Genotypic and phenotypic analyses of two model strains of Cryptococcus neoformans

Abstract

The human pathogenic Cryptococcus neoformans species complex are agents of a common AIDS-defining disease, which causes about 181,000 deaths each year. There are several specific features distinguishing this species from other fungi, including the presence of a polysaccharide capsule and melanin pigment production, both of which contribute to its virulence. A large number of studies about this pathogen used two model strains JEC20 and JEC21. In these studies, these two strains are assumed to be “isogenic”, differ only at the mating type region. Consequently, their phenotypic differences, including virulence, have been attributed to this region. Here, we applied second-generation sequencing and bioinformatics tools to identify sequence polymorphisms between the two genomes. Beside the Mating Type locus, two other regions were found to contain high frequencies of SNPs. To further understand the effects of these loci on the phenotypic differences, four phenotyping assays (mating ability, melanin pigment production, capsule formation, and high temperature growth ability) were conducted on the recombinant progeny obtained from the cross between JEC20 and JEC21. In addition, genomic sequences of these progeny were obtained to identify the complete distributions of other SNPs among the strains. Finally, we identified several novel SNPs contributing to virulence-related traits in this species, which suggest that caution should be placed in attributing phenotypic differences to specific genomic regions in “isogenic” strains derived from classical breeding experiments.