Genome Diversity, Recombination, and Virulence across the Major Lineages of <italic toggle="yes">Paracoccidioides</italic>

ABSTRACT The Paracoccidioides genus includes two species of thermally dimorphic fungi that cause paracoccidioidomycosis, a neglected health-threatening human systemic mycosis endemic to Latin America. To examine the genome evolution and the diversity of Paracoccidioides spp., we conducted whole-geno...

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Autores principales:	José F. Muñoz, Rhys A. Farrer, Christopher A. Desjardins, Juan E. Gallo, Sean Sykes, Sharadha Sakthikumar, Elizabeth Misas, Emily A. Whiston, Eduardo Bagagli, Celia M. A. Soares, Marcus de M. Teixeira, John W. Taylor, Oliver K. Clay, Juan G. McEwen, Christina A. Cuomo
Formato:	article
Lenguaje:	EN
Publicado:	American Society for Microbiology 2016
Materias:	Paracoccidioides evolution genetic recombination genome analysis mycology population genetics Microbiology QR1-502
Acceso en línea:	https://doaj.org/article/6a93c6cabd1e432c99fc2232c16d8d22
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spelling	oai:doaj.org-article:6a93c6cabd1e432c99fc2232c16d8d222021-11-15T15:21:30ZGenome Diversity, Recombination, and Virulence across the Major Lineages of <italic toggle="yes">Paracoccidioides</italic>10.1128/mSphere.00213-162379-5042https://doaj.org/article/6a93c6cabd1e432c99fc2232c16d8d222016-10-01T00:00:00Zhttps://journals.asm.org/doi/10.1128/mSphere.00213-16https://doaj.org/toc/2379-5042ABSTRACT The Paracoccidioides genus includes two species of thermally dimorphic fungi that cause paracoccidioidomycosis, a neglected health-threatening human systemic mycosis endemic to Latin America. To examine the genome evolution and the diversity of Paracoccidioides spp., we conducted whole-genome sequencing of 31 isolates representing the phylogenetic, geographic, and ecological breadth of the genus. These samples included clinical, environmental and laboratory reference strains of the S1, PS2, PS3, and PS4 lineages of P. brasiliensis and also isolates of Paracoccidioides lutzii species. We completed the first annotated genome assemblies for the PS3 and PS4 lineages and found that gene order was highly conserved across the major lineages, with only a few chromosomal rearrangements. Comparing whole-genome assemblies of the major lineages with single-nucleotide polymorphisms (SNPs) predicted from the remaining 26 isolates, we identified a deep split of the S1 lineage into two clades we named S1a and S1b. We found evidence for greater genetic exchange between the S1b lineage and all other lineages; this may reflect the broad geographic range of S1b, which is often sympatric with the remaining, largely geographically isolated lineages. In addition, we found evidence of positive selection for the GP43 and PGA1 antigen genes and genes coding for other secreted proteins and proteases and lineage-specific loss-of-function mutations in cell wall and protease genes; these together may contribute to virulence and host immune response variation among natural isolates of Paracoccidioides spp. These insights into the recent evolutionary events highlight important differences between the lineages that could impact the distribution, pathogenicity, and ecology of Paracoccidioides. IMPORTANCE Characterization of genetic differences between lineages of the dimorphic human-pathogenic fungus Paracoccidioides can identify changes linked to important phenotypes and guide the development of new diagnostics and treatments. In this article, we compared genomes of 31 diverse isolates representing the major lineages of Paracoccidioides spp. and completed the first annotated genome sequences for the PS3 and PS4 lineages. We analyzed the population structure and characterized the genetic diversity among the lineages of Paracoccidioides, including a deep split of S1 into two lineages (S1a and S1b), and differentiated S1b, associated with most clinical cases, as the more highly recombining and diverse lineage. In addition, we found patterns of positive selection in surface proteins and secreted enzymes among the lineages, suggesting diversifying mechanisms of pathogenicity and adaptation across this species complex. These genetic differences suggest associations with the geographic range, pathogenicity, and ecological niches of Paracoccidioides lineages.José F. MuñozRhys A. FarrerChristopher A. DesjardinsJuan E. GalloSean SykesSharadha SakthikumarElizabeth MisasEmily A. WhistonEduardo BagagliCelia M. A. SoaresMarcus de M. TeixeiraJohn W. TaylorOliver K. ClayJuan G. McEwenChristina A. CuomoAmerican Society for MicrobiologyarticleParacoccidioidesevolutiongenetic recombinationgenome analysismycologypopulation geneticsMicrobiologyQR1-502ENmSphere, Vol 1, Iss 5 (2016)
institution	DOAJ
collection	DOAJ
language	EN
topic	Paracoccidioides evolution genetic recombination genome analysis mycology population genetics Microbiology QR1-502
spellingShingle	Paracoccidioides evolution genetic recombination genome analysis mycology population genetics Microbiology QR1-502 José F. Muñoz Rhys A. Farrer Christopher A. Desjardins Juan E. Gallo Sean Sykes Sharadha Sakthikumar Elizabeth Misas Emily A. Whiston Eduardo Bagagli Celia M. A. Soares Marcus de M. Teixeira John W. Taylor Oliver K. Clay Juan G. McEwen Christina A. Cuomo Genome Diversity, Recombination, and Virulence across the Major Lineages of <italic toggle="yes">Paracoccidioides</italic>
description	ABSTRACT The Paracoccidioides genus includes two species of thermally dimorphic fungi that cause paracoccidioidomycosis, a neglected health-threatening human systemic mycosis endemic to Latin America. To examine the genome evolution and the diversity of Paracoccidioides spp., we conducted whole-genome sequencing of 31 isolates representing the phylogenetic, geographic, and ecological breadth of the genus. These samples included clinical, environmental and laboratory reference strains of the S1, PS2, PS3, and PS4 lineages of P. brasiliensis and also isolates of Paracoccidioides lutzii species. We completed the first annotated genome assemblies for the PS3 and PS4 lineages and found that gene order was highly conserved across the major lineages, with only a few chromosomal rearrangements. Comparing whole-genome assemblies of the major lineages with single-nucleotide polymorphisms (SNPs) predicted from the remaining 26 isolates, we identified a deep split of the S1 lineage into two clades we named S1a and S1b. We found evidence for greater genetic exchange between the S1b lineage and all other lineages; this may reflect the broad geographic range of S1b, which is often sympatric with the remaining, largely geographically isolated lineages. In addition, we found evidence of positive selection for the GP43 and PGA1 antigen genes and genes coding for other secreted proteins and proteases and lineage-specific loss-of-function mutations in cell wall and protease genes; these together may contribute to virulence and host immune response variation among natural isolates of Paracoccidioides spp. These insights into the recent evolutionary events highlight important differences between the lineages that could impact the distribution, pathogenicity, and ecology of Paracoccidioides. IMPORTANCE Characterization of genetic differences between lineages of the dimorphic human-pathogenic fungus Paracoccidioides can identify changes linked to important phenotypes and guide the development of new diagnostics and treatments. In this article, we compared genomes of 31 diverse isolates representing the major lineages of Paracoccidioides spp. and completed the first annotated genome sequences for the PS3 and PS4 lineages. We analyzed the population structure and characterized the genetic diversity among the lineages of Paracoccidioides, including a deep split of S1 into two lineages (S1a and S1b), and differentiated S1b, associated with most clinical cases, as the more highly recombining and diverse lineage. In addition, we found patterns of positive selection in surface proteins and secreted enzymes among the lineages, suggesting diversifying mechanisms of pathogenicity and adaptation across this species complex. These genetic differences suggest associations with the geographic range, pathogenicity, and ecological niches of Paracoccidioides lineages.
format	article
author	José F. Muñoz Rhys A. Farrer Christopher A. Desjardins Juan E. Gallo Sean Sykes Sharadha Sakthikumar Elizabeth Misas Emily A. Whiston Eduardo Bagagli Celia M. A. Soares Marcus de M. Teixeira John W. Taylor Oliver K. Clay Juan G. McEwen Christina A. Cuomo
author_facet	José F. Muñoz Rhys A. Farrer Christopher A. Desjardins Juan E. Gallo Sean Sykes Sharadha Sakthikumar Elizabeth Misas Emily A. Whiston Eduardo Bagagli Celia M. A. Soares Marcus de M. Teixeira John W. Taylor Oliver K. Clay Juan G. McEwen Christina A. Cuomo
author_sort	José F. Muñoz
title	Genome Diversity, Recombination, and Virulence across the Major Lineages of <italic toggle="yes">Paracoccidioides</italic>
title_short	Genome Diversity, Recombination, and Virulence across the Major Lineages of <italic toggle="yes">Paracoccidioides</italic>
title_full	Genome Diversity, Recombination, and Virulence across the Major Lineages of <italic toggle="yes">Paracoccidioides</italic>
title_fullStr	Genome Diversity, Recombination, and Virulence across the Major Lineages of <italic toggle="yes">Paracoccidioides</italic>
title_full_unstemmed	Genome Diversity, Recombination, and Virulence across the Major Lineages of <italic toggle="yes">Paracoccidioides</italic>
title_sort	genome diversity, recombination, and virulence across the major lineages of <italic toggle="yes">paracoccidioides</italic>
publisher	American Society for Microbiology
publishDate	2016
url	https://doaj.org/article/6a93c6cabd1e432c99fc2232c16d8d22
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Genome Diversity, Recombination, and Virulence across the Major Lineages of <italic toggle="yes">Paracoccidioides</italic>

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