Each yeast isolate was recovered from a freezer stock and purely cultured on a yeast, peptone, dextrose (YPD) or Sabouraudthetic dextrose (SD) agar plate for 48–60 hr. Next, a single colony was inoculated to another YPD plate and cultured for 24 hr. Approximately 100 µl of yeast cells were used for DNA isolation using the MasterPure Yeast DNA Purification Kit (Epicenter, Madison, WI) according to the manufacturer’s instructions. Alternatively, a single colony was inoculated into 6 ml YPD broth supplemented with 0.5 M NaCl and cultured for 40 hr at 37°, prior to extraction using the MasterPure Yeast DNA Purification Kit (Epicentre) as previously described (Rhodes et al. 2017 (link)).
DNA was sequenced using Illumina technology. For each isolate, a small insert library was constructed and used to generate between 14 and 150 million 101-bp, paired-end reads per isolate, which resulted in 56- to 603-fold average coverage of reads aligned to the H99 genome. In addition, large insert libraries were constructed for 15 isolates (Table S4 ) and also used to generate 101-bp, paired-end reads. Isolates were sequenced at Imperial College London and the Broad Institute (Table S1 ).
DNA was sequenced using Illumina technology. For each isolate, a small insert library was constructed and used to generate between 14 and 150 million 101-bp, paired-end reads per isolate, which resulted in 56- to 603-fold average coverage of reads aligned to the H99 genome. In addition, large insert libraries were constructed for 15 isolates (