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The haplotype-resolved telomere-to-telomere genome and OMICS analyses reveal genetic responses to tapping in rubber tree

Author

Listed:
  • Chaochao Li

    (Chinese Academy of Tropical Agricultural Sciences
    Chinese Academy of Agricultural Sciences
    Chinese Academy of Tropical Agricultural Sciences)

  • Yuan Yuan

    (Chinese Academy of Tropical Agricultural Sciences
    Chinese Academy of Tropical Agricultural Sciences)

  • Zhiyi Nie

    (Chinese Academy of Tropical Agricultural Sciences
    Chinese Academy of Tropical Agricultural Sciences)

  • Tingkai Wu

    (Chinese Academy of Tropical Agricultural Sciences
    Chinese Academy of Tropical Agricultural Sciences)

  • Zhiyuan Wang

    (Chinese Academy of Tropical Agricultural Sciences
    Chinese Academy of Agricultural Sciences
    Chinese Academy of Tropical Agricultural Sciences)

  • Jiangxia Qiao

    (Chinese Academy of Agricultural Sciences)

  • Zhi Deng

    (Chinese Academy of Tropical Agricultural Sciences
    Chinese Academy of Tropical Agricultural Sciences
    Rubber Research Institute)

  • Xiaobo Wang

    (Chinese Academy of Tropical Agricultural Sciences
    Chinese Academy of Tropical Agricultural Sciences
    Rubber Research Institute)

  • Dong Xu

    (Chinese Academy of Tropical Agricultural Sciences
    Chinese Academy of Tropical Agricultural Sciences
    Rubber Research Institute)

  • Xu Wang

    (Chinese Academy of Agricultural Sciences)

  • Shuo Cao

    (Chinese Academy of Agricultural Sciences)

  • Bingqin Li

    (Chinese Academy of Tropical Agricultural Sciences
    Chinese Academy of Tropical Agricultural Sciences)

  • Zewei An

    (Chinese Academy of Tropical Agricultural Sciences
    Chinese Academy of Tropical Agricultural Sciences
    Rubber Research Institute)

  • Wenguan Wu

    (Chinese Academy of Tropical Agricultural Sciences
    Chinese Academy of Tropical Agricultural Sciences
    Rubber Research Institute)

  • Zhongxin Jin

    (Chinese Academy of Tropical Agricultural Sciences
    Chinese Academy of Agricultural Sciences
    Chinese Academy of Tropical Agricultural Sciences)

  • Huasun Huang

    (Chinese Academy of Tropical Agricultural Sciences
    Chinese Academy of Tropical Agricultural Sciences
    Rubber Research Institute)

  • Wei Hu

    (Chinese Academy of Tropical Agricultural Sciences
    Sanya Research Institute of Chinese Academy of Tropical Agricultural Sciences)

  • Yongfeng Zhou

    (Chinese Academy of Agricultural Sciences
    Chinese Academy of Tropical Agricultural Sciences)

  • Han Cheng

    (Chinese Academy of Tropical Agricultural Sciences
    Chinese Academy of Tropical Agricultural Sciences
    Rubber Research Institute)

Abstract

Rubber tree (Hevea brasiliensis) is the primary source of natural rubber and economically important. We present the haplotype-resolved, telomere-to-telomere, gap-free genome assembly of the cultivar CATAS 7-33–97, with both haplotypes containing complete telomeric and centromeric regions. Structural variations, including a 32.71 Mb inversion on chromosome 8, are identified. The fully assembled 36 chromosomes enable comprehensive identification of rubber biosynthesis genes and their allele-specific expression. By integrating transcriptomic and metabolomic data, we reconstruct the rubber biosynthesis pathway and confirm the mevalonate (MVA) pathway as the major carbon source for rapid latex regeneration during tapping. Jasmonic acid (JA) plays a key role in promoting rubber yield by enhancing biosynthetic activity in response to mechanical wounding. We propose a model where JA-induced myelocytomatosis proteins 2 activate mevalonate kinase 1 expression, boosting MVA synthesis and rubber production. These findings provide insights into rubber tree genomics and its molecular response to tapping.

Suggested Citation

  • Chaochao Li & Yuan Yuan & Zhiyi Nie & Tingkai Wu & Zhiyuan Wang & Jiangxia Qiao & Zhi Deng & Xiaobo Wang & Dong Xu & Xu Wang & Shuo Cao & Bingqin Li & Zewei An & Wenguan Wu & Zhongxin Jin & Huasun Hua, 2025. "The haplotype-resolved telomere-to-telomere genome and OMICS analyses reveal genetic responses to tapping in rubber tree," Nature Communications, Nature, vol. 16(1), pages 1-16, December.
    • Handle: RePEc:nat:natcom:v:16:y:2025:i:1:d:10.1038_s41467-025-61527-1
    DOI: 10.1038/s41467-025-61527-1
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    References listed on IDEAS

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    1. Jinquan Chao & Shaohua Wu & Minjing Shi & Xia Xu & Qiang Gao & Huilong Du & Bin Gao & Dong Guo & Shuguang Yang & Shixin Zhang & Yan Li & Xiuli Fan & Chunyan Hai & Liquan Kou & Jiao Zhang & Zhiwei Wang, 2023. "Genomic insight into domestication of rubber tree," Nature Communications, Nature, vol. 14(1), pages 1-13, December.
    2. Junquera, Victoria & Meyfroidt, Patrick & Sun, Zhanli & Latthachack, Phokham & Grêt-Regamey, Adrienne, 2020. "From global drivers to local land-use change: Understanding the northern Laos rubber boom," EconStor Open Access Articles and Book Chapters, ZBW - Leibniz Information Centre for Economics, vol. 109, pages 103-115.
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