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Pan-genome and phylogenomic analyses highlight Hevea species delineation and rubber trait evolution

Author

Listed:
  • Yongjun Fang

    (Chinese Academy of Tropical Agricultural Sciences)

  • Xiaohu Xiao

    (Chinese Academy of Tropical Agricultural Sciences)

  • Jishan Lin

    (Hainan University)

  • Qiang Lin

    (Chinese Academy of Agricultural Sciences)

  • Jiang Wang

    (Hainan University
    Natural Rubber Cooperative Innovation Center of Hainan Province & Ministry of Education of PRC)

  • Kaiye Liu

    (Hainan University
    Natural Rubber Cooperative Innovation Center of Hainan Province & Ministry of Education of PRC)

  • Zhonghua Li

    (Hainan University
    Natural Rubber Cooperative Innovation Center of Hainan Province & Ministry of Education of PRC)

  • Jianfeng Xing

    (Hainan University)

  • Zhenglin Liu

    (Hainan University)

  • Baiyu Wang

    (Guangxi University)

  • Yiying Qi

    (Fujian Agriculture and Forestry University)

  • Xiangyu Long

    (Chinese Academy of Tropical Agricultural Sciences)

  • Xia Zeng

    (Chinese Academy of Tropical Agricultural Sciences)

  • Yanshi Hu

    (Chinese Academy of Tropical Agricultural Sciences)

  • Jiyan Qi

    (Hainan University
    Natural Rubber Cooperative Innovation Center of Hainan Province & Ministry of Education of PRC)

  • Yunxia Qin

    (Chinese Academy of Tropical Agricultural Sciences)

  • Jianghua Yang

    (Chinese Academy of Tropical Agricultural Sciences)

  • Yi Zhang

    (Hainan University
    Natural Rubber Cooperative Innovation Center of Hainan Province & Ministry of Education of PRC)

  • Shengmin Zhang

    (Hainan University
    Natural Rubber Cooperative Innovation Center of Hainan Province & Ministry of Education of PRC)

  • De Ye

    (Hainan University
    Natural Rubber Cooperative Innovation Center of Hainan Province & Ministry of Education of PRC)

  • Jisen Zhang

    (Guangxi University)

  • Jianquan Liu

    (Lanzhou University)

  • Chaorong Tang

    (Hainan University
    Natural Rubber Cooperative Innovation Center of Hainan Province & Ministry of Education of PRC
    Yunnan Institute of Tropical Crops)

Abstract

The para rubber tree (Hevea brasiliensis) is the world’s sole commercial source of natural rubber, a vital industrial raw material. However, the narrow genetic diversity of this crop poses challenges for rubber breeding. Here, we generate high-quality de novo genome assemblies for three H. brasiliensis cultivars, two H. brasiliensis wild accessions, and three other Hevea species (H. nitida, H. pauciflora, and H. benthamiana). Through analyzing genomes of 94 Hevea accessions, we identify five distinct lineages that do not align with their previous species delineations. We discover multiple accessions with hybrid origins between these lineages, indicating incomplete reproductive isolation between them. Only two out of four wild lineages have been introduced to commercial rubber cultivars. Furthermore, we reveal that the rubber production traits emerged following the development of a large REF/SRPP gene cluster and its functional specialization in rubber-producing laticifers within this genus. These findings would enhance rubber breeding and benefit research communities.

Suggested Citation

  • Yongjun Fang & Xiaohu Xiao & Jishan Lin & Qiang Lin & Jiang Wang & Kaiye Liu & Zhonghua Li & Jianfeng Xing & Zhenglin Liu & Baiyu Wang & Yiying Qi & Xiangyu Long & Xia Zeng & Yanshi Hu & Jiyan Qi & Yu, 2024. "Pan-genome and phylogenomic analyses highlight Hevea species delineation and rubber trait evolution," Nature Communications, Nature, vol. 15(1), pages 1-14, December.
  • Handle: RePEc:nat:natcom:v:15:y:2024:i:1:d:10.1038_s41467-024-51031-3
    DOI: 10.1038/s41467-024-51031-3
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    References listed on IDEAS

    as
    1. Ray Ming & Shaobin Hou & Yun Feng & Qingyi Yu & Alexandre Dionne-Laporte & Jimmy H. Saw & Pavel Senin & Wei Wang & Benjamin V. Ly & Kanako L. T. Lewis & Steven L. Salzberg & Lu Feng & Meghan R. Jones , 2008. "The draft genome of the transgenic tropical fruit tree papaya (Carica papaya Linnaeus)," Nature, Nature, vol. 452(7190), pages 991-996, April.
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