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.
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.
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.
Si-Tao Zhu: BGI-Qingdao, Qingdao 266555, China.
Zai-Yun Xiao: Yunnan Institute of Tropical Crops, Jinghong 666100, China.
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.
Yao Yue: BGI-Qingdao, Qingdao 266555, China.
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.
Yu Wu: Yunnan Institute of Tropical Crops, Jinghong 666100, China.
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.
Dan Zhang: Institution of Genomics and Bioinformatics, South China Agricultural University, Guangzhou 510642, China.
Chang-Li Mao: Yunnan Institute of Tropical Crops, Jinghong 666100, China.
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.
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.
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.
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.
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.
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.
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.
