title: Genome Diversity, Recombination, and Virulence across the Major Lineages ofParacoccidioides.
abstract: TheParacoccidioidesgenus 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 ofParacoccidioidesspp., 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 ofP. brasiliensisand also isolates ofParacoccidioides lutziispecies.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 theGP43andPGA1antigen 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 ofParacoccidioidesspp. These insights into the recent evolutionary events highlight important differences between the lineages that could impact the distribution, pathogenicity, and ecology ofParacoccidioides.IMPORTANCECharacterization of genetic differences between lineages of the dimorphic human-pathogenic fungusParacoccidioidescan 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 ofParacoccidioidesspp. 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 ofParacoccidioides, 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 ofParacoccidioideslineages.
authors.affiliation: Cellular and Molecular Biology Unit, Corporación para Investigaciones Biológicas, Medellín, Colombia; Institute of Biology, Universidad de Antioquia, Medellín, Colombia; Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA.
authors.forename: José F
authors.initials: JF
authors.lastname: Muñoz
authors.affiliation: Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA.
authors.forename: Rhys A
authors.identifier: 0000-0001-8456-7458
authors.initials: RA
authors.lastname: Farrer
authors.affiliation: Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA.
authors.forename: Christopher A
authors.initials: CA
authors.lastname: Desjardins
authors.affiliation: Cellular and Molecular Biology Unit, Corporación para Investigaciones Biológicas, Medellín, Colombia; Doctoral Program in Biomedical Sciences, Universidad del Rosario, Bogotá, Colombia.
authors.forename: Juan E
authors.initials: JE
authors.lastname: Gallo
authors.affiliation: Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA.
authors.forename: Sean
authors.initials: S
authors.lastname: Sykes
authors.affiliation: Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA.
authors.forename: Sharadha
authors.initials: S
authors.lastname: Sakthikumar
authors.affiliation: Cellular and Molecular Biology Unit, Corporación para Investigaciones Biológicas, Medellín, Colombia; Institute of Biology, Universidad de Antioquia, Medellín, Colombia.
authors.forename: Elizabeth
authors.initials: E
authors.lastname: Misas
authors.affiliation: Department of Plant and Microbial Biology, University of California, Berkeley, Berkeley, California, USA.
authors.forename: Emily A
authors.initials: EA
authors.lastname: Whiston
authors.affiliation: Instituto de Biociências, Universidade Estadual Paulista, Botucatu, São Paulo, Brazil.
authors.forename: Eduardo
authors.initials: E
authors.lastname: Bagagli
authors.affiliation: Laboratório de Biología Molecular, Instituto de Ciências Biológicas, ICBII, Goiânia, Brazil.
authors.forename: Celia M A
authors.initials: CM
authors.lastname: Soares
authors.affiliation: Instituto de Ciências Biológicas, Universidade de Brasília, Brasília, Distrito Federal, Brazil; Division of Pathogen Genomics, Translational Genomics Research Institute North, Flagstaff, Arizona, USA.
authors.forename: Marcus de M
authors.initials: MM
authors.lastname: Teixeira
authors.affiliation: Department of Plant and Microbial Biology, University of California, Berkeley, Berkeley, California, USA.
authors.forename: John W
authors.initials: JW
authors.lastname: Taylor
authors.affiliation: Cellular and Molecular Biology Unit, Corporación para Investigaciones Biológicas, Medellín, Colombia; School of Medicine and Health Sciences, Universidad del Rosario, Bogotá, Colombia.
authors.forename: Oliver K
authors.initials: OK
authors.lastname: Clay
authors.affiliation: Cellular and Molecular Biology Unit, Corporación para Investigaciones Biológicas, Medellín, Colombia; School of Medicine, Universidad de Antioquia, Medellín, Colombia.
authors.forename: Juan G
authors.initials: JG
authors.lastname: McEwen
authors.affiliation: Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA.
authors.forename: Christina A
authors.identifier: 0000-0002-5778-960X
authors.initials: CA
authors.lastname: Cuomo
keywords: Paracoccidioides; evolution; genetic recombination; genome analysis; mycology; population genetics