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

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 Huang, Wei Hu, Yongfeng Zhou () and Han Cheng ()
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Chaochao Li: Chinese Academy of Tropical Agricultural Sciences
Yuan Yuan: Chinese Academy of Tropical Agricultural Sciences
Zhiyi Nie: Chinese Academy of Tropical Agricultural Sciences
Tingkai Wu: Chinese Academy of Tropical Agricultural Sciences
Zhiyuan Wang: Chinese Academy of Tropical Agricultural Sciences
Jiangxia Qiao: Chinese Academy of Agricultural Sciences
Zhi Deng: Chinese Academy of Tropical Agricultural Sciences
Xiaobo Wang: Chinese Academy of Tropical Agricultural Sciences
Dong Xu: Chinese Academy of Tropical Agricultural Sciences
Xu Wang: Chinese Academy of Agricultural Sciences
Shuo Cao: Chinese Academy of Agricultural Sciences
Bingqin Li: Chinese Academy of Tropical Agricultural Sciences
Zewei An: Chinese Academy of Tropical Agricultural Sciences
Wenguan Wu: Chinese Academy of Tropical Agricultural Sciences
Zhongxin Jin: Chinese Academy of Tropical Agricultural Sciences
Huasun Huang: Chinese Academy of Tropical Agricultural Sciences
Wei Hu: Chinese Academy of Tropical Agricultural Sciences
Yongfeng Zhou: Chinese Academy of Agricultural Sciences
Han Cheng: Chinese Academy of Tropical Agricultural Sciences

Nature Communications, 2025, vol. 16, issue 1, 1-16

Abstract: 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.

Date: 2025
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DOI: 10.1038/s41467-025-61527-1

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