Comparative genomic hybridization in traditional fermentative Saccharomyces cerevisiae yeasts. Saccharomyces cerevisiae

We study the genetics, including microarray karyotyping using comparative genomic hybridization, to explore global changes in the genomic DNA of seven S. cerevisiae strains related to traditional fermentations of very different sources comparing to the sequenced S. cerevisiae laboratory strain (S288C). Our final goal is to determine the adaptive evolution of properties of biotechnological interest in Saccharomyces yeasts. Many copy number variations (CNVs) were observed, especially in genes associated to subtelomeric regions and transposon elements. Among the fermentation strains, differential CNV was observed in genes related to sugar transport and metabolism. An outstanding example of diverse CNV is the gen PUT1, involved in proline assimilation, which correlated with the adaptation of the strains to the presence of this nitrogen source in the media. Overall design: Seven S. cerevisiae strains were obtained from natural environments and different fermentation processes. The S. cerevisiae strain S288C was used as a control for microarray hybridizations. All experiments were performed using duplicate arrays, and Cy5-dCTP and Cy3-dCTP dye-swap assays were performed to reduce dye-specific bias.

本研究聚焦遗传学分析，采用基于比较基因组杂交（comparative genomic hybridization）的微阵列核型分析技术，对7株来源各异的传统发酵用酿酒酵母（Saccharomyces cerevisiae，简称S. cerevisiae）菌株的基因组DNA全局变化进行探究，并与已测序的酿酒酵母实验室菌株S288C开展对照分析。本研究的最终目标是解析酿酒酵母属酵母中具备生物技术应用价值的性状的适应性演化机制。研究中观测到大量拷贝数变异（copy number variation, CNV），尤其富集于亚端粒区域及转座子元件相关基因。在发酵菌株中，与糖转运及代谢相关基因存在差异化的CNV。其中极具代表性的多样化CNV案例为PUT1基因，该基因参与脯氨酸同化过程，与菌株对培养基中该氮源的适应性显著相关。整体实验设计：共获取7株酿酒酵母菌株，均分离自自然环境及不同发酵流程；以已完成全基因组测序的酿酒酵母实验室菌株S288C作为微阵列杂交实验的对照菌株。所有实验均设置重复微阵列，并通过Cy5-dCTP与Cy3-dCTP染料互换实验以降低染料特异性偏倚。