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Patterns of polymorphism and selection in the subgenomes of the allopolyploid Arabidopsis kamchatica

Author

Listed:
  • Timothy Paape

    (University of Zurich
    University of Zurich)

  • Roman V. Briskine

    (University of Zurich
    ETH Zurich
    Functional Genomics Center Zurich)

  • Gwyneth Halstead-Nussloch

    (University of Zurich)

  • Heidi E. L. Lischer

    (University of Zurich
    Swiss Institute of Bioinformatics (SIB))

  • Rie Shimizu-Inatsugi

    (University of Zurich
    University of Zurich)

  • Masaomi Hatakeyama

    (University of Zurich
    University of Zurich
    Swiss Institute of Bioinformatics (SIB)
    Functional Genomics Center Zurich)

  • Kenta Tanaka

    (University of Tsukuba)

  • Tomoaki Nishiyama

    (Kanazawa University)

  • Renat Sabirov

    (Institute of Marine Geology and Geophysics, Far East Branch, Russian Academy of Sciences)

  • Jun Sese

    (Artificial Intelligence Research Center, National Institute of Advanced Industrial Science and Technology (AIST)
    AIST-Tokyo Tech Real World Big-Data Computation Open Innovation Laboratory)

  • Kentaro K. Shimizu

    (University of Zurich
    University of Zurich
    Yokohama City University)

Abstract

Genome duplication is widespread in wild and crop plants. However, little is known about genome-wide selection in polyploids due to the complexity of duplicated genomes. In polyploids, the patterns of purifying selection and adaptive substitutions may be affected by masking owing to duplicated genes or homeologs as well as effective population size. Here, we resequence 25 accessions of the allotetraploid Arabidopsis kamchatica, which is derived from the diploid species A. halleri and A. lyrata. We observe a reduction in purifying selection compared with the parental species. Interestingly, proportions of adaptive non-synonymous substitutions are significantly positive in contrast to most plant species. A recurrent pattern observed in both frequency and divergence–diversity neutrality tests is that the genome-wide distributions of both subgenomes are similar, but the correlation between homeologous pairs is low. This may increase the opportunity of different evolutionary trajectories such as in the HMA4 gene involved in heavy metal hyperaccumulation.

Suggested Citation

  • Timothy Paape & Roman V. Briskine & Gwyneth Halstead-Nussloch & Heidi E. L. Lischer & Rie Shimizu-Inatsugi & Masaomi Hatakeyama & Kenta Tanaka & Tomoaki Nishiyama & Renat Sabirov & Jun Sese & Kentaro , 2018. "Patterns of polymorphism and selection in the subgenomes of the allopolyploid Arabidopsis kamchatica," Nature Communications, Nature, vol. 9(1), pages 1-13, December.
    • Handle: RePEc:nat:natcom:v:9:y:2018:i:1:d:10.1038_s41467-018-06108-1
    DOI: 10.1038/s41467-018-06108-1
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    Cited by:

    1. Reiko Akiyama & Takao Goto & Toshiaki Tameshige & Jiro Sugisaka & Ken Kuroki & Jianqiang Sun & Junichi Akita & Masaomi Hatakeyama & Hiroshi Kudoh & Tanaka Kenta & Aya Tonouchi & Yuki Shimahara & Jun S, 2023. "Seasonal pigment fluctuation in diploid and polyploid Arabidopsis revealed by machine learning-based phenotyping method PlantServation," Nature Communications, Nature, vol. 14(1), pages 1-16, December.
    2. Chow-Lih Yew & Takashi Tsuchimatsu & Rie Shimizu-Inatsugi & Shinsuke Yasuda & Masaomi Hatakeyama & Hiroyuki Kakui & Takuma Ohta & Keita Suwabe & Masao Watanabe & Seiji Takayama & Kentaro K. Shimizu, 2023. "Dominance in self-compatibility between subgenomes of allopolyploid Arabidopsis kamchatica shown by transgenic restoration of self-incompatibility," Nature Communications, Nature, vol. 14(1), pages 1-11, December.

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