Genomic DNA Extraction and Sequencing for C. albicans

For genomic DNA, C. albicans cells were grown in YPD at 30 °C and DNA isolated using a Qiagen Genomic Buffer Set, a Qiagen Genomic-tip 100/G or the MasterPure Yeast DNA Purification kit (Epicentre). DNA was sequenced using Illumina HiSeq 2000 generating 101-bp paired reads. Reads were aligned to the SC5314 reference genome using Burrows–Wheeler Aligner (98 ), and converted to sorted BAM format using Samtools (99 (link)). Picard tools (picard.sourceforge.net/) were used to preprocess the alignments. The Genome Analysis Toolkit (100 (link)) and Pilon (37 (link)) were used to call variant and reference bases from the alignments. Mutations were inspected in IGV (Broad Institute) and annotated using the VCFannotator (Broad Institute). Ploidy, copy number variation, and LOH analyses were performed as described in SI Appendix, Materials and Methods.

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Ene I.V., Farrer R.A., Hirakawa M.P., Agwamba K., Cuomo C.A, & Bennett R.J. (2018). Global analysis of mutations driving microevolution of a heterozygous diploid fungal pathogen. Proceedings of the National Academy of Sciences of the United States of America, 115(37), E8688-E8697.

Publication 2018

Genomic Buffer Set MasterPure Yeast DNA Purification kit HiSeq 2000

Buffer C albicans Cells Copy number variation Genome Mutations Yeast

Corresponding Organization : Providence College

Other organizations : Broad Institute

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Variable analysis

independent variables

Growth of C. albicans cells in YPD at 30 °C

dependent variables

DNA sequencing using Illumina HiSeq 2000 generating 101-bp paired reads
Alignment of reads to the SC5314 reference genome using Burrows–Wheeler Aligner
Conversion of aligned reads to sorted BAM format using Samtools
Preprocessing of alignments using Picard tools
Variant and reference base calling using the Genome Analysis Toolkit and Pilon
Inspection of mutations in IGV (Broad Institute) and annotation using the VCFannotator (Broad Institute)
Ploidy, copy number variation, and LOH analyses

control variables

DNA isolation using a Qiagen Genomic Buffer Set, a Qiagen Genomic-tip 100/G or the MasterPure Yeast DNA Purification kit (Epicentre)

Annotations

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