Biology subjects

Sepulveda, V. E.

Publications and source records attributed to Sepulveda, V. E..

3 recordsLinked to original sources

bioRxiv2026

An ancient gene duplication is implicated in virulence in the human pathogen, Histoplasma

Histoplasma spp. is a dimorphic fungal primary pathogen that infects people worldwide and frequently affects immunosuppressed patients. Previous studies have identified the AMY1 gene product, the -amylase Amy1p, as essential for -glucan production and virulence in Histoplasma capsulatum. We identified two new genes (AMY2 and AMY3) in the Histoplasma genome that encode putative -amylases and made mutants using CRISPR/Cas9 technology, followed by evaluation of their role in -glucan biosynthesis and virulence. We also searched for AMY gene copies in 19 fungal genomes with the goals of identifying orthologs for AMY2 and AMY3, and establishing how many AMY copies existed across different fungi. We found that the number and type of -amylases vary depending on the fungal species; that all -amylases related to Histoplasma Amy1p belong to the GH13_5 subfamily, and all orthologs related to Histoplasmas Amy2p and Amy3p belong to the GH13_1 subfamily. We performed phylogenetic analyses of the three paralogs and revealed that the Histoplasma AMY duplications are ancient. We further established Amy2 is an ortholog of Aspergillus niger AgtA, and Aspergillus nidulans AmyD, and that it is partially involved in Histoplasma -glucan biosynthesis and virulence, while Amy3p is an ortholog of Aspergillus flavus Amy1, and it is dispensable for -glucan biosynthesis and virulence.

microbiology↗

bioRxiv2025

Telomeric assemblies of Paracoccidioides genomes

Paracoccidioides is a genus of dimorphic fungal pathogens endemic to Latin America. We generated long-read de novo assemblies for 11 isolates representing four species of the brasiliensis complex (P. brasiliensis, P. americana, P. restrepiensis, P. venezuelensis) and P. lutzii. These include the first complete telomere-to-telomere assemblies for P. brasiliensis (Pb18) and P. americana (Pb03), each with five chromosomes. Comparative analyses revealed chromosomal fusion and fission events distinguishing P. brasiliensis and P. americana, and a 90 kb tandem duplication in P. americana containing siderophore biosynthesis genes (sid1, sid3, sid4), a cluster of putative virulence factors. Mitochondrial genomes showed conserved gene order but a phylogenetic topology inconsistent with the nuclear tree, suggesting mitochondrial introgression between P. lutzii and P. venezuelensis. RNA transposable elements were enriched near telomeres, correlated with genome size, and most abundant in P. lutzii. These assemblies provide key resources for understanding genome evolution and introgression in Paracoccidioides. SIGNIFICANCESpecies of Paracoccidioides cause paracoccidioidomycosis, a systemic mycosis that remains a major public health problem in Latin America. Despite their clinical importance, genome evolution across the genus is poorly understood owing to the lack of complete reference assemblies. Here, we present the first telomere-to-telomere reference genomes for P. brasiliensis and P. americana, enabling a comprehensive comparison of chromosomal structure across the genus. Our analyses reveal that the nuclear genome is highly dynamic and shaped by large-scale rearrangements and structural variants, including the duplication of a siderophore biosynthesis-related gene cluster linked to virulence. In contrast, the mitochondrial genome is structurally conserved but shows introgression between species, revealing hidden evolutionary exchange. Together, these genomic resources redefine our understanding of Paracoccidioides evolution and provide a foundation for advances in molecular diagnostics, epidemiological surveillance, and studies of fungal pathogenicity.

microbiology↗

bioRxiv2024

Phenotypic characterization of cryptic species in the fungal pathogen Histoplasma

Histoplasmosis is an endemic mycosis that often presents as a respiratory infection in immunocompromised patients. Hundreds of thousands of new infections are reported annually around the world. The etiological agent of the disease, Histoplasma, is a dimorphic fungus commonly found in the soil where it grows as mycelia. Humans can become infected by Histoplasma through inhalation of its spores (conidia) or mycelial particles. The fungi transitions into the yeast phase in the lungs at 37{degrees}C. Once in the lungs, yeast cells reside and proliferate inside alveolar macrophages. We have previously described that Histoplasma is composed of at least five cryptic species that differ genetically, and assigned new names to the lineages. Here we evaluated multiple phenotypic characteristics of 12 strains from five phylogenetic species of Histoplasma to identify phenotypic traits that differentiate between these species: H. capsulatum sensu stricto, H. ohiense, H. mississippiense, H. suramericanum, and an African lineage. We report diagnostic traits for two species. The other three species can be identified by a combination of traits. Our results suggest that 1) there are significant phenotypic differences among the cryptic species of Histoplasma, and 2) that those differences can be used to positively distinguish those species in a clinical setting and for further study of the evolution of this fungal pathogen. IMPORTANCEIdentifying species boundaries is a critical component of evolutionary biology. Genome sequencing and the use of molecular markers have advanced our understanding of the evolutionary history of fungal pathogens, including Histoplasma, and have allowed for the identification of new species. This is especially important in organisms where morphological characteristics cannot be used for this purpose. In this study, we revise the taxonomic status of the four named species of the genus Histoplasma: H. capsulatum sensu stricto, H. ohiense, H. mississippiense, and H. suramericanum and propose the use of species-specific phenotypic traits to aid their identification when genome sequencing is not available. These results have implications not only for evolutionary study of Histoplasma, but also for clinicians, as the Histoplasma species could determine the outcome of disease and treatment needed.

microbiology↗