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Pack-MULE transposable elements mediate gene evolution in plants

Author

Listed:
  • Ning Jiang

    (University of Georgia
    Michigan State University)

  • Zhirong Bao

    (Washington University
    University of Washington)

  • Xiaoyu Zhang

    (University of Georgia
    University of California)

  • Sean R. Eddy

    (Washington University)

  • Susan R. Wessler

    (University of Georgia)

Abstract

Mutator-like transposable elements (MULEs) are found in many eukaryotic genomes and are especially prevalent in higher plants1,2,3. In maize, rice and Arabidopsis a few MULEs were shown to carry fragments of cellular genes4,5,6. These chimaeric elements are called Pack-MULEs in this study. The abundance of MULEs in rice and the availability of most of the genome sequence permitted a systematic analysis of the prevalence and nature of Pack-MULEs in an entire genome. Here we report that there are over 3,000 Pack-MULEs in rice containing fragments derived from more than 1,000 cellular genes. Pack-MULEs frequently contain fragments from multiple chromosomal loci that are fused to form new open reading frames, some of which are expressed as chimaeric transcripts. About 5% of the Pack-MULEs are represented in collections of complementary DNA. Functional analysis of amino acid sequences and proteomic data indicate that some captured gene fragments might be functional. Comparison of the cellular genes and Pack-MULE counterparts indicates that fragments of genomic DNA have been captured, rearranged and amplified over millions of years. Given the abundance of Pack-MULEs in rice and the widespread occurrence of MULEs in all characterized plant genomes, gene fragment acquisition by Pack-MULEs might represent an important new mechanism for the evolution of genes in higher plants.

Suggested Citation

  • 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.
    • Handle: RePEc:nat:nature:v:431:y:2004:i:7008:d:10.1038_nature02953
    DOI: 10.1038/nature02953
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    Cited by:

    1. 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.
    2. 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 Zha, 2022. "Transposable elements orchestrate subgenome-convergent and -divergent transcription in common wheat," Nature Communications, Nature, vol. 13(1), pages 1-16, December.

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