The haplotype-resolved telomere-to-telomere genome and OMICS analyses reveal genetic responses to tapping in rubber tree
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. S...
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Nature Portfolio
2025-07-01
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| Series: | Nature Communications |
| Online Access: | https://doi.org/10.1038/s41467-025-61527-1 |
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| author | 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 Han Cheng |
| author_facet | 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 Han Cheng |
| author_sort | Chaochao Li |
| collection | DOAJ |
| description | 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. |
| format | Article |
| id | doaj-art-c01ed688069b476cbb33467be3714bbc |
| institution | Kabale University |
| issn | 2041-1723 |
| language | English |
| publishDate | 2025-07-01 |
| publisher | Nature Portfolio |
| record_format | Article |
| series | Nature Communications |
| spelling | doaj-art-c01ed688069b476cbb33467be3714bbc2025-08-20T03:46:17ZengNature PortfolioNature Communications2041-17232025-07-0116111610.1038/s41467-025-61527-1The haplotype-resolved telomere-to-telomere genome and OMICS analyses reveal genetic responses to tapping in rubber treeChaochao Li0Yuan Yuan1Zhiyi Nie2Tingkai Wu3Zhiyuan Wang4Jiangxia Qiao5Zhi Deng6Xiaobo Wang7Dong Xu8Xu Wang9Shuo Cao10Bingqin Li11Zewei An12Wenguan Wu13Zhongxin Jin14Huasun Huang15Wei Hu16Yongfeng Zhou17Han Cheng18State Key Laboratory of Tropical Crop Breeding, Ministry of Agriculture and Rural Affairs Key Laboratory of Biology and Genetic Resources of Rubber Tree, Rubber Research Institute, Chinese Academy of Tropical Agricultural SciencesState Key Laboratory of Tropical Crop Breeding, Ministry of Agriculture and Rural Affairs Key Laboratory of Biology and Genetic Resources of Rubber Tree, Rubber Research Institute, Chinese Academy of Tropical Agricultural SciencesState Key Laboratory of Tropical Crop Breeding, Ministry of Agriculture and Rural Affairs Key Laboratory of Biology and Genetic Resources of Rubber Tree, Rubber Research Institute, Chinese Academy of Tropical Agricultural SciencesState Key Laboratory of Tropical Crop Breeding, Ministry of Agriculture and Rural Affairs Key Laboratory of Biology and Genetic Resources of Rubber Tree, Rubber Research Institute, Chinese Academy of Tropical Agricultural SciencesState Key Laboratory of Tropical Crop Breeding, Ministry of Agriculture and Rural Affairs Key Laboratory of Biology and Genetic Resources of Rubber Tree, Rubber Research Institute, Chinese Academy of Tropical Agricultural SciencesState Key Laboratory of Tropical Crop Breeding, Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural SciencesState Key Laboratory of Tropical Crop Breeding, Ministry of Agriculture and Rural Affairs Key Laboratory of Biology and Genetic Resources of Rubber Tree, Rubber Research Institute, Chinese Academy of Tropical Agricultural SciencesState Key Laboratory of Tropical Crop Breeding, Ministry of Agriculture and Rural Affairs Key Laboratory of Biology and Genetic Resources of Rubber Tree, Rubber Research Institute, Chinese Academy of Tropical Agricultural SciencesState Key Laboratory of Tropical Crop Breeding, Ministry of Agriculture and Rural Affairs Key Laboratory of Biology and Genetic Resources of Rubber Tree, Rubber Research Institute, Chinese Academy of Tropical Agricultural SciencesState Key Laboratory of Tropical Crop Breeding, Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural SciencesState Key Laboratory of Tropical Crop Breeding, Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural SciencesState Key Laboratory of Tropical Crop Breeding, Ministry of Agriculture and Rural Affairs Key Laboratory of Biology and Genetic Resources of Rubber Tree, Rubber Research Institute, Chinese Academy of Tropical Agricultural SciencesState Key Laboratory of Tropical Crop Breeding, Ministry of Agriculture and Rural Affairs Key Laboratory of Biology and Genetic Resources of Rubber Tree, Rubber Research Institute, Chinese Academy of Tropical Agricultural SciencesState Key Laboratory of Tropical Crop Breeding, Ministry of Agriculture and Rural Affairs Key Laboratory of Biology and Genetic Resources of Rubber Tree, Rubber Research Institute, Chinese Academy of Tropical Agricultural SciencesState Key Laboratory of Tropical Crop Breeding, Ministry of Agriculture and Rural Affairs Key Laboratory of Biology and Genetic Resources of Rubber Tree, Rubber Research Institute, Chinese Academy of Tropical Agricultural SciencesState Key Laboratory of Tropical Crop Breeding, Ministry of Agriculture and Rural Affairs Key Laboratory of Biology and Genetic Resources of Rubber Tree, Rubber Research Institute, Chinese Academy of Tropical Agricultural SciencesSanya Research Institute, Chinese Academy of Tropical Agricultural SciencesState Key Laboratory of Tropical Crop Breeding, Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural SciencesState Key Laboratory of Tropical Crop Breeding, Ministry of Agriculture and Rural Affairs Key Laboratory of Biology and Genetic Resources of Rubber Tree, Rubber Research Institute, Chinese Academy of Tropical Agricultural SciencesAbstract 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.https://doi.org/10.1038/s41467-025-61527-1 |
| spellingShingle | 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 Han Cheng The haplotype-resolved telomere-to-telomere genome and OMICS analyses reveal genetic responses to tapping in rubber tree Nature Communications |
| title | The haplotype-resolved telomere-to-telomere genome and OMICS analyses reveal genetic responses to tapping in rubber tree |
| title_full | The haplotype-resolved telomere-to-telomere genome and OMICS analyses reveal genetic responses to tapping in rubber tree |
| title_fullStr | The haplotype-resolved telomere-to-telomere genome and OMICS analyses reveal genetic responses to tapping in rubber tree |
| title_full_unstemmed | The haplotype-resolved telomere-to-telomere genome and OMICS analyses reveal genetic responses to tapping in rubber tree |
| title_short | The haplotype-resolved telomere-to-telomere genome and OMICS analyses reveal genetic responses to tapping in rubber tree |
| title_sort | haplotype resolved telomere to telomere genome and omics analyses reveal genetic responses to tapping in rubber tree |
| url | https://doi.org/10.1038/s41467-025-61527-1 |
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