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Molecular plant
02 03, 2020;13 (2): 336-350.

The Chromosome-Based Rubber Tree Genome Provides New Insights into Spurge Genome Evolution and Rubber Biosynthesis.

Jin Liu, Cong Shi, Cheng-Cheng Shi, Wei Li, Qun-Jie Zhang, Yun Zhang, Kui Li, Hui-Fang Lu, Chao Shi, Si-Tao Zhu, Zai-Yun Xiao, Hong Nan, Yao Yue, Xun-Ge Zhu, Yu Wu, Xiao-Ning Hong, Guang-Yi Fan, Yan Tong, Dan Zhang, Chang-Li Mao, Yun-Long Liu, Shi-Jie Hao, Wei-Qing Liu, Mei-Qi Lv, Hai-Bin Zhang, Yuan Liu, Ge-Ran Hu-Tang, Jin-Peng Wang, Jia-Hao Wang, Ying-Huai Sun, Shu-Bang Ni, Wen-Bin Chen, Xing-Cai Zhang, Yuan-Nian Jiao, Evan E Eichler, Guo-Hua Li, Xin Liu, Li-Zhi Gao
Author Information
  1. Jin Liu: Yunnan Institute of Tropical Crops, Jinghong 666100, China; Plant Germplasm and Genomics Center, Germplasm Bank of Wild Species in Southwestern China, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650204, China.
  2. Cong Shi: Plant Germplasm and Genomics Center, Germplasm Bank of Wild Species in Southwestern China, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650204, China; University of Chinese Academy of Sciences, Beijing 100049, China.
  3. Cheng-Cheng Shi: BGI-Qingdao, Qingdao 266555, China.
  4. Wei Li: Institution of Genomics and Bioinformatics, South China Agricultural University, Guangzhou 510642, China.
  5. Qun-Jie Zhang: Institution of Genomics and Bioinformatics, South China Agricultural University, Guangzhou 510642, China.
  6. Yun Zhang: Asia-Pacific Tropical Forestry Germplasm Institution, Southwest China Forestry University, Kunming 650224, China.
  7. Kui Li: School of Life Sciences, Nanjing University, Nanjing 210023, China; Novogene Bioinformatics Institute, Beijing 100083, China.
  8. Hui-Fang Lu: BGI-Shenzhen, Shenzhen 518083, China.
  9. Chao Shi: Plant Germplasm and Genomics Center, Germplasm Bank of Wild Species in Southwestern China, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650204, China.
  10. Si-Tao Zhu: BGI-Qingdao, Qingdao 266555, China.
  11. Zai-Yun Xiao: Yunnan Institute of Tropical Crops, Jinghong 666100, China.
  12. Hong Nan: Plant Germplasm and Genomics Center, Germplasm Bank of Wild Species in Southwestern China, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650204, China; University of Chinese Academy of Sciences, Beijing 100049, China.
  13. Yao Yue: BGI-Qingdao, Qingdao 266555, China.
  14. Xun-Ge Zhu: Plant Germplasm and Genomics Center, Germplasm Bank of Wild Species in Southwestern China, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650204, China; University of Chinese Academy of Sciences, Beijing 100049, China.
  15. Yu Wu: Yunnan Institute of Tropical Crops, Jinghong 666100, China.
  16. Xiao-Ning Hong: BGI-Qingdao, Qingdao 266555, China.
  17. Guang-Yi Fan: BGI-Qingdao, Qingdao 266555, China; BGI-Shenzhen, Shenzhen 518083, China.
  18. Yan Tong: Plant Germplasm and Genomics Center, Germplasm Bank of Wild Species in Southwestern China, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650204, China.
  19. Dan Zhang: Institution of Genomics and Bioinformatics, South China Agricultural University, Guangzhou 510642, China.
  20. Chang-Li Mao: Yunnan Institute of Tropical Crops, Jinghong 666100, China.
  21. Yun-Long Liu: Plant Germplasm and Genomics Center, Germplasm Bank of Wild Species in Southwestern China, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650204, China.
  22. Shi-Jie Hao: BGI-Qingdao, Qingdao 266555, China.
  23. Wei-Qing Liu: BGI-Shenzhen, Shenzhen 518083, China.
  24. Mei-Qi Lv: BGI-Qingdao, Qingdao 266555, China.
  25. Hai-Bin Zhang: Plant Germplasm and Genomics Center, Germplasm Bank of Wild Species in Southwestern China, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650204, China.
  26. Yuan Liu: Plant Germplasm and Genomics Center, Germplasm Bank of Wild Species in Southwestern China, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650204, China.
  27. Ge-Ran Hu-Tang: Plant Germplasm and Genomics Center, Germplasm Bank of Wild Species in Southwestern China, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650204, China; University of Chinese Academy of Sciences, Beijing 100049, China.
  28. Jin-Peng Wang: University of Chinese Academy of Sciences, Beijing 100049, China; State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China.
  29. Jia-Hao Wang: BGI-Qingdao, Qingdao 266555, China.
  30. Ying-Huai Sun: BGI-Shenzhen, Shenzhen 518083, China.
  31. Shu-Bang Ni: Yunnan Institute of Tropical Crops, Jinghong 666100, China.
  32. Wen-Bin Chen: BGI-Shenzhen, Shenzhen 518083, China.
  33. Xing-Cai Zhang: John A. Paulson School of Engineering and Applied Sciences, Harvard University, Cambridge, MA 02138, USA.
  34. Yuan-Nian Jiao: State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China.
  35. Evan E Eichler: Howard Hughes Medical Institute, University of Washington, Seattle, WA 98195, USA.
  36. Guo-Hua Li: Yunnan Institute of Tropical Crops, Jinghong 666100, China.
  37. Xin Liu: BGI-Qingdao, Qingdao 266555, China; BGI-Shenzhen, Shenzhen 518083, China. Electronic address: liuxin@genomics.cn.
  38. Li-Zhi Gao: Plant Germplasm and Genomics Center, Germplasm Bank of Wild Species in Southwestern China, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650204, China; Institution of Genomics and Bioinformatics, South China Agricultural University, Guangzhou 510642, China. Electronic address: lgaogenomics@163.com.
PMID: 31838037 DOI: 10.1016/j.molp.2019.10.017

Abstract

The rubber tree, Hevea brasiliensis, produces natural rubber that serves as an essential industrial raw material. Here, we present a high-quality reference genome for a rubber tree cultivar GT1 using single-molecule real-time sequencing (SMRT) and Hi-C technologies to anchor the ∼1.47-Gb genome assembly into 18 pseudochromosomes. The chromosome-based genome analysis enabled us to establish a model of spurge chromosome evolution, since the common paleopolyploid event occurred before the split of Hevea and Manihot. We show recent and rapid bursts of the three Hevea-specific LTR-retrotransposon families during the last 10 million years, leading to the massive expansion by ∼65.88% (∼970 Mbp) of the whole rubber tree genome since the divergence from Manihot. We identify large-scale expansion of genes associated with whole rubber biosynthesis processes, such as basal metabolic processes, ethylene biosynthesis, and the activation of polysaccharide and glycoprotein lectin, which are important properties for latex production. A map of genomic variation between the cultivated and wild rubber trees was obtained, which contains ∼15.7 million high-quality single-nucleotide polymorphisms. We identified hundreds of candidate domestication genes with drastically lowered genomic diversity in the cultivated but not wild rubber trees despite a relatively short domestication history of rubber tree, some of which are involved in rubber biosynthesis. This genome assembly represents key resources for future rubber tree research and breeding, providing novel targets for improving plant biotic and abiotic tolerance and rubber production.

Keywords

chromosome evolution domestication rubber biosynthesis rubber tree whole-genome duplication

MeSH Term

Chromosome Mapping
Chromosomes, Plant
Domestication
Euphorbia
Evolution, Molecular
Genome, Plant
Hevea
Multigene Family
Plant Proteins
Retroelements
Rubber
Tetraploidy

Chemicals

Plant Proteins
Retroelements
Rubber
Journal Article Research Support, Non-U.S. Gov't

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