IDEAS home Printed from https://ideas.repec.org/a/nat/natcom/v14y2023i1d10.1038_s41467-023-37038-2.html
   My bibliography  Save this article

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

Author

Listed:
  • 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
    as

    Download full text from publisher

    File URL: https://www.nature.com/articles/s41467-023-37038-2
    File Function: Abstract
    Download Restriction: no
    File URL: https://libkey.io/10.1038/s41467-023-37038-2?utm_source=ideas
    LibKey link: if access is restricted and if your library uses this service, LibKey will redirect you to where you can use your library subscription to access this item
    ---><---

    References listed on IDEAS

    as
    1. 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.
    2. 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.
    3. Daniel J. Cosgrove, 2000. "Loosening of plant cell walls by expansins," Nature, Nature, vol. 407(6802), pages 321-326, September.
    4. 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.
    Full references (including those not matched with items on IDEAS)

    Most related items

    These are the items that most often cite the same works as this one and are cited by the same works as this one.
    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. Taikui Zhang & Weichen Huang & Lin Zhang & De-Zhu Li & Ji Qi & Hong Ma, 2024. "Phylogenomic profiles of whole-genome duplications in Poaceae and landscape of differential duplicate retention and losses among major Poaceae lineages," Nature Communications, Nature, vol. 15(1), pages 1-27, December.
    3. Xing Guo & Fang Wang & Dongming Fang & Qiongqiong Lin & Sunil Kumar Sahu & Liuming Luo & Jiani Li & Yewen Chen & Shanshan Dong & Sisi Chen & Yang Liu & Shixiao Luo & Yalong Guo & Huan Liu, 2023. "The genome of Acorus deciphers insights into early monocot evolution," Nature Communications, Nature, vol. 14(1), pages 1-15, December.
    4. Jianxiang Ma & Pengchuan Sun & Dandan Wang & Zhenyue Wang & Jiao Yang & Ying Li & Wenjie Mu & Renping Xu & Ying Wu & Congcong Dong & Nawal Shrestha & Jianquan Liu & Yongzhi Yang, 2021. "The Chloranthus sessilifolius genome provides insight into early diversification of angiosperms," Nature Communications, Nature, vol. 12(1), pages 1-13, December.
    5. Junhui Yuan & Sanjie Jiang & Jianbo Jian & Mingyu Liu & Zhen Yue & Jiabao Xu & Juan Li & Chunyan Xu & Lihong Lin & Yi Jing & Xiaoxiao Zhang & Haixin Chen & Linjuan Zhang & Tao Fu & Shuiyan Yu & Zhangy, 2022. "Genomic basis of the giga-chromosomes and giga-genome of tree peony Paeonia ostii," Nature Communications, Nature, vol. 13(1), pages 1-16, December.
    6. Li Ma & Lingjun Sun & Yinshan Guo & Hong Lin & Zhendong Liu & Kun Li & Xiuwu Guo, 2020. "Transcriptome analysis of table grapes (Vitis vinifera L.) identified a gene network module associated with berry firmness," PLOS ONE, Public Library of Science, vol. 15(8), pages 1-15, August.
    7. Meral Yilmaz & Ömür Baysal & Ragip Soner Sīlme, 2021. "The effect of a seed coating with Origanum vulgare essential oil on Clavibacter michiganensis subsp. michiganensis," Plant Protection Science, Czech Academy of Agricultural Sciences, vol. 57(3), pages 217-225.
    8. Kevin Nota & Jonatan Klaminder & Pascal Milesi & Richard Bindler & Alessandro Nobile & Tamara Steijn & Stefan Bertilsson & Brita Svensson & Shun K. Hirota & Ayumi Matsuo & Urban Gunnarsson & Heikki Se, 2022. "Norway spruce postglacial recolonization of Fennoscandia," Nature Communications, Nature, vol. 13(1), pages 1-9, December.
    9. Xiao Feng & Qipian Chen & Weihong Wu & Jiexin Wang & Guohong Li & Shaohua Xu & Shao Shao & Min Liu & Cairong Zhong & Chung-I Wu & Suhua Shi & Ziwen He, 2024. "Genomic evidence for rediploidization and adaptive evolution following the whole-genome triplication," Nature Communications, Nature, vol. 15(1), pages 1-15, December.

    More about this item

    Statistics

    Access and download statistics

    Corrections

    All material on this site has been provided by the respective publishers and authors. You can help correct errors and omissions. When requesting a correction, please mention this item's handle: RePEc:nat:natcom:v:14:y:2023:i:1:d:10.1038_s41467-023-37038-2. See general information about how to correct material in RePEc.

    If you have authored this item and are not yet registered with RePEc, we encourage you to do it here. This allows to link your profile to this item. It also allows you to accept potential citations to this item that we are uncertain about.

    If CitEc recognized a bibliographic reference but did not link an item in RePEc to it, you can help with this form .

    If you know of missing items citing this one, you can help us creating those links by adding the relevant references in the same way as above, for each refering item. If you are a registered author of this item, you may also want to check the "citations" tab in your RePEc Author Service profile, as there may be some citations waiting for confirmation.

    For technical questions regarding this item, or to correct its authors, title, abstract, bibliographic or download information, contact: Sonal Shukla or Springer Nature Abstracting and Indexing (email available below). General contact details of provider: http://www.nature.com .

    Please note that corrections may take a couple of weeks to filter through the various RePEc services.

    IDEAS is a RePEc service. RePEc uses bibliographic data supplied by the respective publishers.