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Whole genome analysis illustrates global clonal population structure of the ubiquitous dermatophyte pathogen Trichophyton rubrum

Gabriela F. Persinoti, Diego A. Martinez, Wenjun Li, Aylin Döğen, R. Blake Billmyre, Anna Averette, Jonathan M. Goldberg, Terrance Shea, Sarah Young, Qiandong Zeng, Brian G. Oliver, Richard Barton, Banu Metin, Süleyha Hilmioğlu-Polat, View ORCID ProfileMacit Ilkit, Yvonne Gräser, View ORCID ProfileNilce M. Martinez-Rossi, Theodore C. White, Joseph Heitman, View ORCID ProfileChristina A. Cuomo
doi: https://doi.org/10.1101/261743
Gabriela F. Persinoti
*Department of Genetics, Ribeirão Preto Medical School, University of São Paulo, Brazil
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Diego A. Martinez
†Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, USA
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Wenjun Li
‡Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, North Carolina, USA
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Aylin Döğen
‡Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, North Carolina, USA
§Department of Pharmaceutical Microbiology, Faculty of Pharmacy, University of Mersin, Mersin, Turkey
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R. Blake Billmyre
‡Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, North Carolina, USA
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Anna Averette
‡Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, North Carolina, USA
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Jonathan M. Goldberg
†Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, USA
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Terrance Shea
†Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, USA
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Sarah Young
†Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, USA
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Qiandong Zeng
†Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, USA
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Brian G. Oliver
**Center for Infectious Disease Research, Seattle, Washington, USA
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Richard Barton
††University of Leeds, Leeds, United Kingdom
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Banu Metin
‡‡Department of Food Engineering, Faculty of Engineering and Natural Sciences, Istanbul Sabahattin Zaim University, Istanbul, Turkey
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Süleyha Hilmioğlu-Polat
§§Department of Microbiology, Faculty of Medicine, University of Ege, Izmir, Turkey
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Macit Ilkit
***Division of Mycology, Department of Microbiology, Faculty of Medicine University of çukurova, Adana, Turkey
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  • ORCID record for Macit Ilkit
Yvonne Gräser
†††Institute of Microbiology and Hygiene, University Medicine Berlin - Charité, Berlin, Germany
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Nilce M. Martinez-Rossi
*Department of Genetics, Ribeirão Preto Medical School, University of São Paulo, Brazil
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Theodore C. White
‡‡‡School of Biological Sciences, University of Missouri-Kansas City, Kansas City, Missouri, USA
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Joseph Heitman
‡Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, North Carolina, USA
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  • For correspondence: cuomo@broadinstitute.org heitm001@duke.edu
Christina A. Cuomo
†Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, USA
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  • ORCID record for Christina A. Cuomo
  • For correspondence: cuomo@broadinstitute.org heitm001@duke.edu
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Abstract

Dermatophytes include fungal species that infect humans, as well as those which also infect other animals or only grow in the environment. The dermatophyte species Trichophyton rubrum is a frequent cause of skin infection in immunocompetent individuals. While members of the T. rubrum species complex have been further categorized based on various morphologies, the population structure and ability to undergo sexual reproduction are not well understood. In this study, we analyze a large set of T. rubrum and Trichophyton interdigitale isolates to examine mating types, evidence of mating, and genetic variation. We find that nearly all isolates of T. rubrum are of a single mating type, and that incubation with T. rubrum morphotype megninii isolates of the other mating type failed to induce sexual development. While the region around the mating type locus is characterized by a higher frequency of SNPs compared to other genomic regions, we find that the population is remarkably clonal, with highly conserved gene content, low levels of variation, and little evidence of recombination These results support a model of recent transition to asexual growth when this species specialized to growth on human hosts.

Data access: Genome sequence data is available in NCBI under the Umbrella BioProject PRJNA186851.

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The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY 4.0 International license.
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Posted February 08, 2018.
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Whole genome analysis illustrates global clonal population structure of the ubiquitous dermatophyte pathogen Trichophyton rubrum
Gabriela F. Persinoti, Diego A. Martinez, Wenjun Li, Aylin Döğen, R. Blake Billmyre, Anna Averette, Jonathan M. Goldberg, Terrance Shea, Sarah Young, Qiandong Zeng, Brian G. Oliver, Richard Barton, Banu Metin, Süleyha Hilmioğlu-Polat, Macit Ilkit, Yvonne Gräser, Nilce M. Martinez-Rossi, Theodore C. White, Joseph Heitman, Christina A. Cuomo
bioRxiv 261743; doi: https://doi.org/10.1101/261743
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Whole genome analysis illustrates global clonal population structure of the ubiquitous dermatophyte pathogen Trichophyton rubrum
Gabriela F. Persinoti, Diego A. Martinez, Wenjun Li, Aylin Döğen, R. Blake Billmyre, Anna Averette, Jonathan M. Goldberg, Terrance Shea, Sarah Young, Qiandong Zeng, Brian G. Oliver, Richard Barton, Banu Metin, Süleyha Hilmioğlu-Polat, Macit Ilkit, Yvonne Gräser, Nilce M. Martinez-Rossi, Theodore C. White, Joseph Heitman, Christina A. Cuomo
bioRxiv 261743; doi: https://doi.org/10.1101/261743

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