Gene flow contributes to diversification of the major fungal pathogen Candida albicans

Ropars, Jeanne; Maufrais, Corinne; Diogo, Dorothée; Marcet‐Houben, Marina; Perin, Aurélie; Sertour, Natacha; Mosca, Kevin; Permal, Emmanuelle; Laval, Guillaume; Bouchier, Christiane; Ma, Laurence; Schwartz, Katja; Voelz, Kerstin; May, Robin C.; Poulain, Julie; Battail, Christophe; Wincker, Patrick; Borman, Andrew M.; Chowdhary, Anuradha; Fan, Shang­rong; Kim, Soo Hyun; Pape, Patrice Le; Romeo, Orazio; Shin, Jong Hee; Gabaldón, Toni; Sherlock, Gavin; Bougnoux, Marie‐Elisabeth; d’Enfert, Christophe

doi:10.1038/s41467-018-04787-4

Cited by 141 publications

(259 citation statements)

References 73 publications

(83 reference statements)

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“…23 When it takes place, DNA sequencing allows tracking the region of the origin of an infectious agent. 24 Geographic races sometimes demonstrate clinical predilections 25 and peculiar drug-resistance properties. 26 Here, using a sample of T mentagrophytes and T interdigitale isolates from Iran and all available in GenBank ITS region sequences of the TMTISG, we were able to demonstrate that more than a half of observed genetic diversity within the species complex belonged to genotypes with geographically restricted ranges.…”

Section: Discussionmentioning

confidence: 99%

Trichophyton mentagrophytes and T interdigitale genotypes are associated with particular geographic areas and clinical manifestations

Taghipour

Pchelin

Mahmoudabadi

et al. 2019

Mycoses

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Summary The fungi Trichophyton mentagrophytes and T interdigitale account for significant amount of dermatophytosis cases worldwide. These two dermatophytes form a species complex and have a number of ribosomal internal transcribed spacer (ITS) region genotypes, allowing simultaneous species identification and strain typing. Our aim was to describe the geographic distribution of T mentagrophytes/T interdigitale ITS region genotypes and find an association between the genotypes and clinical presentations of respective infections. We performed rDNA ITS region sequencing in 397 Iranian T mentagrophytes/T interdigitale isolates and analysed all available in GenBank entries with sequences of this kind. For the study, 515 clinical annotations were available. Statistical analysis was performed by chi‐squared test and Spearman rank correlation analysis. A total of 971 sequences belonged to genotypes with at least 10 geographic annotations and were classified on the basis of exclusive occurrence in a particular region or high relative contribution to a regional sample. We discerned Asian and Oceanian (“” Type V, “” Type VIII, “”), European (“” Type III, “” Type III*, “” Type VI) and cosmopolitan (“” Type I, “” Type II, “” Type II* and “” Type XXIV) genotypes. There was statistically significant difference in the ITS genotype distribution between different affected body sites. Trichophyton mentagrophytes “” Type VIII correlated with tinea cruris, T mentagrophytes “” Type V correlated with tinea corporis, T interdigitale “” Type II correlated with tinea pedis and onychomycosis. Trichophyton mentagrophytes and T interdigitale genotypes can be associated with distinct geographic locations and particular clinical presentations.

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Section: Discussionmentioning

confidence: 99%

Trichophyton mentagrophytes and T interdigitale genotypes are associated with particular geographic areas and clinical manifestations

Taghipour

Pchelin

Mahmoudabadi

et al. 2019

Mycoses

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“…This type of event leads to a decrease of the genetic variability allowing the expression of recessive alleles, and therefore can result in a beneficial adaptation in some environments. The prevalence of LOH events has recently been observed in several yeast species such as S. cerevisiae (Peter, et al 2018), Candida albicans (Ropars, et al 2018) and Kluyveromyces marxianus (Ortiz-Merino, et al 2018). Moreover, previous studies of B. bruxellensis isolates revealed the presence of several regions which underwent LOH.…”

Section: Genomes Are Punctuated By a Few Loss-of-heterozygosity Regionsmentioning

confidence: 94%

“…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.…”

Section: Introductionmentioning

confidence: 99%

High complexity and degree of genetic variation inBrettanomyces bruxellensispopulation

Gounot

Neuvéglise

Freel

et al. 2019

Preprint

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AbstractGenome-wide characterization of genetic variants of a large population of individuals within the same species is essential to have a deeper insight into its evolutionary history as well as the genotype-phenotype relationship. Population genomic surveys have been performed in multiple yeast species, including the two model organisms, Saccharomyces cerevisiae and Schizosaccharomyces pombe. In this context, we sought to explore an uncharacterized yeast species, Brettanomyces bruxellensis, which is a major cause of wine spoilage but also can contribute to the specific flavor profile of some Belgium beers. We have completely sequenced the genome of 53 B. bruxellensis strains isolated worldwide. The annotation of the reference genome allowed us to define the gene content of this species. As previously suggested, our genomic data clearly highlighted that genetic diversity variation is related to ploidy level, which is variable in the B. bruxellensis species. Genomes are punctuated by multiple loss-of-heterozygosity regions while aneuploidies as well as segmental duplications are uncommon. Interestingly, triploid genomes are more prone to gene copy number variation than diploids. Finally, the pangenome of the species was reconstructed and was found to be small with few accessory genes compared to S. cerevisiae. The pangenome is composed of 4,923 core ORFs and 303 ORFs that are variable within the population. All these results highlight the different trajectories of species evolution and consequently the interest of establishing population genomic surveys in more populations.

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“…1Molecular 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 …”

Section: Resolving Puzzles From Genomics Footprintsmentioning

confidence: 99%

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

Gabaldón

Fairhead

2018

Curr Genet

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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.

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Gene flow contributes to diversification of the major fungal pathogen Candida albicans

Cited by 141 publications

References 73 publications

Trichophyton mentagrophytes and T interdigitale genotypes are associated with particular geographic areas and clinical manifestations

Trichophyton mentagrophytes and T interdigitale genotypes are associated with particular geographic areas and clinical manifestations

High complexity and degree of genetic variation inBrettanomyces bruxellensispopulation

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

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