Comparative Phylogenomics of Pathogenic and Nonpathogenic Species

Abstract

The Ascomycete Onygenales order embraces a diverse group of mammalian pathogens, including the yeast-forming dimorphic fungal pathogens Histoplasma capsulatum, Paracoccidioides spp. and Blastomyces dermatitidis, the dermatophytes Microsporum spp. and Trichopyton spp., the spherule-forming dimorphic fungal pathogens in the genus Coccidioides, and many nonpathogens. Although genomes for all of the aforementioned pathogenic species are available, only one nonpathogen had been sequenced. Here, we enhance comparative phylogenomics in Onygenales by adding genomes for Amauroascus mutatus, Amauroascus niger, Byssoonygena ceratinophila, and Chrysosporium queenslandicum—four nonpathogenic Onygenales species, all of which are more closely related to Coccidioides spp. than any other known Onygenales species. Phylogenomic detection of gene family expansion and contraction can provide clues to fungal function but is sensitive to taxon sampling. By adding additional nonpathogens, we show that LysM domain-containing proteins, previously thought to be expanding in some Onygenales, are contracting in the Coccidioides-Uncinocarpus clade, as are the self-nonself recognition Het loci. The denser genome sampling presented here highlights nearly 800 genes unique to Coccidiodes, which have significantly fewer known protein domains and show increased expression in the endosporulating spherule, the parasitic phase unique to Coccidioides spp. These genomes provide insight to gene family expansion/contraction and patterns of individual gene gain/loss in this diverse order—both major drivers of evolutionary change. Our results suggest that gene family expansion/contraction can lead to adaptive radiations that create taxonomic orders, while individual gene gain/loss likely plays a more significant role in branch-specific phenotypic changes that lead to adaptation for species or genera.

Local population structure and patterns of Western Hemisphere dispersal forCoccidioides spp., the fungal cause of Valley Fever

“…The Coccidioides genomic adaptations to mammalian hosts (e.g., expansion of protease and keratinase gene families) (8,36) and the hypothesis that the patchy distribution of Coccidioides in soil is due to the fungal association with mammal carcasses (i.e., dead hosts) and burrows (31, 37) comport with a theory that distribution is related to distinct movement events of infected animals. Although multiple North American mammal species can be infected, rodents, canids, and humans are highly susceptible to succumbing to the disease, allowing infecting strains to reenter into the soil upon death (1,38), and therefore may be considered the most likely "vectors" of transmission of Coccidioides from one locale to another.…”

Validating Genomewide Predictions of Genetic Variance in a Contemporary Breeding Program

“…Marker genotypes were imputed using the expectation maximization algorithm implemented in the rrBLUP package in R (Endelman, 2011). This marker set and genetic map (Muñoz-Amatriaín et al, 2011) have been used in studies of genomewide selection, association mapping, and population genetics of North American barley germplasm (Lorenz et al, 2012;Pauli et al, 2014;Poets et al, 2016). To infer genetic map positions, we first obtained physical and genetic map information on 3072 array-based SNPs developed during the Barley Coordinated Agricultural Project (BCAP) (Close et al, 2009).…”

Coccidioides immitis and posadasii; A review of their biology, genomics, pathogenesis, and host immunity

“…Coccidioides species are fungi within Ascomycete division, Eurotiomycetes class, Onygenales order [2,3]. This order includes a variety of dimorphic human pathogens capable of causing invasive disease in immunologically normal hosts, including Histoplasma capsulatum, Paracoccidioides spp., and Blastomyces spp.…”