Genomic correlates of virulence and morphological phase transitions in pathogenic Onygenales fungi

The programme of modern whole-genome comparative omics for fungi was well described by Bowman, Taylor and White (1996, Mol Phylogenet Evol) at its outset: “because pathogenicity apparently has arisen independently multiple times ... comparative examination of several pathogens and their closest relatives should provide a basis for discerning general principles of pathogen evolution. Understanding the acquisition of pathogenicity may help us understand the emergence of new fungal pathogens”. The design of such genome-wide studies are in a sense analogous to the case-control design: one compares pathogenic species with closely related non-pathogenic species (macroevolution), and more virulent strains with relatively avirulent strains of the same species (microevoluion), in order to recognize and investigate key differences in otherwise similar genomes that could shed light on the molecular and cellular bases of pathogenicity or virulence in the studied fungi. To obtain the data allowing such comparative analyses, we have worked together with next-generation sequencing labs in the Broad Institute of MIT and Harvard (Cambridge, MA) and the University of Illinois (Urbana-Champaign, IL), and collaborated with the Broad Institute and the CDC (Atlanta, GA) for analyses. Our initial focus (2010-2016) was on the Onygenales, which constitute an ideal ‘phylogenetic Galapagos’ in which closely related fungi show an impressive phenotypic diversity (morphology, pathogenicity, geographic and ecological niches) that is ideal for the comparative programme. Furthermore, many of the Onygenales fungi that cause systemic (not superficial) mycoses in human have a double lifestyle: as a saprophyte, and as a parasite of human or other animals. The two phases or modes of existence correspond to two morphologically very different states, e.g., mycelia/conidia vs. yeast, spherules or adiaspores; typically change of temperature upon inhalation or prolonged physical contact with the animal host triggers a phase transition (duration ~ days) amounting to a fundamental reorganization of important parts of the transcriptome. Since such fungi cannot develop full-fledged virulence while in the saprophytic form but only in the parasitic form, the observation and documenting of gene-expression changes during and after the phase transition can give further clues to processes enabling pathogenicity/virulence. We have published a series of papers since 2012 describing our genome-wide comparative or transcriptomic analyses for the Onygenales genera Blastomyces, Emmonsia, the emerging pathogen Emergomyces, and Paracoccidioides, all of which correspond to pathogens of human and/or other animals, and for Spiromastix and Polytolypa, which so far have not been identified with disease or a non-saprophytic phase. We are now branching out also to analyze, and compare at the whole-genome level, fungi outside the Onygenales order, such as recently emerging drug-resistant pathogens of the Candida genus. Due to the increasing availability in recent years of whole genome assemblies and annotations, provided and made publicly available by other groups, we foresee also accelerated analyses or collaborations along the same lines for other pathogenic and pathogen-related fungi in the near future.