Transposable Elements Orchestrate Subgenome-Convergent and -Divergent Transcription in Common Wheat
    作者: Yuyun Zhang, Zijuan Li, Jinyi Liu, Yu’e Zhang, Luhuan Ye, Yuan Peng, Haoyu Wang, Huishan Diao, Yu Ma, Yili Zhuang, Meiyue Wang, Yilin Xie, Tengfei Tang, Wan Teng, Yiping Tong, Wenli Zhang, Zhaobo Lang, Yongbiao Xue and Yijing Zhang
    刊物名称: Nature Communications
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    摘要:
    The success of common wheat as a global staple crop was largely attributed to its genomic diversity and redundancy due to the merge of different genomes, giving rise to the major question how subgenome-divergent and –convergent transcription is mediated and harmonized in a single cell. Here, we create a catalog of genome-wide transcription factor-binding sites (TFBSs) to assemble a common wheat regulatory network on an unprecedented scale. A significant proportion of subgenome-divergent TFBSs are derived from differential expansions of particular transposable elements (TEs) in diploid progenitors, which contribute to subgenome-divergent transcription. Whereas subgenome-convergent transcription is associated with balanced TF binding at loci derived from TE expansions before diploid divergence. These TFBSs have retained in parallel during evolution of each diploid, despite extensive unbalanced turnover of the flanking TEs. Thus, the differential evolutionary selection of paleo- and neo-TEs contribute to subgenome-convergent and -divergent regulation in common wheat, highlighting the influence of TE repertory plasticity on transcriptional plasticity in polyploid.