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Genome biology of the paleotetraploid perennial biomass crop Miscanthus

Author

Listed:
  • Therese Mitros

    (University of California
    University of Illinois)

  • Adam M. Session

    (University of California
    U.S. Department of Energy Joint Genome Institute)

  • Brandon T. James

    (University of Illinois
    HudsonAlpha Biotechnology Institute)

  • Guohong Albert Wu

    (U.S. Department of Energy Joint Genome Institute)

  • Mohammad B. Belaffif

    (University of Illinois
    HudsonAlpha Biotechnology Institute)

  • Lindsay V. Clark

    (University of Illinois
    University of Illinois)

  • Shengqiang Shu

    (U.S. Department of Energy Joint Genome Institute)

  • Hongxu Dong

    (University of Illinois)

  • Adam Barling

    (University of Illinois)

  • Jessica R. Holmes

    (University of Illinois
    University of Illinois)

  • Jessica E. Mattick

    (University of Illinois
    Loyola University Chicago)

  • Jessen V. Bredeson

    (University of California)

  • Siyao Liu

    (University of Illinois
    University of North Carolina)

  • Kerrie Farrar

    (Aberystwyth University, Gogerddan)

  • Katarzyna Głowacka

    (Institute of Plant Genetics, Polish Academy of Sciences
    University of Nebraska-Lincoln)

  • Stanisław Jeżowski

    (Institute of Plant Genetics, Polish Academy of Sciences)

  • Kerrie Barry

    (U.S. Department of Energy Joint Genome Institute)

  • Won Byoung Chae

    (University of Illinois
    Dankook University)

  • John A. Juvik

    (University of Illinois)

  • Justin Gifford

    (University of Illinois)

  • Adebosola Oladeinde

    (University of Illinois)

  • Toshihiko Yamada

    (Field Science Center for Northern Biosphere)

  • Jane Grimwood

    (U.S. Department of Energy Joint Genome Institute
    HudsonAlpha Biotechnology Institute)

  • Nicholas H. Putnam

    (Dovetail Genomics)

  • Jose Vega

    (Earlham Institute, Norwich Research Park Innovation Centre)

  • Susanne Barth

    (Oak Park Research Centre)

  • Manfred Klaas

    (Oak Park Research Centre)

  • Trevor Hodkinson

    (The University of Dublin)

  • Laigeng Li

    (Institute of Plant Physiology and Ecology, Chinese Academy of Sciences)

  • Xiaoli Jin

    (Zhejiang University)

  • Junhua Peng

    (HuaZhi Rice Biotech Company)

  • Chang Yeon Yu

    (Kangwon National University)

  • Kweon Heo

    (Kangwon National University)

  • Ji Hye Yoo

    (Kangwon National University)

  • Bimal Kumar Ghimire

    (Konkuk University)

  • Iain S. Donnison

    (Aberystwyth University, Gogerddan)

  • Jeremy Schmutz

    (U.S. Department of Energy Joint Genome Institute
    HudsonAlpha Biotechnology Institute)

  • Matthew E. Hudson

    (University of Illinois
    University of Illinois
    University of Illinois)

  • Erik J. Sacks

    (University of Illinois
    University of Illinois
    University of Illinois)

  • Stephen P. Moose

    (University of Illinois
    University of Illinois
    University of Illinois)

  • Kankshita Swaminathan

    (University of Illinois
    HudsonAlpha Biotechnology Institute)

  • Daniel S. Rokhsar

    (University of California
    University of Illinois
    U.S. Department of Energy Joint Genome Institute
    Okinawa Institute of Science and Technology Graduate University)

Abstract

Miscanthus is a perennial wild grass that is of global importance for paper production, roofing, horticultural plantings, and an emerging highly productive temperate biomass crop. We report a chromosome-scale assembly of the paleotetraploid M. sinensis genome, providing a resource for Miscanthus that links its chromosomes to the related diploid Sorghum and complex polyploid sugarcanes. The asymmetric distribution of transposons across the two homoeologous subgenomes proves Miscanthus paleo-allotetraploidy and identifies several balanced reciprocal homoeologous exchanges. Analysis of M. sinensis and M. sacchariflorus populations demonstrates extensive interspecific admixture and hybridization, and documents the origin of the highly productive triploid bioenergy crop M. × giganteus. Transcriptional profiling of leaves, stem, and rhizomes over growing seasons provides insight into rhizome development and nutrient recycling, processes critical for sustainable biomass accumulation in a perennial temperate grass. The Miscanthus genome expands the power of comparative genomics to understand traits of importance to Andropogoneae grasses.

Suggested Citation

  • Therese Mitros & Adam M. Session & Brandon T. James & Guohong Albert Wu & Mohammad B. Belaffif & Lindsay V. Clark & Shengqiang Shu & Hongxu Dong & Adam Barling & Jessica R. Holmes & Jessica E. Mattick, 2020. "Genome biology of the paleotetraploid perennial biomass crop Miscanthus," Nature Communications, Nature, vol. 11(1), pages 1-11, December.
    • Handle: RePEc:nat:natcom:v:11:y:2020:i:1:d:10.1038_s41467-020-18923-6
    DOI: 10.1038/s41467-020-18923-6
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    Citations

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    Cited by:

    1. Yanting Shen & Wanying Li & Ying Zeng & Zhipeng Li & Yiqiong Chen & Jixiang Zhang & Hong Zhao & Lingfang Feng & Dongming Ma & Xiaolu Mo & Puyue Ouyang & Lili Huang & Zheng Wang & Yuannian Jiao & Hong-, 2022. "Chromosome-level and haplotype-resolved genome provides insight into the tetraploid hybrid origin of patchouli," Nature Communications, Nature, vol. 13(1), pages 1-15, December.
    2. Aiping Song & Jiangshuo Su & Haibin Wang & Zhongren Zhang & Xingtan Zhang & Yves Peer & Fei Chen & Weimin Fang & Zhiyong Guan & Fei Zhang & Zhenxing Wang & Likai Wang & Baoqing Ding & Shuang Zhao & Li, 2023. "Analyses of a chromosome-scale genome assembly reveal the origin and evolution of cultivated chrysanthemum," Nature Communications, Nature, vol. 14(1), pages 1-15, December.
    3. José Cerca & Bent Petersen & José Miguel Lazaro-Guevara & Angel Rivera-Colón & Siri Birkeland & Joel Vizueta & Siyu Li & Qionghou Li & João Loureiro & Chatchai Kosawang & Patricia Jaramillo Díaz & Gon, 2022. "The genomic basis of the plant island syndrome in Darwin’s giant daisies," Nature Communications, Nature, vol. 13(1), pages 1-13, December.
    4. Adam M. Session & Daniel S. Rokhsar, 2023. "Transposon signatures of allopolyploid genome evolution," Nature Communications, Nature, vol. 14(1), pages 1-14, December.
    5. 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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