Genome Organization and Copy-Number Variation Reveal Clues to Virulence Evolution in Coccidioides posadasii

Abstract

The human fungal pathogen Coccidioides spp. causes valley fever, a treatment-refractory and sometimes deadly disease prevalent in arid regions of the western hemisphere. Fungal virulence in the mammalian host hinges on a switch between growth as hyphae and as large spherules containing infectious spores. How these virulence programs are encoded in the genome remains poorly understood. Drawing on Coccidioides genomic resources, we first discovered a new facet of genome organization in this system: spherule-gene islands, clusters of genes physically linked in the genome that exhibited specific mRNA induction in the spherule phase. Next, we surveyed copy-number variation genome-wide among strains of C. posadasii. Emerging from this catalog were spherule-gene islands with striking presence-absence differentiation between C. posadasii populations, a pattern expected from virulence factors subjected to different selective pressures across habitats. Finally, analyzing single-nucleotide differences across C. posadasii strains, we identified signatures of natural selection in spherule-expressed genes. Together, our data establish spherule-gene islands as candidate determinants of virulence and targets of selection in Coccidioides.

Keywords: Coccidioides; copy number variation; fungal pathogens; genome organization; virulence.

Figure 1

Secondary metabolite clusters with life cycle-specific upregulation. Each circle reports expression patterns from one secondary metabolite cluster. In a given circle, brightly colored areas and overlaid black numbers report the proportion and number, respectively, of genes in the cluster induced in the indicated life cycle phase of C. posadasii. Clusters with such expression signals in only one life cycle phase are marked with an asterisk.

Figure 2

Spherule-gene and hyphae-gene islands. Each panel reports the results of a test for genomic regions over-represented among genes induced in one C. posadasii life cycle phase. The x-axis reports the chromosome positions of a given genomic window, and the y-axis reports the number of genes in the window upregulated in spherules (A) or hyphae (B). The dashed line reports the maximum number of genes of the respective induction behavior expected in a window under a null model. Stars indicate windows overlapping with secondary metabolite clusters from Figure 1, and inset tracks indicate windows in a highly variable region of chromosome III (see below).

Figure 3

Copy number variants and their proximity to transposons across C. posadasii strains. (A) In the main panel, each row reports the results of quantification of copy number in the indicated strain relative to the C. posadasii reference assembly (Teixeira et al., 2021). The x-axis reports genome location, and the color scale reports copy number. At the top, the y-axis reports the V_ST metric of population differentiation of the copy number; rows underneath report transposon and gene locations. Only results from chromosome I are shown; the remaining chromosomes are reported in Figure S2. (B) The x-axis reports the distance between a copy number variant (CNV) boundary and the nearest transposon; the y-axis reports the proportion of CNVs with the transposon distance on the x, as a kernel density estimate.

Figure 4

Widespread deletions in a spherule-expressed locus. In the main panel, data are as in Figure 3 and Supplementary Figure S3, except that only a region of chromosome III is shown, and strains were clustered using Euclidean distance and average linkage. For a version showing windows overlapping transposons, see Supplementary Figure S4. Cells on the left report strain population: Arizona, green; Caribbean, yellow; Texas/Mexico/South America, pink.

Figure 5

Paralogy in the copy number-variable chromosome III region. Axes report position in the C. posadasii Silveira reference genome in the chromosome III locus from Figure 4. Black points report nucleotide identity. Colored stars identify inferred gene duplications discussed in the Section 4.1.