Credit41_In_Lab_Evolution

Different strains of Saccharomyces cerevisiae were treated with Credit41, then isolated and sequenced. Whole genome sequencing of GSY147(S288c backgroud), YJM789, AWRI1631 and RM11, grown in YPD, YM or YM supplemented with WYF, treated or not with Cr41, using Illumina Miseq. The cells were grown for 6 passages, then screened for resistance. A single colony of resistant cells was used for genomic DNA extraction using phenol-chloroform method (Hirt, 1967). The library was built using Quanta-bio sparq DNA frag and library kit and sequenced on an Illumina Miseq platform. Basecalls performed with Illumina’s FASTQ Generation (v1.0.0) available in BaseSpace. The data for all strains was then aligned to S288c reference (release R64-2-1) by creating an index using GATK-4.1.1.0. The GATK HaplotypeCaller was used to generate the vcf files.研究人员采用Credit41（后文简称Cr41）处理不同酿酒酵母（Saccharomyces cerevisiae）菌株，随后对其开展分离与测序工作。针对在YPD、YM或添加WYF的YM培养基中培养、经Cr41处理或未处理的GSY147（S288c背景菌株）、YJM789、AWRI1631及RM11菌株，研究人员采用因美纳（Illumina）MiSeq测序平台开展全基因组测序。所有菌株经6代传代培养后，筛选获得耐药菌株；取耐药菌株的单菌落，采用酚-氯仿法（Hirt, 1967）提取基因组DNA。使用Quanta-bio Sparq DNA片段化与文库构建试剂盒构建测序文库，并在因美纳MiSeq测序平台上完成测序。碱基识别工作通过BaseSpace平台内置的Illumina FASTQ生成工具（v1.0.0）完成。随后将所有菌株的测序数据比对至S288c参考基因组（版本R64-2-1），比对前通过基因组分析工具包（Genome Analysis Toolkit，GATK）4.1.1.0构建参考基因组索引；最终使用GATK单倍型调用器（HaplotypeCaller）生成VCF格式变异检测文件。