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Draft genome of spinach and transcriptome diversity of 120 Spinacia accessions

Author

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  • Chenxi Xu

    (Development and Collaborative Innovation Center of Plant Germplasm Resources, College of Life and Environmental Sciences, Shanghai Normal University)

  • Chen Jiao

    (Boyce Thompson Institute, Cornell University)

  • Honghe Sun

    (Boyce Thompson Institute, Cornell University)

  • Xiaofeng Cai

    (Development and Collaborative Innovation Center of Plant Germplasm Resources, College of Life and Environmental Sciences, Shanghai Normal University)

  • Xiaoli Wang

    (Development and Collaborative Innovation Center of Plant Germplasm Resources, College of Life and Environmental Sciences, Shanghai Normal University)

  • Chenhui Ge

    (Development and Collaborative Innovation Center of Plant Germplasm Resources, College of Life and Environmental Sciences, Shanghai Normal University)

  • Yi Zheng

    (Boyce Thompson Institute, Cornell University)

  • Wenli Liu

    (Boyce Thompson Institute, Cornell University)

  • Xuepeng Sun

    (Boyce Thompson Institute, Cornell University)

  • Yimin Xu

    (Boyce Thompson Institute, Cornell University)

  • Jie Deng

    (Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences)

  • Zhonghua Zhang

    (Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences)

  • Sanwen Huang

    (Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences)

  • Shaojun Dai

    (Development and Collaborative Innovation Center of Plant Germplasm Resources, College of Life and Environmental Sciences, Shanghai Normal University)

  • Beiquan Mou

    (USDA-Agricultural Research Service, Crop Improvement and Protection Research Unit)

  • Quanxi Wang

    (Development and Collaborative Innovation Center of Plant Germplasm Resources, College of Life and Environmental Sciences, Shanghai Normal University)

  • Zhangjun Fei

    (Development and Collaborative Innovation Center of Plant Germplasm Resources, College of Life and Environmental Sciences, Shanghai Normal University
    Boyce Thompson Institute, Cornell University
    USDA-Agricultural Research Service, Robert W. Holley Center for Agriculture and Health)

  • Quanhua Wang

    (Development and Collaborative Innovation Center of Plant Germplasm Resources, College of Life and Environmental Sciences, Shanghai Normal University)

Abstract

Spinach is an important leafy vegetable enriched with multiple necessary nutrients. Here we report the draft genome sequence of spinach (Spinacia oleracea, 2n=12), which contains 25,495 protein-coding genes. The spinach genome is highly repetitive with 74.4% of its content in the form of transposable elements. No recent whole genome duplication events are observed in spinach. Genome syntenic analysis between spinach and sugar beet suggests substantial inter- and intra-chromosome rearrangements during the Caryophyllales genome evolution. Transcriptome sequencing of 120 cultivated and wild spinach accessions reveals more than 420 K variants. Our data suggests that S. turkestanica is likely the direct progenitor of cultivated spinach and spinach domestication has a weak bottleneck. We identify 93 domestication sweeps in the spinach genome, some of which are associated with important agronomic traits including bolting, flowering and leaf numbers. This study offers insights into spinach evolution and domestication and provides resources for spinach research and improvement.

Suggested Citation

  • Chenxi Xu & Chen Jiao & Honghe Sun & Xiaofeng Cai & Xiaoli Wang & Chenhui Ge & Yi Zheng & Wenli Liu & Xuepeng Sun & Yimin Xu & Jie Deng & Zhonghua Zhang & Sanwen Huang & Shaojun Dai & Beiquan Mou & Qu, 2017. "Draft genome of spinach and transcriptome diversity of 120 Spinacia accessions," Nature Communications, Nature, vol. 8(1), pages 1-10, August.
    • Handle: RePEc:nat:natcom:v:8:y:2017:i:1:d:10.1038_ncomms15275
    DOI: 10.1038/ncomms15275
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    Cited by:

    1. Guoliang Li & Qing Meng & Zhiyuan Liu & Zhaosheng Xu & Helong Zhang & Wei Qian, 2020. "Management of the Tolerance to Bolting for Spinach (Spinacia Oleracea L.)- Retrospect and Prospects," Biomedical Journal of Scientific & Technical Research, Biomedical Research Network+, LLC, vol. 28(1), pages 21260-21264, June.
    2. Octavio R. Salazar & Ke Chen & Vanessa J. Melino & Muppala P. Reddy & Eva Hřibová & Jana Čížková & Denisa Beránková & Juan Pablo Arciniegas Vega & Lina María Cáceres Leal & Manuel Aranda & Lukasz Jare, 2024. "SOS1 tonoplast neo-localization and the RGG protein SALTY are important in the extreme salinity tolerance of Salicornia bigelovii," Nature Communications, Nature, vol. 15(1), pages 1-21, December.
    3. Xiaofeng Cai & Xuepeng Sun & Chenxi Xu & Honghe Sun & Xiaoli Wang & Chenhui Ge & Zhonghua Zhang & Quanxi Wang & Zhangjun Fei & Chen Jiao & Quanhua Wang, 2021. "Genomic analyses provide insights into spinach domestication and the genetic basis of agronomic traits," Nature Communications, Nature, vol. 12(1), pages 1-12, December.
    4. Jorge F. S. Ferreira & Devinder Sandhu & Xuan Liu & Jonathan J. Halvorson, 2018. "Spinach ( Spinacea oleracea L.) Response to Salinity: Nutritional Value, Physiological Parameters, Antioxidant Capacity, and Gene Expression," Agriculture, MDPI, vol. 8(10), pages 1-16, October.

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