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.

橡胶树巴西橡胶树（Hevea brasiliensis）生产天然橡胶，可作为必不可少的工业原料。在这里，我们使用单分子实时测序（SMRT）和Hi-C技术将橡胶树品种GT1的高质量参考基因组固定在18个假染色体上，将其1.47-Gb基因组锚定。基于染色体的基因组分析使我们能够建立大范围染色体进化的模型，因为常见的古多倍体事件发生在三叶胶和Manihot分裂之前。我们展示了三个三叶橡胶的近期和快速爆发在过去千万年特异性LTR-反转录转座子的家庭，因为从分歧导致大规模扩张在整个橡胶树基因组~65.88％（~970 MBP）木薯。我们确定了与整个橡胶生物合成过程相关的基因的大规模扩展，例如基础代谢过程，乙烯生物合成以及多糖和糖蛋白凝集素的激活，这是乳胶生产的重要特性。获得了栽培橡胶树和野生橡胶树之间的基因组变异图，其中包含约1570万个高质量的单核苷酸多态性。尽管橡胶树的驯化历史相对较短，但我们在栽培的而非野生的橡胶树中鉴定了数百种基因组多样性大大降低的候选驯化基因，其中有些驯化基因与橡胶生物合成有关。这个基因组组装代表了未来橡胶树研究和育种的关键资源，