PMID- 34934463 OWN - NLM STAT- PubMed-not-MEDLINE LR - 20240404 IS - 0166-0616 (Print) IS - 1872-9797 (Electronic) IS - 0166-0616 (Linking) VI - 100 DP - 2021 Sep TI - Exploring genetic diversity, population structure, and phylogeography in Paracoccidioides species using AFLP markers. PG - 100131 LID - 10.1016/j.simyco.2021.100131 [doi] LID - 100131 AB - Paracoccidioidomycosis (PCM) is a life-threatening systemic fungal infection acquired after inhalation of Paracoccidioides propagules from the environment. The main agents include members of the P. brasiliensis complex (phylogenetically-defined species S1, PS2, PS3, and PS4) and P. lutzii. DNA-sequencing of protein-coding loci (e.g., GP43, ARF, and TUB1) is the reference method for recognizing Paracoccidioides species due to a lack of robust phenotypic markers. Thus, developing new molecular markers that are informative and cost-effective is key to providing quality information to explore genetic diversity within Paracoccidioides. We report using new amplified fragment length polymorphism (AFLP) markers and mating-type analysis for genotyping Paracoccidioides species. The bioinformatic analysis generated 144 in silico 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 in vitro to genotype 165 Paracoccidioides isolates recovered from across a vast area of South America. Considering the overall scored AFLP markers in vitro (67-87 fragments), the values of polymorphism information content (PIC = 0.3345-0.3456), marker index (MI = 0.0018), effective multiplex ratio (E = 44.6788-60.3818), resolving power (Rp = 22.3152-34.3152), discriminating power (D = 0.5183-0.5553), expected heterozygosity (H = 0.4247-0.4443), and mean heterozygosity (H (avp) = 0.00002-0.00004), demonstrated the utility of AFLP markers to speciate Paracoccidioides and to dissect both deep and fine-scale genetic structures. Analysis of molecular variance (AMOVA) revealed that the total genetic variance (65-66 %) was due to variability among P. brasiliensis complex and P. lutzii (PhiPT = 0.651-0.658, P < 0.0001), supporting a highly structured population. Heterothallism was the exclusive mating strategy, and the distributions of MAT1-1 or MAT1-2 idiomorphs were not significantly skewed (1:1 ratio) for P. brasiliensis s. str. (chi(2) = 1.025; P = 0.3113), P. venezuelensis (chi(2) = 0.692; P = 0.4054), and P. lutzii (chi(2) = 0.027; P = 0.8694), supporting random mating within each species. In contrast, skewed distributions were found for P. americana (chi(2) = 8.909; P = 0.0028) and P. restrepiensis (chi(2) = 4.571; P = 0.0325) with a preponderance of MAT1-1. Geographical distributions confirmed that P. americana, P. restrepiensis, and P. lutzii are more widespread than previously thought. P. brasiliensis s. str. is by far the most 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 Paracoccidioides species, guiding disease-control strategies to mitigate PCM. CI - (c) 2021 Westerdijk Fungal Biodiversity Institute. Production and hosting by ELSEVIER B.V. FAU - Roberto, T N AU - Roberto TN AD - Laboratory of Emerging Fungal Pathogens, Department of Microbiology, Immunology, and Parasitology, Discipline of Cellular Biology, Federal University of Sao Paulo (UNIFESP), Sao Paulo, 04023062, Brazil. FAU - de Carvalho, J A AU - de Carvalho JA AD - Laboratory of Emerging Fungal Pathogens, Department of Microbiology, Immunology, and Parasitology, Discipline of Cellular Biology, Federal University of Sao Paulo (UNIFESP), Sao Paulo, 04023062, Brazil. AD - Department of Medicine, Discipline of Infectious Diseases, Federal University of Sao Paulo (UNIFESP), Sao Paulo, 04023062, Brazil. FAU - Beale, M A AU - Beale MA AD - Parasites and Microbes Programme, Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SA, UK. FAU - Hagen, F AU - Hagen F AD - Department of Medical Mycology, Westerdijk Fungal Biodiversity Institute, Uppsalalaan 8, 3584CT, Utrecht, the Netherlands. AD - Department of Medical Microbiology, University Medical Center Utrecht, Heidelberglaan 100, 3584 CX, Utrecht, the Netherlands. AD - Laboratory of Medical Mycology, Jining No. 1 People's Hospital, Jining, Shandong, People's Republic of China. FAU - Fisher, M C AU - Fisher MC AD - MRC Center for Global Infectious Disease Analysis, School of Public Health, Imperial College London, London, W2 1PG, UK. FAU - Hahn, R C AU - Hahn RC AD - Laboratory of Mycology/Research, Faculty of Medicine, Federal University of Mato Grosso, Cuiaba, 78060900, Brazil. AD - Julio Muller University Hospital, Federal University of Mato Grosso, Cuiaba, 78048902, Brazil. FAU - de Camargo, Z P AU - de Camargo ZP AD - Laboratory of Emerging Fungal Pathogens, Department of Microbiology, Immunology, and Parasitology, Discipline of Cellular Biology, Federal University of Sao Paulo (UNIFESP), Sao Paulo, 04023062, Brazil. AD - Department of Medicine, Discipline of Infectious Diseases, Federal University of Sao Paulo (UNIFESP), Sao Paulo, 04023062, Brazil. FAU - Rodrigues, A M AU - Rodrigues AM AD - Laboratory of Emerging Fungal Pathogens, Department of Microbiology, Immunology, and Parasitology, Discipline of Cellular Biology, Federal University of Sao Paulo (UNIFESP), Sao Paulo, 04023062, Brazil. AD - Department of Medicine, Discipline of Infectious Diseases, Federal University of Sao Paulo (UNIFESP), Sao Paulo, 04023062, Brazil. LA - eng GR - WT_/Wellcome Trust/United Kingdom GR - 206194/WT_/Wellcome Trust/United Kingdom GR - MR/R015600/1/MRC_/Medical Research Council/United Kingdom PT - Journal Article DEP - 20211130 PL - Netherlands TA - Stud Mycol JT - Studies in mycology JID - 8411984 PMC - PMC8645518 OTO - NOTNLM OT - AFLP OT - AMOVA OT - Endemic mycosis OT - Genetic diversity OT - Mating-type OT - Paracoccidioides OT - Paracoccidioidomycosis EDAT- 2021/12/23 06:00 MHDA- 2021/12/23 06:01 PMCR- 2021/11/30 CRDT- 2021/12/22 06:48 PHST- 2021/12/22 06:48 [entrez] PHST- 2021/12/23 06:00 [pubmed] PHST- 2021/12/23 06:01 [medline] PHST- 2021/11/30 00:00 [pmc-release] AID - S0166-0616(21)00018-X [pii] AID - 100131 [pii] AID - 10.1016/j.simyco.2021.100131 [doi] PST - epublish SO - Stud Mycol. 2021 Nov 30;100:100131. doi: 10.1016/j.simyco.2021.100131. eCollection 2021 Sep.