties of *Candida albicans*, as determined by multilocus sequence typing. J Clin Microbiol 43:5601–5613. https://doi.org/10.1128/JCM.43.11.5601-5613.2005