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Evidence for positive selection in putative virulence factors within the Paracoccidioides brasiliensis species complex.

Matute DR, Quesada-Ocampo LM, Rauscher JT, McEwen JG - PLoS Negl Trop Dis (2008)

Bottom Line: Here, we present evidence indicating that several replacement mutations in gp43 are under positive balancing selection.The other three genes (fks, cdc42 and p27) show very little variation among the P. brasiliensis lineages and appear to be under positive directional selection.We present our results within an evolutionary framework that may be applicable for studying adaptation and pathogenesis in P. brasiliensis and other pathogenic fungi.

View Article: PubMed Central - PubMed

Affiliation: Department of Ecology and Evolution, University of Chicago, Chicago, Illinois, USA. danielricardomatute@gmail.com

ABSTRACT
Paracoccidioides brasiliensis is a dimorphic fungus that is the causative agent of paracoccidioidomycosis, the most important prevalent systemic mycosis in Latin America. Recently, the existence of three genetically isolated groups in P. brasiliensis was demonstrated, enabling comparative studies of molecular evolution among P. brasiliensis lineages. Thirty-two gene sequences coding for putative virulence factors were analyzed to determine whether they were under positive selection. Our maximum likelihood-based approach yielded evidence for selection in 12 genes that are involved in different cellular processes. An in-depth analysis of four of these genes showed them to be either antigenic or involved in pathogenesis. Here, we present evidence indicating that several replacement mutations in gp43 are under positive balancing selection. The other three genes (fks, cdc42 and p27) show very little variation among the P. brasiliensis lineages and appear to be under positive directional selection. Our results are consistent with the more general observations that selective constraints are variable across the genome, and that even in the genes under positive selection, only a few sites are altered. We present our results within an evolutionary framework that may be applicable for studying adaptation and pathogenesis in P. brasiliensis and other pathogenic fungi.

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Related in: MedlinePlus

The phylogeny of H. capsulatum, P. brasiliensis Pb18, and P. brasiliensis Pb01 .N1 is the common ancestor of the three branches of the tree.
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pntd-0000296-g001: The phylogeny of H. capsulatum, P. brasiliensis Pb18, and P. brasiliensis Pb01 .N1 is the common ancestor of the three branches of the tree.

Mentions: Using a distance-based Bayesian method, the ancestral sequences were reconstructed (i.e. the common ancestor of the three branches of the tree (N1 in Figure 1)), using the Ancestor software [36] for each gene in the dataset. The predicted sequence of each ancestral state was given a probability, with a 95% or higher cut-off. To test for positive selection we calculated the dN and dS values for each branch of the phylogeny (Figure 1) using the random effect likelihood method of Pond and Frost [37],[38], available in HyPhy [38]. The distance from the common ancestor of the last common ancestor of the two P. brasiliensis groups was calculated using an optimal model of nucleic acid selection. Similar results were obtained with other models (HKY85, TN93, and REV).


Evidence for positive selection in putative virulence factors within the Paracoccidioides brasiliensis species complex.

Matute DR, Quesada-Ocampo LM, Rauscher JT, McEwen JG - PLoS Negl Trop Dis (2008)

The phylogeny of H. capsulatum, P. brasiliensis Pb18, and P. brasiliensis Pb01 .N1 is the common ancestor of the three branches of the tree.
© Copyright Policy
Related In: Results  -  Collection

Show All Figures
getmorefigures.php?uid=PMC2553485&req=5

pntd-0000296-g001: The phylogeny of H. capsulatum, P. brasiliensis Pb18, and P. brasiliensis Pb01 .N1 is the common ancestor of the three branches of the tree.
Mentions: Using a distance-based Bayesian method, the ancestral sequences were reconstructed (i.e. the common ancestor of the three branches of the tree (N1 in Figure 1)), using the Ancestor software [36] for each gene in the dataset. The predicted sequence of each ancestral state was given a probability, with a 95% or higher cut-off. To test for positive selection we calculated the dN and dS values for each branch of the phylogeny (Figure 1) using the random effect likelihood method of Pond and Frost [37],[38], available in HyPhy [38]. The distance from the common ancestor of the last common ancestor of the two P. brasiliensis groups was calculated using an optimal model of nucleic acid selection. Similar results were obtained with other models (HKY85, TN93, and REV).

Bottom Line: Here, we present evidence indicating that several replacement mutations in gp43 are under positive balancing selection.The other three genes (fks, cdc42 and p27) show very little variation among the P. brasiliensis lineages and appear to be under positive directional selection.We present our results within an evolutionary framework that may be applicable for studying adaptation and pathogenesis in P. brasiliensis and other pathogenic fungi.

View Article: PubMed Central - PubMed

Affiliation: Department of Ecology and Evolution, University of Chicago, Chicago, Illinois, USA. danielricardomatute@gmail.com

ABSTRACT
Paracoccidioides brasiliensis is a dimorphic fungus that is the causative agent of paracoccidioidomycosis, the most important prevalent systemic mycosis in Latin America. Recently, the existence of three genetically isolated groups in P. brasiliensis was demonstrated, enabling comparative studies of molecular evolution among P. brasiliensis lineages. Thirty-two gene sequences coding for putative virulence factors were analyzed to determine whether they were under positive selection. Our maximum likelihood-based approach yielded evidence for selection in 12 genes that are involved in different cellular processes. An in-depth analysis of four of these genes showed them to be either antigenic or involved in pathogenesis. Here, we present evidence indicating that several replacement mutations in gp43 are under positive balancing selection. The other three genes (fks, cdc42 and p27) show very little variation among the P. brasiliensis lineages and appear to be under positive directional selection. Our results are consistent with the more general observations that selective constraints are variable across the genome, and that even in the genes under positive selection, only a few sites are altered. We present our results within an evolutionary framework that may be applicable for studying adaptation and pathogenesis in P. brasiliensis and other pathogenic fungi.

Show MeSH
Related in: MedlinePlus