Data from: Adaptation of a polyphagous herbivore to a novel host plant extensively shapes the transcriptome of herbivore and host

Generalist arthropod herbivores rapidly adapt to a broad range of host plants. However, the extent of transcriptional reprogramming in the herbivore and its hosts associated with adaptation remains poorly understood. Using the spider mite Tetranychus urticae and tomato as models with available genomic resources, we investigated the reciprocal genomewide transcriptional changes in both spider mite and tomato as a consequence of mite's adaptation to tomato. We transferred a genetically diverse mite population from bean to tomato where triplicated populations were allowed to propagate for 30 generations. Evolving populations greatly increased their reproductive performance on tomato relative to their progenitors when reared under identical conditions, indicative of genetic adaptation. Analysis of transcriptional changes associated with mite adaptation to tomato revealed two main components. First, adaptation resulted in a set of mite genes that were constitutively downregulated, independently of the host. These genes were mostly of an unknown function. Second, adapted mites mounted an altered transcriptional response that had greater amplitude of changes when re-exposed to tomato, relative to nonadapted mites. This gene set was enriched in genes encoding detoxifying enzymes and xenobiotic transporters. Besides the direct effects on mite gene expression, adaptation also indirectly affected the tomato transcriptional responses, which were attenuated upon feeding of adapted mites, relative to the induced responses by nonadapted mite feeding. Thus, constitutive downregulation and increased transcriptional plasticity of genes in a herbivore may play a central role in adaptation to host plants, leading to both a higher detoxification potential and reduced production of plant defence compounds.广食性节肢动物植食者可快速适应宽泛范围的寄主植物。然而，目前学界对植食者及其寄主在适应过程中所涉及的转录重编程（transcriptional reprogramming）程度，仍缺乏深入认知。本研究以具备可用基因组资源的二斑叶螨（Tetranychus urticae）与番茄为模式体系，探究了叶螨适应番茄时，二者之间发生的双向全基因组转录变化。我们将遗传背景多样的叶螨种群从菜豆转移至番茄，设置三组重复种群使其繁殖30代。在相同饲养条件下，经过适应演化的种群在番茄上的繁殖性能较其祖先种群显著提升，这一表型特征证实其发生了遗传适应。对叶螨适应番茄相关的转录变化分析显示，存在两类核心调控模式：其一，适应过程使一组叶螨基因呈现组成型下调表达，且该调控不受寄主植物种类影响；此类基因大多功能未知。其二，相较于未适应的叶螨种群，适应后的叶螨在再次接触番茄时，其转录响应的变化幅度更大且响应模式发生重塑。该基因集显著富集于编码解毒酶与异生物质转运蛋白的基因。除对叶螨基因表达的直接调控作用外，适应过程还间接影响了番茄的转录响应：相较于未适应叶螨取食所诱导的番茄转录响应，适应叶螨取食后番茄的转录响应被显著削弱。综上，植食者体内基因的组成型下调与转录可塑性提升，可能在寄主植物适应过程中发挥核心作用，可同时增强其解毒潜力并降低植物防御化合物的生成。