CRISPR-Cas9 editing induces Loss of Heterozygosity in the pathogenic yeast Candida parapsilosis

Genetic manipulation is often used to study gene function. However, unplanned genome changes (including Single Nucleotide Polymorphisms (SNPs), aneuploidy and Loss of Heterozygosity (LOH)) can affect the phenotypic traits of the engineered strains. Here, we show that CRISPR-Cas9 editing can induce LOH in the diploid human pathogenic yeast Candida parapsilosis. We sequenced the genomes of ten isolates that were edited with CRISPR-Cas9 and found that the designed changes were present in nine. However, we also observed LOH in all isolates, and aneuploidy in two isolates. LOH occurred most commonly downstream of the Cas9 cut site and extended to the telomere in three isolates. In two isolates we observed LOH on chromosomes that were not targeted by CRISPR-Cas9. Two different isolates exhibited cysteine and methionine auxotrophy caused by LOH at a heterozygous site in MET10, approximately 11 and 157 kb downstream from the Cas9 target site, respectively. C. parapsilosis isolates have relatively low levels of heterozygosity. However, our results show that mutation complementation to confirm observed phenotypes is important even when using CRISPR-Cas9, which is now the gold standard of genetic engineering.IMPORTANCECRISPR-Cas9 has greatly streamlined gene editing, and is now the gold standard and first choice for genetic engineering. However, we show that in diploid species extra care should be taken in confirming the cause of any phenotypic changes observed. We show that the Cas9-induced double strand break is often associated with loss of heterozygosity in the asexual diploid human fungal pathogen Candida parapsilosis. This can result in deleterious heterozygous variants (e.g. stop gain in one allele) becoming homozygous resulting in unplanned phenotypic changes. Our results stress the importance of mutation complementation even when using CRISPR-Cas9.