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In this article, we compared genomes of 31 diverse isolates representing the major lineages of\n            <jats:italic>Paracoccidioides<\/jats:italic>\n            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\n            <jats:italic>Paracoccidioides<\/jats:italic>\n            , 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\n            <jats:italic>Paracoccidioides<\/jats:italic>\n            lineages.\n          <\/jats:p>","DOI":"10.1128\/msphere.00213-16","type":"journal-article","created":{"date-parts":[[2016,9,29]],"date-time":"2016-09-29T02:39:15Z","timestamp":1475116755000},"update-policy":"https:\/\/doi.org\/10.1128\/asmj-crossmark-policy-page","source":"Crossref","is-referenced-by-count":99,"title":["Genome Diversity, Recombination, and Virulence across the Major Lineages of\n            <i>Paracoccidioides<\/i>"],"prefix":"10.1128","volume":"1","author":[{"given":"Jos\u00e9 F.","family":"Mu\u00f1oz","sequence":"first","affiliation":[{"name":"Cellular and Molecular Biology Unit, Corporaci\u00f3n para Investigaciones Biol\u00f3gicas, Medell\u00edn, Colombia"},{"name":"Institute of Biology, Universidad de Antioquia, Medell\u00edn, Colombia"},{"name":"Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-8456-7458","authenticated-orcid":false,"given":"Rhys A.","family":"Farrer","sequence":"additional","affiliation":[{"name":"Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Christopher A.","family":"Desjardins","sequence":"additional","affiliation":[{"name":"Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Juan E.","family":"Gallo","sequence":"additional","affiliation":[{"name":"Cellular and Molecular Biology Unit, Corporaci\u00f3n para Investigaciones Biol\u00f3gicas, Medell\u00edn, Colombia"},{"name":"Doctoral Program in Biomedical Sciences, Universidad del Rosario, Bogot\u00e1, Colombia"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Sean","family":"Sykes","sequence":"additional","affiliation":[{"name":"Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Sharadha","family":"Sakthikumar","sequence":"additional","affiliation":[{"name":"Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Elizabeth","family":"Misas","sequence":"additional","affiliation":[{"name":"Cellular and Molecular Biology Unit, Corporaci\u00f3n para Investigaciones Biol\u00f3gicas, Medell\u00edn, Colombia"},{"name":"Institute of Biology, Universidad de Antioquia, Medell\u00edn, Colombia"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Emily A.","family":"Whiston","sequence":"additional","affiliation":[{"name":"Department of Plant and Microbial Biology, University of California, Berkeley, Berkeley, California, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Eduardo","family":"Bagagli","sequence":"additional","affiliation":[{"name":"Instituto de Bioci\u00eancias, Universidade Estadual Paulista, Botucatu, S\u00e3o Paulo, Brazil"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Celia M. 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