Evolutionary rewiring of wheat abiotic stress responsive network by lineage-specific transposable elements I

The yield of wheat is highly impacted by environmental stresses. The combinatorial regulation of sequence-specific transcription factors(TFs) defines a regulatory network that underlies plant stress responses. Here we created a comprehensive catalog of genomic binding sites of 115 TFs underlying abiotic stress responses by leveraging DAP-seq in Triticum Urartu, along with epigenomic profiles. The majority of gene distant TF binding sites(TFBS) are embedded in transposable elements(TEs), whose functional relevance was supported by a signature of purifying selection and active epigenomic features. Furthermore, ~30% non-TE TFBS share high sequence similarity with TE-embeded TFBS, potentially derived from Triticeae-specific TEs and have almost no sequence homology in non-Triticeae species. The expansion of TE-derived TFBS in wheat linked to wheat-specific stress responsive genes, suggesting that TEs are an important driving force for regulatory innovation. Altogether, TEs have significantly and continuously shaped regulatory network in wheat adaptation. In order to delineate the major TF regulatory circuitry to abiotic stresses in Triticum Urartu, we performed DAP-seq to obtain a genome-wide binding profile of stress response TFs, ChIP-seq for three well-studied histone modifications (including H3K9ac, H3K4me3 and H3K27me3), DNase-seq, Bisulphite-seq and RNA-seq in 5 stresses.