Transposable elements orchestrate subgenome-convergent and -divergent transcription in common wheat

Yuyun Zhang, Zijuan Li, Jinyi Liu, Yu’e Zhang, Luhuan Ye, Yuan Peng, Haoyu Wang, Huishan Diao, Yu Ma, Meiyue Wang, Yilin Xie, Tengfei Tang, Yili Zhuang, Wan Teng, Yiping Tong, Wenli Zhang, Zhaobo Lang (), Yongbiao Xue () and Yijing Zhang ()
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Yuyun Zhang: Chinese Academy of Sciences
Zijuan Li: Chinese Academy of Sciences
Jinyi Liu: Chinese Academy of Sciences
Yu’e Zhang: University of the Chinese Academy of Sciences
Luhuan Ye: Chinese Academy of Sciences
Yuan Peng: Chinese Academy of Sciences
Haoyu Wang: Chinese Academy of Sciences
Huishan Diao: Fudan University
Yu Ma: Chinese Academy of Sciences
Meiyue Wang: Fudan University
Yilin Xie: Chinese Academy of Sciences
Tengfei Tang: Chinese Academy of Sciences
Yili Zhuang: Chinese Academy of Sciences
Wan Teng: University of the Chinese Academy of Sciences
Yiping Tong: University of the Chinese Academy of Sciences
Wenli Zhang: Nanjing Agricultural University, No.1 Weigang
Zhaobo Lang: Chinese Academy of Sciences
Yongbiao Xue: University of the Chinese Academy of Sciences
Yijing Zhang: Fudan University

Nature Communications, 2022, vol. 13, issue 1, 1-16

Abstract: Abstract 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.

Date: 2022
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DOI: 10.1038/s41467-022-34290-w

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