The human fungal pathogenParacoccidioides brasiliensis(Onygenales: Ajellomycetaceae) is a complex of two species: phylogenetic evidence from five mitochondrial markers

Abstract

Paracoccidioides brasiliensis is the aetiological agent of paracoccidioidomycosis, the most important systemic mycosis in Latin America. In order to study the diversity of P. brasiliensis mitochondrial genes, to evaluate previous taxonomic proposals, and to explore the hypothesis that the previously described ''divergent isolate'' B30 (also called Pb01) could represent a new P. brasiliensis species, we undertook a molecular phylogenetic analysis based on five mitochondrial markers. Mitochondrial sequences of 59 P. brasiliensis isolates obtained from clinical and environmental samples, and the orthologous genes from outgroup species, are reported and analysed using parsimony and Bayesian methods. The combined data set comprised 2364 characters, of which 426 were informative. One of the studied strains presented a 376-nt insertion at the apocytochrome b (cob) gene. The corresponding sequence had a high similarity (79%) with an intron found in the Neurospora crassa cob gene. Interestingly, this intron is absent in the previously published sequence of the P. brasiliensis mitochondrial genome. Our trees were moderately congruent with the previous P. brasiliensis taxonomic proposals. Furthermore, we identified a new monophyletic group of strains within P. brasiliensis. Nevertheless, the phylogenetic species recognition (PSR) analyses described here suggested that these groups of strains could represent geographical variants rather than different Paracoccidioides cryptic species. In addition, and as previously proposed by other authors, these analyses supported the existence of a new specie of Paracoccidioides, which includes the previously described, divergent isolate B30 ⁄ Pb01. This is the first report providing evidence, independent of nuclear markers, for the split of this important human pathogen into two species. We support the formal description of the B30 ⁄ Pb01 as new specie.ÓThe Willi Hennig Society 2010.

Genus Paracoccidioides: Species Recognition and Biogeographic Aspects

“…Although Matute et al [7] have considered S1 a single species despite its paraphyletic nature, we are led to suppose that a partial and insufficient sampling may be masking the true phylogeography of S1 isolates on account of its wide geographic distribution together with the fragmentation observed in the formation of a Venezuelan subpopulation [19]. We believe that ecological studies, such as those that aim to isolate or detect the cryptic species in the environment, rather than in migratory patients, would be helpful to clarify some uncertainties about the speciation within the genus Paracoccidioides .…”

New insights into a complex fungal pathogen: the case of Paracoccidioides spp.

“…Regarding its phylogenetic classification, P . brasiliensis S1 is widely distributed throughout South America, PS2 has been identified only in Brazil and Venezuela, PS3 is apparently restricted to regions of Colombia and PS4 has to date been reported only from Venezuela (Matute et al ., ; Salgado‐Salazar et al ., ; Theodoro et al ., ). The other species, P .…”

“…brasiliensis , considered to be a complex of four distinct phylogenetic lineages (S1, PS2, PS3 and PS4), and the recently described P . lutzii (formerly 'Pb01‐like') (Matute et al ., ; Teixeira et al ., ; Salgado‐Salazar et al ., ; Theodoro et al ., ; Teixeira et al ., ).…”

Paracoccidioidesgenomes reflect high levels of species divergence and little interspecific gene flow

“…Since recombination in Paracoccidioides occurs but seems to be rare, and there is a high level of linkage disequilibrium across the genome (see Results), we studied each supercontig as an unlinked loci. Since mtDNA shows evidence of interspecific gene transfer (Salgado-Salazar et al 2010;, we focused only on nuclear genomes We obtained whole supercontig sequences for each individual from the .VCF file using the FastaAlternateReferenceMaker tool in GATK, re-aligned them using Mafft v. 7 (Katoh and Standley 2013), and used them to build Maximum Likelihood (ML) trees using RAxML version 8.2.9 (Stamatakis 2006). We inferred individual trees for each of the largest six supercontigs, which encompass 62% of the genome.…”