Genome Evolution and Innovation across the Four Major Lineages of Cryptococcus gattii

Abstract

Cryptococcus gattii is a fungal pathogen of humans, causing pulmonary infections in otherwise healthy hosts. To characterize genomic variation among the four major lineages of C. gattii (VGI, -II, -III, and -IV), we generated, annotated, and compared 16 de novo genome assemblies, including the first for the rarely isolated lineages VGIII and VGIV. By identifying syntenic regions across assemblies, we found 15 structural rearrangements, which were almost exclusive to the VGI-III-IV lineages. Using synteny to inform orthology prediction, we identified a core set of 87% of C. gattii genes present as single copies in all four lineages. Remarkably, 737 genes are variably inherited across lineages and are overrepresented for response to oxidative stress, mitochondrial import, and metal binding and transport. Specifically, VGI has an expanded set of iron-binding genes thought to be important to the virulence of Cryptococcus, while VGII has expansions in the stress-related heat shock proteins relative to the other lineages. We also characterized genes uniquely absent in each lineage, including a copper transporter absent from VGIV, which influences Cryptococcus survival during pulmonary infection and the onset of meningoencephalitis. Through inclusion of population-level data for an additional 37 isolates, we identified a new transcontinental clonal group that we name VGIIx, mitochondrial recombination between VGII and VGIII, and positive selection of multidrug transporters and the iron-sulfur protein aconitase along multiple branches of the phylogenetic tree. Our results suggest that gene expansion or contraction and positive selection have introduced substantial variation with links to mechanisms of pathogenicity across this species complex.

Microevolutionary traits and comparative population genomics of the emerging pathogenic fungus Cryptococcus gattii

“…phagocytosis, IPR, vomocytosis, cryptococcal mitochondrial tubularization and macrophage death) in replicate (3X–8X) over a timecourse of macrophage interaction (0, 18, 24 and 48 h). First, we measured the maximal intracellular proliferate potential ( T max ; commonly referred to as IPR) for 20 isolates of C. gattii including four of the six named subclades (the outbreak clades VGIIa and VGIIc, the recently described VGIIx [24], and VGIIb; figure 1 and electronic supplementary material, table S2). These strains were selected, according to previous literature and strain detail knowledge, to represent a balanced collection of strains (i) from the North Pacific C. gattii outbreak, (ii) from environmental origin, and (iii) representing the different molecular groups.…”

“…The first gene (CNBG_1370) is a 1 : 1 orthologue of C. neoformans H99 Utr2 gene (with homology to chitin transglycolase), which is potentially involved in capsule biosynthesis [35]. In C. gattii, this gene is under selection in the recently named VGIIx subclade [24] with d N = 0.0063, d S = 0.0059, ω = 1.0792. The second gene (CNBG_0047) is in an orthogroup with C. neoformans H99 Cap64-like proteins Cas31 and Cas3, and under selection in VGIIb ( d N = 0.0028, d S = 0.0023, ω = 1.2242).…”

“…We found 113 genes with significant differences () after Benjamini–Hochberg (BH) multiple correction. Previously when we calculated these values for VGIIa (subset 5 in [24]) for non-fixed differences across multiple isolates with BH correction and q -value < 0.01, without adjusting the NS sites parameter, we identified an almost entirely distinct list of 87 genes, apart from two genes that were identified in both (CNBG_5460 (Fungal Zn(2)-Cys(6) binuclear cluster domain) and CNBG_4219 (domain of unknown function 1708)). Again, no PFAM or GO-term from these genes was enriched (according to two-tailed Fisher's exact test with q -value FDR).…”

Tackling emerging fungal threats to animal health, food security and ecosystem resilience

“…A pertinent example is expounded by Farrer [13], where comparative genomics were used to analyse lineages of the basidiomycete fungus Cryptococcus gattii that are emerging as a cause of fatal human meningitis across the Pacific Northwest of the USA and Canada. These, and accompanying analyses [14], have shown that four major genetic lineages of C. gattii occur exhibiting extensive genome diversification that is associated with variation in virulence. Broad-scale interlineage processes, such as gene expansion/contraction and mitochondrial recombination, through to fine-scale intralineage microevolutionary events, such as positive selection of single-nucleotide polymorphisms, were shown to be associated with variation in virulence across this species.…”

Transcriptional heterogeneity ofCryptococcus gattiiVGII compared with non-VGII lineages underpins key pathogenicity pathways

“…Orthologs to genes of known function in C. neoformans H99 were identified in C. 676 gattii R265 using OrthoMCL (48) across 16 isolates as previously described (7). 677…”