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The Spirodela polyrhiza genome reveals insights into its neotenous reduction fast growth and aquatic lifestyle

Author

Listed:
  • W. Wang

    (Waksman Institute of Microbiology, Rutgers University)

  • G. Haberer

    (MIPS/IBIS, Institute for Bioinformatics and System Biology, Helmholtz Center Munich, German Research Center for Environmental Health (GmbH))

  • H. Gundlach

    (MIPS/IBIS, Institute for Bioinformatics and System Biology, Helmholtz Center Munich, German Research Center for Environmental Health (GmbH))

  • C. Gläßer

    (MIPS/IBIS, Institute for Bioinformatics and System Biology, Helmholtz Center Munich, German Research Center for Environmental Health (GmbH)
    Present address: Center for Molecular Biology, University of Heidelberg, Im Neuenheimer Feld 282, D-69120 Heidelberg, Germany)

  • T. Nussbaumer

    (MIPS/IBIS, Institute for Bioinformatics and System Biology, Helmholtz Center Munich, German Research Center for Environmental Health (GmbH))

  • M.C. Luo

    (University of California)

  • A. Lomsadze

    (Georgia Institute of Technology)

  • M. Borodovsky

    (Georgia Institute of Technology)

  • R.A. Kerstetter

    (Waksman Institute of Microbiology, Rutgers University
    Present address: The Genome Analysis Center, Monsanto Company, 800 N Lindbergh Boulevard, St Louis, Missouri 63167, USA)

  • J. Shanklin

    (Brookhaven National Laboratory)

  • D.W. Byrant

    (Donald Danforth Plant Science Center)

  • T.C. Mockler

    (Donald Danforth Plant Science Center)

  • K.J. Appenroth

    (University of Jena)

  • J. Grimwood

    (DOE Joint Genome Institute
    HudsonAlpha Institute for Biotechnology)

  • J. Jenkins

    (HudsonAlpha Institute for Biotechnology)

  • J. Chow

    (DOE Joint Genome Institute)

  • C. Choi

    (DOE Joint Genome Institute)

  • C. Adam

    (DOE Joint Genome Institute)

  • X.-H. Cao

    (Leibniz-Institute of Plant Genetics and Crop Plant Research (IPK))

  • J. Fuchs

    (Leibniz-Institute of Plant Genetics and Crop Plant Research (IPK))

  • I. Schubert

    (Leibniz-Institute of Plant Genetics and Crop Plant Research (IPK))

  • D. Rokhsar

    (DOE Joint Genome Institute)

  • J. Schmutz

    (DOE Joint Genome Institute
    HudsonAlpha Institute for Biotechnology)

  • T.P. Michael

    (Waksman Institute of Microbiology, Rutgers University
    Present address: Ibis Bioscience, Suite 150, 2251 Faraday Avenue, Carlsbad, California 92008, USA)

  • K.F.X. Mayer

    (MIPS/IBIS, Institute for Bioinformatics and System Biology, Helmholtz Center Munich, German Research Center for Environmental Health (GmbH))

  • J Messing

    (Waksman Institute of Microbiology, Rutgers University)

Abstract

The subfamily of the Lemnoideae belongs to a different order than other monocotyledonous species that have been sequenced and comprises aquatic plants that grow rapidly on the water surface. Here we select Spirodela polyrhiza for whole-genome sequencing. We show that Spirodela has a genome with no signs of recent retrotranspositions but signatures of two ancient whole-genome duplications, possibly 95 million years ago (mya), older than those in Arabidopsis and rice. Its genome has only 19,623 predicted protein-coding genes, which is 28% less than the dicotyledonous Arabidopsis thaliana and 50% less than monocotyledonous rice. We propose that at least in part, the neotenous reduction of these aquatic plants is based on readjusted copy numbers of promoters and repressors of the juvenile-to-adult transition. The Spirodela genome, along with its unique biology and physiology, will stimulate new insights into environmental adaptation, ecology, evolution and plant development, and will be instrumental for future bioenergy applications.

Suggested Citation

  • W. Wang & G. Haberer & H. Gundlach & C. Gläßer & T. Nussbaumer & M.C. Luo & A. Lomsadze & M. Borodovsky & R.A. Kerstetter & J. Shanklin & D.W. Byrant & T.C. Mockler & K.J. Appenroth & J. Grimwood & J., 2014. "The Spirodela polyrhiza genome reveals insights into its neotenous reduction fast growth and aquatic lifestyle," Nature Communications, Nature, vol. 5(1), pages 1-13, May.
    • Handle: RePEc:nat:natcom:v:5:y:2014:i:1:d:10.1038_ncomms4311
    DOI: 10.1038/ncomms4311
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    Cited by:

    1. David Wickell & Li-Yaung Kuo & Hsiao-Pei Yang & Amra Dhabalia Ashok & Iker Irisarri & Armin Dadras & Sophie de Vries & Jan de Vries & Yao-Moan Huang & Zheng Li & Michael S. Barker & Nolan T. Hartwick , 2021. "Underwater CAM photosynthesis elucidated by Isoetes genome," Nature Communications, Nature, vol. 12(1), pages 1-13, December.
    2. Youru WANG, 2016. "Callus induction and frond regeneration in Spirodela polyrhiza," Czech Journal of Genetics and Plant Breeding, Czech Academy of Agricultural Sciences, vol. 52(3), pages 114-119.
    3. Jessen V. Bredeson & Jessica B. Lyons & Ibukun O. Oniyinde & Nneka R. Okereke & Olufisayo Kolade & Ikenna Nnabue & Christian O. Nwadili & Eva Hřibová & Matthew Parker & Jeremiah Nwogha & Shengqiang Sh, 2022. "Chromosome evolution and the genetic basis of agronomically important traits in greater yam," Nature Communications, Nature, vol. 13(1), pages 1-16, December.
    4. Liang Ma & Ke-Wei Liu & Zhen Li & Yu-Yun Hsiao & Yiying Qi & Tao Fu & Guang-Da Tang & Diyang Zhang & Wei-Hong Sun & Ding-Kun Liu & Yuanyuan Li & Gui-Zhen Chen & Xue-Die Liu & Xing-Yu Liao & Yu-Ting Ji, 2023. "Diploid and tetraploid genomes of Acorus and the evolution of monocots," Nature Communications, Nature, vol. 14(1), pages 1-18, December.

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