Genome Sequencing of IMX2538 Yeast Strain

IMX2538 (35-deletions prototrophic strain) was sequenced using 300-bp paired-end sequencing reads prepared with the MiSeq reagent kit v3 on an Illumina MiSeq sequencer (Illumina, San Diego, CA). To this end, extracted DNA was mechanically sheared to 550 bp with the M220 ultrasonicator (Covaris, Wolburn, MA) and subsequently the TruSeq DNA PCR-Free Library preparation kit (Illumina) was employed to make a six-strain library. The samples were quantified by quantitative PCR on a Rotor-Gene Q PCR cycler (Qiagen) using the KAPA library quantification kit (Kapa Biosystems, Wilmington, MA). Library integrity and fragment size were determined with a Tapestation 2200 system (Agilent Technologies). Sequencing reads were mapped onto the CEN.PK113-7D (163 (link)) reference genome using the Burrows-Wheeler alignment (BWA) tool (version 0.7.15) (164 (link)) and further processed using SAMtools (version 1.3.1) (165 (link)) and Pilon (with -vcf setting; version 1.18) (166 (link)) to identify SNPs. The sequence was analyzed by visualizing the generated .bam files in the Integrative Genomics Viewer (IGV) software (version 2.4.0) (167 (link)). Chromosomal copy number was estimated by the Magnolya algorithm (version 0.15) (168 (link)).