Lehrstuhl für Technische Mikrobiologie, Technische Universität München, Freising, Germany.
PLoS One. 2020 Sep 23;15(9):e0238924. doi: 10.1371/journal.pone.0238924. eCollection 2020.
In this work the potential of comparative transcriptomics was explored of Saccharomyces (S.) cerevisiae and S. pastorianus for their discrimination. This way an alternative should be demonstrated to comparative genomics, which can be difficult as a result of their aneuoploid genomes composed of mosaics of the parental genomes. Strains were selected according to their application in beer brewing, i.e. top and bottom fermenting yeasts. Comparative transcriptomics was performed for four strains each of commercially available S. cerevisiae (top fermenting) and Saccharomyces pastorianus (bottom fermenting) brewing yeasts grown at two different temperatures to mid-exponential growth phase. A non-reference based approach was chosen in the form of alignment against a de novo assembled brewery-associated pan transcriptome to exclude bias introduced by manual selection of reference genomes. The result is an analysis workflow for self-contained comparative transcriptomics of Saccharomyces yeasts including, but not limited to, the analysis of core and accessory gene expression, functional analysis and metabolic classification. The functionality of this workflow is demonstrated along the principal differentiation of accessory transcriptomes of S. cerevisiae versus S. pastorianus strains. Hence, this work provides a concept enabling studies under different brewing conditions.
在这项工作中，探索了酿酒酵母（Saccharomyces cerevisiae）和巴氏酵母（Saccharomyces pastorianus）的比较转录组学潜力，以对它们进行区分。由于它们的非整倍体基因组是由双亲基因组的嵌合体组成的，因此这为比较基因组学提供了一种替代方法，但这种方法可能会很困难。根据它们在啤酒酿造中的应用，选择了菌株，即顶部发酵酵母和底部发酵酵母。对四种商业上可用的酿酒酵母（顶部发酵）和巴氏酵母（底部发酵）酿造酵母进行了比较转录组学研究，这些酵母在两种不同的温度下生长到中指数生长期。选择了一种非参考的方法，即与从头组装的啤酒厂相关的泛转录组进行比对，以排除手动选择参考基因组引入的偏差。结果是一种酿酒酵母（Saccharomyces）自我包含的比较转录组学分析工作流程，包括但不限于核心基因和辅助基因表达、功能分析和代谢分类的分析。该工作流程的功能通过 S. cerevisiae 菌株与 S. pastorianus 菌株辅助转录组的主要差异来证明。因此，这项工作提供了一种在不同酿造条件下进行研究的概念。
