Knowledge of the number and nature of genetic changes responsible for adaptation is essential for understanding and predicting evolutionary trajectories. Here, we study the genomic basis of compensatory adaptation to the fitness cost of fungicide resistance in experimentally evolved strains of the filamentous fungus Aspergillus nidulans The original selection experiment tracked the fitness recovery of lines founded by an ancestral strain that was resistant to fludioxonil, but paid a fitness cost in the absence of the fungicide. We obtained whole-genome sequence data for the ancestral A. nidulans strain and eight experimentally evolved strains. We find that fludioxonil resistance in the ancestor was likely conferred by a mutation in histidine kinase nikA, part of the two-component signal transduction system of the high-osmolarity glycerol (HOG) stress response pathway. To compensate for the pleiotropic negative effects of the resistance mutation, the subsequent fitness gains observed in the evolved lines were likely caused by secondary modification of HOG pathway activity. Candidate genes for the compensatory fitness increases were significantly overrepresented by stress response functions, and some were specifically associated with the HOG pathway itself. Parallel evolution at the gene level was rare among evolved lines. There was a positive relationship between the predicted number of adaptive steps, estimated from fitness data, and the number of genomic mutations, determined by whole-genome sequencing. However, the number of genomic mutations was, on average, 8.45 times greater than the number of adaptive steps inferred from fitness data. This research expands our understanding of the genetic basis of adaptation in multicellular eukaryotes and lays out a framework for future work on the genomics of compensatory adaptation in A. nidulans.

译文

了解负责适应的遗传变化的数量和性质对于理解和预测进化轨迹至关重要。在这里,我们研究了在实验进化的丝状真菌构巢曲霉菌株中,对杀真菌剂抗性的适应性成本进行补偿性适应的基因组基础。最初的选择实验跟踪了由祖先菌株建立的品系的适应性恢复,该品系对氟二氧嘧啶具有抗性,但在没有杀真菌剂的情况下支付了健身费用。我们获得了祖先的A.Niddulans菌株和八个实验进化的菌株的全基因组序列数据。我们发现,祖先的氟二氧杂环素抗性可能是由组氨酸激酶nikA的突变赋予的,该突变是高渗透压甘油 (HOG) 应激反应途径的两组分信号转导系统的一部分。为了补偿抗性突变的多效性负面影响,在进化系中观察到的随后的适应性增益可能是由HOG途径活性的二次修饰引起的。代偿性适应性增加的候选基因显着被应激反应功能所代表,其中一些与HOG途径本身特别相关。在进化品系中,基因水平的平行进化很少见。根据适应性数据估算的自适应步骤的预测数量与通过全基因组测序确定的基因组突变数量之间存在正相关关系。然而,基因组突变的数量平均比从适应性数据推断的适应性步骤的数量大8.45倍。这项研究扩大了我们对多细胞真核生物适应的遗传基础的理解,并为未来在a.Niddulans的补偿性适应基因组学方面的工作奠定了框架。

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