More than 80% of the wheat genome consists of transposable elements (TEs), which act as major drivers of wheat genome evolution. However, their contributions to the regulatory evolution of wheat adaptations remain largely unclear. Here, we created genome-binding maps for 53 transcription factors (TFs) underlying environmental responses by leveraging DAP-seq in Triticum urartu, together with epigenomic profiles. Most TF binding sites (TFBSs) located distally from genes are embedded in TEs, whose functional relevance is supported by purifying selection and active epigenomic features. About 24% of the non-TE TFBSs share significantly high sequence similarity with TE-embedded TFBSs. These non-TE TFBSs have almost no homologous sequences in non-Triticeae species and are potentially derived from Triticeae-specific TEs. The expansion of TE-derived TFBS linked to wheat-specific gene responses, suggesting TEs are an important driving force for regulatory innovations. Altogether, TEs have been significantly and continuously shaping regulatory networks related to wheat genome evolution and adaptation.

中文翻译：

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谱系特异性转座元件对小麦转录调控网络的进化重新布线

超过 80% 的小麦基因组由转座元件 (TE) 组成，它们是小麦基因组进化的主要驱动力。然而，它们对小麦适应的调控进化的贡献在很大程度上仍不清楚。在这里，我们利用乌拉尔图小麦中的 DAP-seq 以及表观基因组图谱，创建了 53 个环境反应背后的转录因子 (TF) 的基因组结合图谱。大多数位于基因远端的 TF 结合位点 (TFBS) 嵌入在 TE 中，其功能相关性得到纯化选择和活跃表观基因组特征的支持。大约 24% 的非 TE TFBS 与 TE 嵌入的 TFBS 具有显着高的序列相似性。这些非 TE TFBS 在非小麦科物种中几乎没有同源序列，并且可能源自小麦科特异性 TE。TE 衍生的 TFBS 的扩展与小麦特异性基因反应相关，这表明 TE 是监管创新的重要驱动力。总而言之，TE 一直在显着且持续地塑造与小麦基因组进化和适应相关的监管网络。