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The Torreya grandis genome illuminates the origin and evolution of gymnosperm-specific sciadonic acid biosynthesis

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  • Heqiang Lou

    (Zhejiang A&F University)

  • Lili Song

    (Zhejiang A&F University)

  • Xiaolong Li

    (Zhejiang A&F University
    Ministry of Agriculture and Rural Affairs)

  • Hailing Zi

    (Novogene Bioinformatics Institute)

  • Weijie Chen

    (Zhejiang A&F University)

  • Yadi Gao

    (Zhejiang A&F University)

  • Shan Zheng

    (Zhejiang A&F University)

  • Zhangjun Fei

    (Cornell University
    U.S. Department of Agriculture-Agricultural Research Service, Robert W. Holley Center for Agriculture and Health)

  • Xuepeng Sun

    (Zhejiang A&F University
    Ministry of Agriculture and Rural Affairs)

  • Jiasheng Wu

    (Zhejiang A&F University)

Abstract

Torreya plants produce dry fruits with assorted functions. Here, we report the 19-Gb chromosome-level genome assembly of T. grandis. The genome is shaped by ancient whole-genome duplications and recurrent LTR retrotransposon bursts. Comparative genomic analyses reveal key genes involved in reproductive organ development, cell wall biosynthesis and seed storage. Two genes encoding a C18 Δ9-elongase and a C20 Δ5-desaturase are identified to be responsible for sciadonic acid biosynthesis and both are present in diverse plant lineages except angiosperms. We demonstrate that the histidine-rich boxes of the Δ5-desaturase are crucial for its catalytic activity. Methylome analysis reveals that methylation valleys of the T. grandis seed genome harbor genes associated with important seed activities, including cell wall and lipid biosynthesis. Moreover, seed development is accompanied by DNA methylation changes that possibly fuel energy production. This study provides important genomic resources and elucidates the evolutionary mechanism of sciadonic acid biosynthesis in land plants.

Suggested Citation

  • Heqiang Lou & Lili Song & Xiaolong Li & Hailing Zi & Weijie Chen & Yadi Gao & Shan Zheng & Zhangjun Fei & Xuepeng Sun & Jiasheng Wu, 2023. "The Torreya grandis genome illuminates the origin and evolution of gymnosperm-specific sciadonic acid biosynthesis," Nature Communications, Nature, vol. 14(1), pages 1-15, December.
    • Handle: RePEc:nat:natcom:v:14:y:2023:i:1:d:10.1038_s41467-023-37038-2
    DOI: 10.1038/s41467-023-37038-2
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    1. Liangsheng Zhang & Fei Chen & Xingtan Zhang & Zhen Li & Yiyong Zhao & Rolf Lohaus & Xiaojun Chang & Wei Dong & Simon Y. W. Ho & Xing Liu & Aixia Song & Junhao Chen & Wenlei Guo & Zhengjia Wang & Yingy, 2020. "The water lily genome and the early evolution of flowering plants," Nature, Nature, vol. 577(7788), pages 79-84, January.
    2. Daniel J. Cosgrove, 2000. "Loosening of plant cell walls by expansins," Nature, Nature, vol. 407(6802), pages 321-326, September.
    3. Björn Nystedt & Nathaniel R. Street & Anna Wetterbom & Andrea Zuccolo & Yao-Cheng Lin & Douglas G. Scofield & Francesco Vezzi & Nicolas Delhomme & Stefania Giacomello & Andrey Alexeyenko & Riccardo Vi, 2013. "The Norway spruce genome sequence and conifer genome evolution," Nature, Nature, vol. 497(7451), pages 579-584, May.
    4. Tao Wan & Zhiming Liu & Ilia J. Leitch & Haiping Xin & Gillian Maggs-Kölling & Yanbing Gong & Zhen Li & Eugene Marais & Yiying Liao & Can Dai & Fan Liu & Qijia Wu & Chi Song & Yadong Zhou & Weichang H, 2021. "The Welwitschia genome reveals a unique biology underpinning extreme longevity in deserts," Nature Communications, Nature, vol. 12(1), pages 1-15, December.
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