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

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 pseudo-chromosomes. 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 ten million years (MYR), leading to the massive expansion ∼60.44% (∼890 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 the latex production. We report the first map of genomic variation between the cultivated and wild rubber trees and obtained ∼15.7 million high-quality single nucleotide polymorphisms (SNPs). 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, some of which are involved in the rubber biosynthesis. This genome assembly represents key resources for future rubber tree breeding programs providing novel gene targets to improve biotic and abiotic tolerance and rubber production.