Dataset Information

Genomic diversity of the human pathogen Paracoccidioides across the South American continent.

ABSTRACT: Paracoccidioidomycosis (PCM) is a life-threatening systemic mycosis widely reported in the Gran Chaco ecosystem. The disease is caused by different species from the genus Paracoccidioides, which are all endemic to South and Central America. Here, we sequenced and analyzed 31 isolates of Paracoccidioides across South America, with particular focus on isolates from Argentina and Paraguay. The de novo sequenced isolates were compared with publicly available genomes. Phylogenetics and population genomics revealed that PCM in Argentina and Paraguay is caused by three distinct Paracoccidioides genotypes, P. brasiliensis (S1a and S1b) and P. restrepiensis (PS3). P. brasiliensis S1a isolates from Argentina are frequently associated with chronic forms of the disease. Our results suggest the existence of extensive molecular polymorphism among Paracoccidioides species, and provide a framework to begin to dissect the connection between genotypic differences in the pathogen and the clinical outcomes of the disease.

SUBMITTER: Teixeira MM

PROVIDER: S-EPMC7385733 | biostudies-literature | 2020 Jul

REPOSITORIES: biostudies-literature

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Genomic diversity of the human pathogen Paracoccidioides across the South American continent.

Teixeira Marcus de Melo MM Cattana Maria Emilia ME Matute Daniel R DR Muñoz José F JF Arechavala Alicia A Isbell Kristin K Schipper Rafael R Santiso Gabriela G Tracogna Fernanda F Sosa María de Los Ángeles MLÁ Cech Norma N Alvarado Primavera P Barreto Laura L Chacón Yone Y Ortellado Juana J Lima Cleoni Mendes de CM Chang Marilene Rodrigues MR Niño-Vega Gustavo G Yasuda Maria Aparecida Shikanai MAS Felipe Maria Sueli Soares MSS Negroni Ricardo R Cuomo Christina A CA Barker Bridget B Giusiano Gustavo G

Fungal genetics and biology : FG & B 20200420

Paracoccidioidomycosis (PCM) is a life-threatening systemic mycosis widely reported in the Gran Chaco ecosystem. The disease is caused by different species from the genus Paracoccidioides, which are all endemic to South and Central America. Here, we sequenced and analyzed 31 isolates of Paracoccidioides across South America, with particular focus on isolates from Argentina and Paraguay. The de novo sequenced isolates were compared with publicly available genomes. Phylogenetics and population gen ...[more]

PMID: 32325168

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Project description:BackgroundBovine leukocyte antigens (BoLAs) are used extensively as markers of disease and immunological traits in cattle. However, until now, characterization of BoLA gene polymorphisms in Zebu breeds using high resolution typing methods has been poor. Here, we used a polymerase chain reaction sequence-based typing (PCR-SBT) method to sequence exon 2 of the BoLA class II DRB3 gene from 421 cattle (116 Bolivian Nellore, 110 Bolivian Gir, and 195 Peruvian Nellore-Brahman). Data from 1416 Taurine and Zebu samples were also included in the analysis.ResultsWe identified 46 previously reported alleles and no novel variants. Of note, 1/3 of the alleles were detected only in Zebu cattle. Comparison of the degree of genetic variability at the population and sequence levels with genetic distance in the three above mentioned breeds and nine previously reported breeds revealed that Zebu breeds had a gene diversity score higher than 0.86, a nucleotide diversity score higher than 0.06, and a mean number of pairwise differences greater than 16, being similar to those estimated for other cattle breeds. A neutrality test revealed that only Nellore-Brahman cattle showed the even gene frequency distribution expected under a balanced selection scenario. The FST index and the exact G test showed significant differences across all cattle populations (FST = 0.057; p < 0.001). Neighbor-joining trees and principal component analysis identified two major clusters: one comprising mainly European Taurine breeds and a second comprising Zebu breeds. This is consistent with the historical and geographical origin of these breeds. Some of these differences may be explained by variation of amino acid motifs at antigen-binding sites.ConclusionsThe results presented herein show that the historical divergence between Taurine and Zebu cattle breeds is a result of origin, selection, and adaptation events, which would explain the observed differences in BoLA-DRB3 gene diversity between the two major bovine types. This allelic information will be important for investigating the relationship between the major histocompatibility complex and disease, and contribute to an ongoing effort to catalog bovine MHC allele frequencies according to breed and location.

Dataset Information

Genomic diversity of the human pathogen Paracoccidioides across the South American continent.

Publications

Genomic diversity of the human pathogen Paracoccidioides across the South American continent.

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