IDEAS home Printed from https://ideas.repec.org/a/nat/natcom/v11y2020i1d10.1038_s41467-020-15040-2.html
   My bibliography  Save this article

Gene clustering and copy number variation in alkaloid metabolic pathways of opium poppy

Author

Listed:
  • Qiushi Li

    (University of Calgary
    China Academy of Chinese Medical Sciences)

  • Sukanya Ramasamy

    (University of Calgary)

  • Pooja Singh

    (University of Calgary)

  • Jillian M. Hagel

    (University of Calgary
    Willow Biosciences Inc.)

  • Sonja M. Dunemann

    (University of Calgary)

  • Xue Chen

    (University of Calgary
    Willow Biosciences Inc.)

  • Rongji Chen

    (University of Calgary)

  • Lisa Yu

    (University of Calgary)

  • Joseph E. Tucker

    (Willow Biosciences Inc.
    University of Calgary)

  • Peter J. Facchini

    (University of Calgary
    Willow Biosciences Inc.)

  • Sam Yeaman

    (University of Calgary)

Abstract

Genes in plant secondary metabolic pathways enable biosynthesis of a range of medically and industrially important compounds, and are often clustered on chromosomes. Here, we study genomic clustering in the benzylisoquinoline alkaloid (BIA) pathway in opium poppy (Papaver somniferum), exploring relationships between gene expression, copy number variation, and metabolite production. We use Hi-C to improve the existing draft genome assembly, yielding chromosome-scale scaffolds that include 35 previously unanchored BIA genes. We find that co-expression of BIA genes increases within clusters and identify candidates with unknown function based on clustering and covariation in expression and alkaloid production. Copy number variation in critical BIA genes correlates with stark differences in alkaloid production, linking noscapine production with an 11-gene deletion, and increased thebaine/decreased morphine production with deletion of a T6ODM cluster. Our results show that the opium poppy genome is still dynamically evolving in ways that contribute to medically and industrially important phenotypes.

Suggested Citation

  • Qiushi Li & Sukanya Ramasamy & Pooja Singh & Jillian M. Hagel & Sonja M. Dunemann & Xue Chen & Rongji Chen & Lisa Yu & Joseph E. Tucker & Peter J. Facchini & Sam Yeaman, 2020. "Gene clustering and copy number variation in alkaloid metabolic pathways of opium poppy," Nature Communications, Nature, vol. 11(1), pages 1-13, December.
    • Handle: RePEc:nat:natcom:v:11:y:2020:i:1:d:10.1038_s41467-020-15040-2
    DOI: 10.1038/s41467-020-15040-2
    as

    Download full text from publisher

    File URL: https://www.nature.com/articles/s41467-020-15040-2
    File Function: Abstract
    Download Restriction: no
    File URL: https://libkey.io/10.1038/s41467-020-15040-2?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
    ---><---

    Citations

    Citations are extracted by the CitEc Project, subscribe to its RSS feed for this item.
    as


    Cited by:

    1. Theresa Catania & Yi Li & Thilo Winzer & David Harvey & Fergus Meade & Anna Caridi & Andrew Leech & Tony R. Larson & Zemin Ning & Jiyang Chang & Yves Peer & Ian A. Graham, 2022. "A functionally conserved STORR gene fusion in Papaver species that diverged 16.8 million years ago," Nature Communications, Nature, vol. 13(1), pages 1-11, December.
    2. Xiaofei Yang & Shenghan Gao & Li Guo & Bo Wang & Yanyan Jia & Jian Zhou & Yizhuo Che & Peng Jia & Jiadong Lin & Tun Xu & Jianyong Sun & Kai Ye, 2021. "Three chromosome-scale Papaver genomes reveal punctuated patchwork evolution of the morphinan and noscapine biosynthesis pathway," Nature Communications, Nature, vol. 12(1), pages 1-14, December.
    3. Natali Ozber & Samuel C. Carr & Jeremy S. Morris & Siyu Liang & Jacinta L. Watkins & Kristian M. Caldo & Jillian M. Hagel & Kenneth K. S. Ng & Peter J. Facchini, 2022. "Alkaloid binding to opium poppy major latex proteins triggers structural modification and functional aggregation," Nature Communications, Nature, vol. 13(1), pages 1-16, 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:11:y:2020:i:1:d:10.1038_s41467-020-15040-2. 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.

    We have no bibliographic references for this item. You can help adding them by using 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.