Comparative genomic analyses of the human fungal pathogens Coccidioides and their relatives

Abstract

While most Ascomycetes tend to associate principally with plants, the dimorphic fungi Coccidioides immitis and Coccidioides posadasii are primary pathogens of immunocompetent mammals, including humans. Infection results from environmental exposure to Coccidiodies, which is believed to grow as a soil saprophyte in arid deserts. To investigate hypotheses about the life history and evolution of Coccidioides, the genomes of several Onygenales, including C. immitis and C. posadasii; a close, nonpathogenic relative, Uncinocarpus reesii; and a more diverged pathogenic fungus, Histoplasma capsulatum, were sequenced and compared with those of 13 more distantly related Ascomycetes. This analysis identified increases and decreases in gene family size associated with a host/substrate shift from plants to animals in the Onygenales. In addition, comparison among Onygenales genomes revealed evolutionary changes in Coccidioides that may underlie its infectious phenotype, the identification of which may facilitate improved treatment and prevention of coccidioidomycosis. Overall, the results suggest that Coccidioides species are not soil saprophytes, but that they have evolved to remain associated with their dead animal hosts in soil, and that Coccidioides metabolism genes, membrane-related proteins, and putatively antigenic compounds have evolved in response to interaction with an animal host.

Figure 1.

Evidence of mutational bias associated with repetitive regions of the Coccidioides genomes. For both the C. immitis and C. posadasii genomes, each 1-kb nonoverlapping window of sequence was categorized into a repeat class. Classification is based on the number of homologous copies (n) of that window identified within the genome: nonrepetitive, low (n < 6), mid (n = 6–20), and high (n > 20). The mean GC percentage, the mean CpG frequency, and the fraction of elements with a CpG frequency less than 0.010 were measured for each repeat class. The results indicate that repeats in Coccidioides tend to exhibit a paucity of CpG dinucleotides compared with nonrepetitive regions.

Figure 2.

A timeline of genomic changes that underlie the evolution of pathogenicity in Coccidioides. A RAxML-generated maximum likelihood phylogeny based on an alignment of 1148 concatenated genes that comprise 46,890 unambiguously aligned amino acid sites following the removal of gaps was used as a starting point to perform nonparametric rate smoothing. Divergence times were subsequently estimated from the smoothed phylogeny by applying a calibration of 215 Mya for the Pezizomycotina origin as in the method of Taylor and Berbee (2006). The significant evolutionary events identified in the hierarchical comparative genomic analysis of the Coccidioides lineage are overlaid onto the phylogeny. Taken together, they suggest that a gradual progression of evolutionary events ultimately yielded the pathogenic phenotype of Coccidioides. (A) Gene family reductions associated with the metabolism of plant material were coupled with a growth substrate transition from plant to animal material. (B) Subsequent expansions in proteases and keratinases led to a nutritional association with mammals in a nonpathogenic fashion. (C) The acquisition and adaptation of genes involved in metabolism, membrane biology, and mycotoxin production led to metabolic and morphological phenotypes that enabled survival within a live host, ultimately resulting in disease. (D) Secreted proteins, metabolism genes, and secondary metabolism genes that are shared between the two Coccidioides species have been subject to positive selection since they diverged. This suggests that Coccidioides may experience on-going adaptation in response to host immune system selection pressures.

Figure 3.

The evolution of gene family size in the Eurotiomycetes gene family size evolution was evaluated across seven Eurotiomycetes and two Sordariomycete outgroups. The columns capture the size of selected gene families across the taxa, with Coccidioides gene family contractions and expansions represented by numbers in the light and dark gray boxes, respectively (specific information regarding gene family function can be found in the main text). Taxa are listed on the lefthand side according to their phylogenetic orientation and represented by four letter identifiers: Anid indicates Aspergillus nidulans; Afum, Aspergillus fumigatus; Ater, Aspergillus terreus; Hcap, Histoplasma capsulatum; Uree, Uncinocarpus reesii; Cimm, Coccidioides immitis; Cpos, Coccidioides posadasii; Ncra, Neurospora crassa; and Fgra, Fusarium graminearum.