To extract genomic DNA, ∼109 cells grown overnight in YPD at 30°C were processed using the Qiagen Genomic Buffer Set and the Qiagen Genomic-tip 100/G. Lyticase (Sigma, L2524) was used to enzymatically digest the fungal cell wall. Two libraries were constructed with average insert sizes of 197 bases and 2.5 kilobases (Supplemental Table S2) as previously described (Fisher et al. 2011 (link); Grad et al. 2012 (link)) and were sequenced on an Illumina HiSeq to generate 101 base paired-end reads.
For SNP calling, reads were aligned to the SC5314 genome (version A21-s02-m01-r01;http://www.candidagenome.org ) using BWA 0.5.9 (Li and Durbin 2010 (link)) and variants identified with GATK (McKenna et al. 2010 (link)). Genomic regions exhibiting copy number variation were identified from GC normalized read depth. Potential inversions and translocations identified from alignments of the de novo assemblies were validated by evaluating read support using BreakDancer (Chen et al. 2009 (link)).
The Illumina reads for each strain were assembled using ALLPATHS-LG (Gnerre et al. 2011 (link)), and genes were predicted for each assembly. Both the assemblies and SNPs were used to evaluate variation in gene content and sequence. For detailed DNA sequence analysis methods, see Supplemental Material.
For SNP calling, reads were aligned to the SC5314 genome (version A21-s02-m01-r01;
The Illumina reads for each strain were assembled using ALLPATHS-LG (Gnerre et al. 2011 (link)), and genes were predicted for each assembly. Both the assemblies and SNPs were used to evaluate variation in gene content and sequence. For detailed DNA sequence analysis methods, see Supplemental Material.
