Abstract
<jats:p>The diploid ascomycetous yeast Candida parapsilosis accounts for an increasing proportion of invasive Candida infections, highlighting the need for improved genome resources to support studies of pathogenesis and antifungal drug resistance. Here, a Pacific Biosciences (PacBio) HiFi read set was used to generate a collapsed haploid nuclear genome assembly and to explore phased diploid genome structure for C. parapsilosis strain CDC 317, the strain used for the current GenBank reference assembly. The assembly read set represented approximately 50× genome coverage, had a mean read length of 22.1 kb, with 96.4% of read bases with FASTQ quality scores ≥Q60. The collapsed HiFi assembly resolved eight telomere-bounded nuclear chromosomes and revealed a translocation artifact between chromosomes 4 and 5 in the reference assembly. Comparisons between haplotype-resolved assemblies confirmed high nucleotide-level homozygosity between homologous chromosomes, while revealing previously unrecognized localized structural heterozygosity on chromosome 8. Additional haplotype-level sequence variation occurred in genes encoding large, repeat-rich cell-surface glycoproteins. These results refine understanding of the CDC 317 genome structure and provide HiFi read and assembly resources to support studies of C. parapsilosis clinically relevant traits.</jats:p>