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Genome sequence of the date palm Phoenix dactylifera L

Author

Listed:
  • Ibrahim S. Al-Mssallem

    (Joint Center for Genomics Research, King Abdulaziz City for Science and Technology and Chinese Academy of Sciences
    College of Agriculture and Food Sciences, King Faisal University)

  • Songnian Hu

    (Joint Center for Genomics Research, King Abdulaziz City for Science and Technology and Chinese Academy of Sciences
    CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences)

  • Xiaowei Zhang

    (Joint Center for Genomics Research, King Abdulaziz City for Science and Technology and Chinese Academy of Sciences
    CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences)

  • Qiang Lin

    (Joint Center for Genomics Research, King Abdulaziz City for Science and Technology and Chinese Academy of Sciences
    CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences)

  • Wanfei Liu

    (Joint Center for Genomics Research, King Abdulaziz City for Science and Technology and Chinese Academy of Sciences
    CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences)

  • Jun Tan

    (Joint Center for Genomics Research, King Abdulaziz City for Science and Technology and Chinese Academy of Sciences)

  • Xiaoguang Yu

    (Joint Center for Genomics Research, King Abdulaziz City for Science and Technology and Chinese Academy of Sciences
    CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences)

  • Jiucheng Liu

    (Joint Center for Genomics Research, King Abdulaziz City for Science and Technology and Chinese Academy of Sciences
    CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences)

  • Linlin Pan

    (Joint Center for Genomics Research, King Abdulaziz City for Science and Technology and Chinese Academy of Sciences
    CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences)

  • Tongwu Zhang

    (Joint Center for Genomics Research, King Abdulaziz City for Science and Technology and Chinese Academy of Sciences
    CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences)

  • Yuxin Yin

    (Joint Center for Genomics Research, King Abdulaziz City for Science and Technology and Chinese Academy of Sciences
    CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences)

  • Chengqi Xin

    (Joint Center for Genomics Research, King Abdulaziz City for Science and Technology and Chinese Academy of Sciences
    CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences)

  • Hao Wu

    (Joint Center for Genomics Research, King Abdulaziz City for Science and Technology and Chinese Academy of Sciences
    CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences)

  • Guangyu Zhang

    (Joint Center for Genomics Research, King Abdulaziz City for Science and Technology and Chinese Academy of Sciences
    CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences)

  • Mohammed M. Ba Abdullah

    (Joint Center for Genomics Research, King Abdulaziz City for Science and Technology and Chinese Academy of Sciences)

  • Dawei Huang

    (Joint Center for Genomics Research, King Abdulaziz City for Science and Technology and Chinese Academy of Sciences
    CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences)

  • Yongjun Fang

    (Joint Center for Genomics Research, King Abdulaziz City for Science and Technology and Chinese Academy of Sciences
    CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences)

  • Yasser O. Alnakhli

    (Joint Center for Genomics Research, King Abdulaziz City for Science and Technology and Chinese Academy of Sciences)

  • Shangang Jia

    (Joint Center for Genomics Research, King Abdulaziz City for Science and Technology and Chinese Academy of Sciences
    CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences)

  • An Yin

    (Joint Center for Genomics Research, King Abdulaziz City for Science and Technology and Chinese Academy of Sciences
    CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences)

  • Eman M. Alhuzimi

    (Joint Center for Genomics Research, King Abdulaziz City for Science and Technology and Chinese Academy of Sciences)

  • Burair A. Alsaihati

    (Joint Center for Genomics Research, King Abdulaziz City for Science and Technology and Chinese Academy of Sciences)

  • Saad A. Al-Owayyed

    (Joint Center for Genomics Research, King Abdulaziz City for Science and Technology and Chinese Academy of Sciences)

  • Duojun Zhao

    (Joint Center for Genomics Research, King Abdulaziz City for Science and Technology and Chinese Academy of Sciences
    CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences)

  • Sun Zhang

    (Joint Center for Genomics Research, King Abdulaziz City for Science and Technology and Chinese Academy of Sciences
    CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences)

  • Noha A. Al-Otaibi

    (Joint Center for Genomics Research, King Abdulaziz City for Science and Technology and Chinese Academy of Sciences)

  • Gaoyuan Sun

    (Joint Center for Genomics Research, King Abdulaziz City for Science and Technology and Chinese Academy of Sciences
    CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences)

  • Majed A. Majrashi

    (Joint Center for Genomics Research, King Abdulaziz City for Science and Technology and Chinese Academy of Sciences)

  • Fusen Li

    (Joint Center for Genomics Research, King Abdulaziz City for Science and Technology and Chinese Academy of Sciences
    CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences)

  • Tala

    (Joint Center for Genomics Research, King Abdulaziz City for Science and Technology and Chinese Academy of Sciences
    CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences)

  • Jixiang Wang

    (Joint Center for Genomics Research, King Abdulaziz City for Science and Technology and Chinese Academy of Sciences
    CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences)

  • Quanzheng Yun

    (Joint Center for Genomics Research, King Abdulaziz City for Science and Technology and Chinese Academy of Sciences
    CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences)

  • Nafla A. Alnassar

    (Joint Center for Genomics Research, King Abdulaziz City for Science and Technology and Chinese Academy of Sciences)

  • Lei Wang

    (Joint Center for Genomics Research, King Abdulaziz City for Science and Technology and Chinese Academy of Sciences
    CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences)

  • Meng Yang

    (Joint Center for Genomics Research, King Abdulaziz City for Science and Technology and Chinese Academy of Sciences
    CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences)

  • Rasha F. Al-Jelaify

    (Joint Center for Genomics Research, King Abdulaziz City for Science and Technology and Chinese Academy of Sciences)

  • Kan Liu

    (Joint Center for Genomics Research, King Abdulaziz City for Science and Technology and Chinese Academy of Sciences
    CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences)

  • Shenghan Gao

    (Joint Center for Genomics Research, King Abdulaziz City for Science and Technology and Chinese Academy of Sciences
    CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences)

  • Kaifu Chen

    (Joint Center for Genomics Research, King Abdulaziz City for Science and Technology and Chinese Academy of Sciences
    CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences)

  • Samiyah R. Alkhaldi

    (Joint Center for Genomics Research, King Abdulaziz City for Science and Technology and Chinese Academy of Sciences)

  • Guiming Liu

    (Joint Center for Genomics Research, King Abdulaziz City for Science and Technology and Chinese Academy of Sciences
    CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences)

  • Meng Zhang

    (Joint Center for Genomics Research, King Abdulaziz City for Science and Technology and Chinese Academy of Sciences
    CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences)

  • Haiyan Guo

    (Joint Center for Genomics Research, King Abdulaziz City for Science and Technology and Chinese Academy of Sciences
    CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences)

  • Jun Yu

    (Joint Center for Genomics Research, King Abdulaziz City for Science and Technology and Chinese Academy of Sciences
    CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences)

Abstract

Date palm (Phoenix dactylifera L.) is a cultivated woody plant species with agricultural and economic importance. Here we report a genome assembly for an elite variety (Khalas), which is 605.4 Mb in size and covers >90% of the genome (~671 Mb) and >96% of its genes (~41,660 genes). Genomic sequence analysis demonstrates that P. dactylifera experienced a clear genome-wide duplication after either ancient whole genome duplications or massive segmental duplications. Genetic diversity analysis indicates that its stress resistance and sugar metabolism-related genes tend to be enriched in the chromosomal regions where the density of single-nucleotide polymorphisms is relatively low. Using transcriptomic data, we also illustrate the date palm’s unique sugar metabolism that underlies fruit development and ripening. Our large-scale genomic and transcriptomic data pave the way for further genomic studies not only on P. dactylifera but also other Arecaceae plants.

Suggested Citation

  • Ibrahim S. Al-Mssallem & Songnian Hu & Xiaowei Zhang & Qiang Lin & Wanfei Liu & Jun Tan & Xiaoguang Yu & Jiucheng Liu & Linlin Pan & Tongwu Zhang & Yuxin Yin & Chengqi Xin & Hao Wu & Guangyu Zhang & M, 2013. "Genome sequence of the date palm Phoenix dactylifera L," Nature Communications, Nature, vol. 4(1), pages 1-9, October.
    • Handle: RePEc:nat:natcom:v:4:y:2013:i:1:d:10.1038_ncomms3274
    DOI: 10.1038/ncomms3274
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    Cited by:

    1. Jessen V. Bredeson & Jessica B. Lyons & Ibukun O. Oniyinde & Nneka R. Okereke & Olufisayo Kolade & Ikenna Nnabue & Christian O. Nwadili & Eva Hřibová & Matthew Parker & Jeremiah Nwogha & Shengqiang Sh, 2022. "Chromosome evolution and the genetic basis of agronomically important traits in greater yam," Nature Communications, Nature, vol. 13(1), pages 1-16, December.
    2. Nanqiao Liao & Zhongyuan Hu & Jinshan Miao & Xiaodi Hu & Xiaolong Lyu & Haitian Fang & Yi-Mei Zhou & Ahmed Mahmoud & Guancong Deng & Yi-Qing Meng & Kejia Zhang & Yu-Yuan Ma & Yuelin Xia & Meng Zhao & , 2022. "Chromosome-level genome assembly of bunching onion illuminates genome evolution and flavor formation in Allium crops," Nature Communications, Nature, vol. 13(1), pages 1-15, December.
    3. 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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