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The main agents include members of the\n                    <jats:italic>P. brasiliensis<\/jats:italic>\n                    complex (phylogenetically-defined species S1, PS2, PS3, and\n PS4) and\n                    <jats:italic>P. lutzii<\/jats:italic>\n                    . DNA-sequencing of protein-coding loci (e.g.,\n                    <jats:italic>GP43<\/jats:italic>\n                    ,\n                    <jats:italic>ARF<\/jats:italic>\n                    , and\n                    <jats:italic>TUB1<\/jats:italic>\n                    ) is the reference method for recognizing\n                    <jats:italic>Paracoccidioides<\/jats:italic>\n                    species due to a lack of robust phenotypic markers. Thus, developing new molecular markers that are informative\n and cost-effective is key to providing quality information to explore genetic diversity within\n                    <jats:italic>Paracoccidioides<\/jats:italic>\n                    . We report using new amplified fragment length polymorphism (AFLP) markers and mating-type analysis for genotyping\n                    <jats:italic>Paracoccidioides<\/jats:italic>\n                    species. The bioinformatic analysis\n generated 144\n                    <jats:italic>in silico<\/jats:italic>\n                    AFLP profiles, highlighting two discriminatory primer pairs combinations (#1 EcoRI-AC\/MseI-CT and #2 EcoRI-AT\/MseI-CT). The combinations #1 and #2 were used\n                    <jats:italic>in vitro<\/jats:italic>\n                    to genotype 165\n                    <jats:italic>Paracoccidioides<\/jats:italic>\n                    isolates recovered from across a vast area of\n South America. Considering the overall scored AFLP markers\n                    <jats:italic>in vitro<\/jats:italic>\n                    (67-87 fragments), the values of polymorphism information content (\n                    <jats:italic>PIC<\/jats:italic>\n                    = 0.3345-0.3456), marker index (\n                    <jats:italic>MI<\/jats:italic>\n                    = 0.0018), effective multiplex ratio (\n                    <jats:italic>E<\/jats:italic>\n                    = 44.6788-60.3818), resolving power (\n                    <jats:italic>Rp<\/jats:italic>\n                    =\n 22.3152-34.3152), discriminating power (\n                    <jats:italic>D<\/jats:italic>\n                    = 0.5183-0.5553), expected heterozygosity (\n                    <jats:italic>H<\/jats:italic>\n                    = 0.4247-0.4443), and mean heterozygosity (\n                    <jats:italic>H<\/jats:italic>\n                    &lt;inf&gt;\n                    <jats:italic>avp<\/jats:italic>\n                    &lt;\/inf&gt; = 0.00002-0.00004), demonstrated the utility of AFLP markers to speciate\n                    <jats:italic>Paracoccidioides<\/jats:italic>\n                    and to\n dissect both deep and fine-scale genetic structures. Analysis of molecular variance (AMOVA) revealed that the total genetic variance (65-66\u00a0%) was due to variability among\n                    <jats:italic>P. brasiliensis<\/jats:italic>\n                    complex and\n                    <jats:italic>P. lutzii<\/jats:italic>\n                    (PhiPT = 0.651-0.658,\n                    <jats:italic>P<\/jats:italic>\n                    \u00a0&lt;\u00a00.0001), supporting\n a highly structured population. Heterothallism was the exclusive mating strategy, and the distributions of\n                    <jats:italic>MAT1-1<\/jats:italic>\n                    or\n                    <jats:italic>MAT1-2<\/jats:italic>\n                    idiomorphs were not significantly skewed (1:1 ratio) for\n                    <jats:italic>P. brasiliensis s. str.<\/jats:italic>\n                    (\u03c7\n                    <jats:sup>2<\/jats:sup>\n                    = 1.025;\n                    <jats:italic>P<\/jats:italic>\n                    = 0.3113),\n                    <jats:italic>P. venezuelensis<\/jats:italic>\n                    (\u03c7\n                    <jats:sup>2<\/jats:sup>\n                    = 0.692;\n                    <jats:italic>P<\/jats:italic>\n                    = 0.4054), and\n                    <jats:italic>P. lutzii<\/jats:italic>\n                    (\u03c7\n                    <jats:sup>2<\/jats:sup>\n                    = 0.027;\n                    <jats:italic>P<\/jats:italic>\n                    = 0.8694), supporting random mating within each species. In contrast, skewed distributions were found for\n                    <jats:italic>P. americana<\/jats:italic>\n                    (\u03c7\n                    <jats:sup>2<\/jats:sup>\n                    = 8.909;\n                    <jats:italic>P<\/jats:italic>\n                    = 0.0028) and\n                    <jats:italic>P. restrepiensis<\/jats:italic>\n                    (\u03c7\n                    <jats:sup>2<\/jats:sup>\n                    = 4.571;\n                    <jats:italic>P<\/jats:italic>\n                    = 0.0325) with a preponderance of\n                    <jats:italic>MAT1-1<\/jats:italic>\n                    . Geographical distributions confirmed that\n                    <jats:italic>P. americana<\/jats:italic>\n                    ,\n                    <jats:italic>P. restrepiensis<\/jats:italic>\n                    , and\n                    <jats:italic>P. lutzii<\/jats:italic>\n                    are more widespread than previously thought.\n                    <jats:italic>P. brasiliensis s. str.<\/jats:italic>\n                    is by far the most\n widely occurring lineage in Latin America countries, occurring in all regions of Brazil. Our new DNA fingerprint assay proved to be rapid, reproducible, and highly discriminatory, to give insights into the taxonomy, ecology, and epidemiology of\n                    <jats:italic>Paracoccidioides<\/jats:italic>\n                    species, guiding disease-control\n strategies to mitigate PCM.\n                  <\/jats:p>","DOI":"10.1016\/j.simyco.2021.100131","type":"journal-article","created":{"date-parts":[[2021,11,30]],"date-time":"2021-11-30T20:30:43Z","timestamp":1638304243000},"page":"100131-100131","source":"Crossref","is-referenced-by-count":28,"title":["Exploring genetic diversity, population structure, and phylogeography in\n                    <i>Paracoccidioides<\/i>\n                    species using AFLP markers"],"prefix":"10.3114","volume":"100","author":[{"given":"T.N.","family":"Roberto","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"J.A.","family":"de Carvalho","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"M.A.","family":"Beale","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"F.","family":"Hagen","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"M.C.","family":"Fisher","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"R.C.","family":"Hahn","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Z.P.","family":"de Camargo","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"A.M.","family":"Rodrigues","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"1645","reference":[{"key":"10.1016\/j.simyco.2021.100131_bib1","doi-asserted-by":"crossref","DOI":"10.1371\/journal.pntd.0007742","article-title":"A\u00a0hidden battle in the dirt: Soil amoebae interactions with Paracoccidioides spp","volume":"13","author":"Albuquerque","year":"2019","journal-title":"PLoS Neglected Tropical Diseases"},{"key":"10.1016\/j.simyco.2021.100131_bib2","doi-asserted-by":"crossref","first-page":"368","DOI":"10.4269\/ajtmh.16-0254","article-title":"Paracoccidioidomycosis in Brazilian patients with and without human immunodeficiency virus infection","volume":"96","author":"Almeida","year":"2017","journal-title":"American Journal of Tropical Medicine and Hygiene"},{"key":"10.1016\/j.simyco.2021.100131_bib3","first-page":"125","article-title":"Estudos comparativos do granuloma coccidi\u00f3idico nos Estados Unidos e no Brasil. 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