Overdominant and partially dominant mutations drive clonal adaptation in diploid Saccharomyces cerevisiae
Overdominant and partially dominant mutations drive clonal adaptation in diploid Saccharomyces cerevisiae
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DOI：
10.1093/genetics/iyac061
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发表时间：
2022-04-18
期刊：
影响因子：
3.3
通讯作者：
Lang, Gregory, I
中科院分区：
文献类型：
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作者：
Aggeli, Dimitra;Marad, Daniel A.;Lang, Gregory, I
在实验进化中，适应性靶标的识别通常依赖于广泛的复制和基因重建。另一种方法是通过产生包含进化突变随机组合的分离体池，直接检测进化克隆中的所有突变。在这里，我们将这种方法应用于从4个二倍体群体中分离出来的6个酿酒酵母无性系，这些无性系在富葡萄糖培养基中无性系进化了2000代。相对于祖先，每个克隆包含17-26个突变。我们通过将进化克隆的孢子培养物与祖先的条形码单倍体进行大量交配，获得了创始克隆与进化克隆之间的中间基因型。我们对得到的条形码二倍体进行了大规模竞争，并通过条形码测序在实验和替代环境中量化了适应度。我们使用基于条形码的适应度分析和对一部分分离子的全基因组测序来估计进化突变的平均适应度效应。与我们之前对单倍体进化克隆的研究相反，我们发现二倍体携带较少的有益突变，在它们产生的环境中具有适度的适应性效应（高达5.4%）。与理论预期一致，重构实验表明，所有具有可检测到的适应度效应的突变都表现出对祖先等位基因的某种程度的优势，并且大多数是过显性的。在替代环境中具有较低适应度效应的基因型使我们能够确定驱动我们系统适应的条件。
Identification of adaptive targets in experimental evolution typically relies on extensive replication and genetic reconstruction. An alternative approach is to directly assay all mutations in an evolved clone by generating pools of segregants that contain random combinations of evolved mutations. Here, we apply this method to 6 Saccharomyces cerevisiae clones isolated from 4 diploid populations that were clonally evolved for 2,000 generations in rich glucose medium. Each clone contains 17-26 mutations relative to the ancestor. We derived intermediate genotypes between the founder and the evolved clones by bulk mating sporulated cultures of the evolved clones to a barcoded haploid version of the ancestor. We competed the resulting barcoded diploids en masse and quantified fitness in the experimental and alternative environments by barcode sequencing. We estimated average fitness effects of evolved mutations using barcode-based fitness assays and whole-genome sequencing for a subset of segregants. In contrast to our previous work with haploid evolved clones, we find that diploids carry fewer beneficial mutations, with modest fitness effects (up to 5.4%) in the environment in which they arose. In agreement with theoretical expectations, reconstruction experiments show that all mutations with a detectable fitness effect manifest some degree of dominance over the ancestral allele, and most are overdominant. Genotypes with lower fitness effects in alternative environments allowed us to identify conditions that drive adaptation in our system.