Analysis of clinical Candida parapsilosis isolates reveals copy number variation in key fluconazole resistance genes

We used whole-genome sequencing to analyze a collection of 35 fluconazole-resistant and 7 susceptible isolates together with coverage analysis and GWAS techniques to identify new mechanisms of fluconazole resistance. Phylogenetic analysis shows that although the collection is diverse, two persistent clinical lineages were identified. We identified copy number variation (CNV) of two genes, and , in resistant isolates. Two strains have a CNV at the locus; the entire ORF is amplified in one, and only the promoter region is amplified in the other. We show that the annotated telomeric gene is actually an artifactual fusion of two highly similar neighboring genes due to an assembly error in the CDC317 reference genome. We report highly variable copy numbers of the region across the collection. Several strains have increased the expansion of the two genes into a tandem array of new chimeric genes. Other strains have experienced a deletion between the two genes creating a single gene with a reciprocal chimerism. We find translocations, duplications, and gene conversion across the gene family in the species complex, showing that it is a highly dynamic family.