Duplication and DNA segmental loss in the rice genome: implications for diploidization

Authors

  • Xiyin Wang,

    1. College of Life Sciences, National Laboratory of Plant Genetic Engineering and Protein Engineering, Center of Bioinformatics, Peking University, Beijing 100871, China,
    2. Beijing Genomics Institute/Center of Genomics and Bioinformatics, Chinese Academy of Sciences, Beijing 101300, China,
    3. College of Mathematics, Hebei Polytechnic University, Tangshan, Hebei 063009, China,
    4. These authors contributed equally to this work
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  • Xiaoli Shi,

    1. College of Life Sciences, National Laboratory of Plant Genetic Engineering and Protein Engineering, Center of Bioinformatics, Peking University, Beijing 100871, China,
    2. Beijing Genomics Institute/Center of Genomics and Bioinformatics, Chinese Academy of Sciences, Beijing 101300, China,
    3. These authors contributed equally to this work
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  • Bailin Hao,

    1. Beijing Genomics Institute/Center of Genomics and Bioinformatics, Chinese Academy of Sciences, Beijing 101300, China,
    2. Institute of Theoretical Physics, Academia Sinica, Beijing 100080, China;
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  • Song Ge,

    Corresponding author
    1. Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China;
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  • Jingchu Luo

    Corresponding author
    1. College of Life Sciences, National Laboratory of Plant Genetic Engineering and Protein Engineering, Center of Bioinformatics, Peking University, Beijing 100871, China,
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Authors for correspondence: Jingchu LuoTel: +86 10 62757281Fax: +86 10 62759001Email: luojc@pku.edu.cn

Song GeTel: +86 10 62591431x6097Fax: +86 10 62590843Email: gesong@ns.ibcas.ac.cn

Summary

  • • Large-scale duplication events have been recently uncovered in the rice genome, but different interpretations were proposed regarding the extent of the duplications.
  • • Through analysing the 370 Mb genome sequences assembled into 12 chromosomes of Oryza sativa subspecies indica, we detected 10 duplicated blocks on all 12 chromosomes that contained 47% of the total predicted genes. Based on the phylogenetic analysis, we inferred that this was a result of a genome duplication that occurred c. 70 million years ago, supporting the polyploidy origin of the rice genome. In addition, a segmental duplication was also identified involving chromosomes 11 and 12, which occurred c. 5 million years ago.
  • • Following the duplications, there have been large-scale chromosomal rearrangements and deletions. About 30–65% of duplicated genes were lost shortly after the duplications, leading to a rapid diploidization.
  • • Together with other lines of evidence, we propose that polyploidization is still an ongoing process in grasses of polyploidy origins.

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