WGS of SC5314x529L parasexual progeny

SC5314 and 529L were mated to one another and concerted chromosome loss was induced by plating on pre-sporulation agar medium at 37C for 7 days. Colonies were screened for ploidy by flow cytometry. Cells were cultured overnight in YPD at 30 °C and genomic DNA for each strain was isolated from ~108 cells using the Zymo Research Quick-DNA™ Fungal/Bacterial Miniprep Kit according to the manufacturer’s instructions (Zymo, Irvine, CA). DNA libraries were prepared using NEBNext® Ultra™ II FS DNA Library Prep Kit for Illumina (New England Biolabs, Ipswich, MA). Prepared libraries were sequenced for 150 bp paired-end reads on an Illumina Novaseq platform at the Novogene Sequencing Facility. The reads were trimmed using trimmomatic 0.39 (with default parameters except slidingwindow:4:30, maxinfo:100:1, headcrop:12, and minlen:50) to get rid of the adaptor content in the sequences Using bowtie2 v2.2.6, the trimmed reads were aligned against the SC5314 reference genome (version A21-s02-m09-r10) obtained from the Candida Genome Database (www.candidagenome.org). The aligned SAM files were then converted to the BAM format using samtools v1.7.