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DNA transposons mediate duplications via transposition-independent and -dependent mechanisms in metazoans

Author

Listed:
  • Shengjun Tan

    (Chinese Academy of Sciences
    Chinese Academy of Sciences)

  • Huijing Ma

    (Chinese Academy of Sciences
    Chinese Academy of Sciences
    University of Chinese Academy of Sciences)

  • Jinbo Wang

    (Chinese Academy of Sciences
    Chinese Academy of Sciences)

  • Man Wang

    (Peking University Cancer Hospital & Institute)

  • Mengxia Wang

    (Chinese Academy of Sciences
    Chinese Academy of Sciences
    University of Chinese Academy of Sciences)

  • Haodong Yin

    (Chinese Academy of Sciences
    University of Chinese Academy of Sciences)

  • Yaqiong Zhang

    (Chinese Academy of Sciences
    Chinese Academy of Sciences)

  • Xinying Zhang

    (Chinese Academy of Sciences
    University of Chinese Academy of Sciences)

  • Jieyu Shen

    (Chinese Academy of Sciences
    Chinese Academy of Sciences
    University of Chinese Academy of Sciences)

  • Danyang Wang

    (University of Chinese Academy of Sciences
    Chinese Academy of Sciences)

  • Graham L. Banes

    (University of Wisconsin–Madison
    Chinese Academy of Sciences)

  • Zhihua Zhang

    (University of Chinese Academy of Sciences
    Chinese Academy of Sciences)

  • Jianmin Wu

    (Peking University Cancer Hospital & Institute)

  • Xun Huang

    (University of Chinese Academy of Sciences
    Chinese Academy of Sciences)

  • Hua Chen

    (University of Chinese Academy of Sciences
    Chinese Academy of Sciences
    Chinese Academy of Sciences)

  • Siqin Ge

    (Chinese Academy of Sciences
    University of Chinese Academy of Sciences)

  • Chun-Long Chen

    (PSL Research University, CNRS UMR 3244
    Sorbonne University)

  • Yong E. Zhang

    (Chinese Academy of Sciences
    Chinese Academy of Sciences
    University of Chinese Academy of Sciences
    Chinese Academy of Sciences)

Abstract

Despite long being considered as “junk”, transposable elements (TEs) are now accepted as catalysts of evolution. One example is Mutator-like elements (MULEs, one type of terminal inverted repeat DNA TEs, or TIR TEs) capturing sequences as Pack-MULEs in plants. However, their origination mechanism remains perplexing, and whether TIR TEs mediate duplication in animals is almost unexplored. Here we identify 370 Pack-TIRs in 100 animal reference genomes and one Pack-TIR (Ssk-FB4) family in fly populations. We find that single-copy Pack-TIRs are mostly generated via transposition-independent gap filling, and multicopy Pack-TIRs are likely generated by transposition after replication fork switching. We show that a proportion of Pack-TIRs are transcribed and often form chimeras with hosts. We also find that Ssk-FB4s represent a young protein family, as supported by proteomics and signatures of positive selection. Thus, TIR TEs catalyze new gene structures and new genes in animals via both transposition-independent and -dependent mechanisms.

Suggested Citation

  • Shengjun Tan & Huijing Ma & Jinbo Wang & Man Wang & Mengxia Wang & Haodong Yin & Yaqiong Zhang & Xinying Zhang & Jieyu Shen & Danyang Wang & Graham L. Banes & Zhihua Zhang & Jianmin Wu & Xun Huang & H, 2021. "DNA transposons mediate duplications via transposition-independent and -dependent mechanisms in metazoans," Nature Communications, Nature, vol. 12(1), pages 1-14, December.
    • Handle: RePEc:nat:natcom:v:12:y:2021:i:1:d:10.1038_s41467-021-24585-9
    DOI: 10.1038/s41467-021-24585-9
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    References listed on IDEAS

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    1. Ning Jiang & Zhirong Bao & Xiaoyu Zhang & Sean R. Eddy & Susan R. Wessler, 2004. "Pack-MULE transposable elements mediate gene evolution in plants," Nature, Nature, vol. 431(7008), pages 569-573, September.
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