Wheat centromeric retrotransposons: the new ones take a major role in centromeric structure

Authors

  • Baochun Li,

    1. Key Laboratory of Crop Gene Resource and Germplasm Enhancement, Ministry of Agriculture, Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, China
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    • These authors contributed equally to this work.
  • Frédéric Choulet,

    1. INRA, UMR1095, Genetic Diversity and Ecophysiology of Cereals, Clermont-Ferrand, France
    2. University Blaise Pascal, UMR1095, Genetic Diversity and Ecophysiology of Cereals, Clermont-Ferrand, France
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    • These authors contributed equally to this work.
  • Yanfang Heng,

    1. Key Laboratory of Crop Gene Resource and Germplasm Enhancement, Ministry of Agriculture, Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, China
    2. National Maize Improvement Centre, China Agricultural University, Beijing, China
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    • These authors contributed equally to this work.
  • Weiwei Hao,

    1. Key Laboratory of Crop Gene Resource and Germplasm Enhancement, Ministry of Agriculture, Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, China
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  • Etienne Paux,

    1. INRA, UMR1095, Genetic Diversity and Ecophysiology of Cereals, Clermont-Ferrand, France
    2. University Blaise Pascal, UMR1095, Genetic Diversity and Ecophysiology of Cereals, Clermont-Ferrand, France
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  • Zhao Liu,

    1. Key Laboratory of Crop Gene Resource and Germplasm Enhancement, Ministry of Agriculture, Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, China
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  • Wei Yue,

    1. Key Laboratory of Crop Gene Resource and Germplasm Enhancement, Ministry of Agriculture, Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, China
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  • Weiwei Jin,

    Corresponding author
    1. National Maize Improvement Centre, China Agricultural University, Beijing, China
    • Key Laboratory of Crop Gene Resource and Germplasm Enhancement, Ministry of Agriculture, Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, China
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  • Catherine Feuillet,

    Corresponding author
    1. INRA, UMR1095, Genetic Diversity and Ecophysiology of Cereals, Clermont-Ferrand, France
    2. University Blaise Pascal, UMR1095, Genetic Diversity and Ecophysiology of Cereals, Clermont-Ferrand, France
    • Key Laboratory of Crop Gene Resource and Germplasm Enhancement, Ministry of Agriculture, Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, China
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  • Xueyong Zhang

    Corresponding author
    • Key Laboratory of Crop Gene Resource and Germplasm Enhancement, Ministry of Agriculture, Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, China
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For correspondence (e-mails weiweijin@cau.edu.cn, catherine.feuillet@clermont.inra.fr and xueyongz@caas.net.cn).

Summary

The physical map of the hexaploid wheat chromosome 3B was screened using centromeric DNA probes. A 1.1-Mb region showing the highest number of positive bacterial artificial chromosome (BAC) clones was fully sequenced and annotated, revealing that 96% of the DNA consisted of transposable elements, mainly long terminal repeat (LTR) retrotransposons (88%). Estimation of the insertion time of the transposable elements revealed that CRW (also called Cereba) and Quinta are the youngest elements at the centromeres of common wheat (Triticum spp.) and its diploid ancestors, with Quinta being younger than CRW in both diploid and hexaploid wheats. Chromatin immunoprecipitation experiments revealed that both CRW and Quinta families are targeted by the centromere-specific histone H3 variant CENH3. Immuno colocalization of retroelements and CENH3 antibody indicated that a higher proportion of Quinta than CRWs was associated with CENH3, although CRWs were more abundant. Long arrays of satellite repeats were also identified in the wheat centromere regions, but they lost the ability to bind with CENH3. In addition to transposons, two functional genes and one pseudogene were identified. The gene density in the centromere appeared to be between three and four times lower than the average gene density of chromosome 3B. Comparisons with related grasses also indicated a loss of microcollinearity in this region. Finally, comparison of centromeric sequences of Aegilops tauschii (DD), Triticum boeoticum (AA) and hexaploid wheat revealed that the centromeres in both the polyploids and diploids are still undergoing dynamic changes, and that the new CRWs and Quintas may have undertaken the core role in kinetochore formation.

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