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

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, Yunxia Qin, Jianghua Yang, Yi Zhang, Shengmin Zhang, Ye De, Jisen Zhang, Jianquan Liu () and Chaorong Tang ()
Additional contact information
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
Kaiye Liu: Hainan University
Zhonghua Li: Hainan University
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
Yunxia Qin: Chinese Academy of Tropical Agricultural Sciences
Jianghua Yang: Chinese Academy of Tropical Agricultural Sciences
Yi Zhang: Hainan University
Shengmin Zhang: Hainan University
Ye De: Hainan University
Jisen Zhang: Guangxi University
Jianquan Liu: Lanzhou University
Chaorong Tang: Hainan University

Nature Communications, 2024, vol. 15, issue 1, 1-14

Abstract: 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.

Date: 2024
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DOI: 10.1038/s41467-024-51031-3

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