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 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.

High-quality de novo assembly of the Eucommia ulmoides haploid genome provides new insights into evolution and rubber biosynthesis

“…Its main function is to add IPP to the precursor in the trans configuration. According to the chain length of the product, it can be divided into short-chain and long-chain TPTs, where short-chain TPTs are widely found in plants, mainly including geranyl GPS, FPS, and GGPS 5 , 52 , 89 , 90 . However, the long-chain TPT responsible for adding IPP to precursors for long-chain TPI rubber elongation is still unknown.…”

Structural and Functional Annotation of Transposable Elements Revealed a Potential Regulation of Genes Involved in Rubber Biosynthesis by TE-Derived siRNA Interference in Hevea brasiliensis

“…SRPPs were identified in many plants (rubber and non-rubber producing), while REFs were not found in other plants [1]. They have been shown to be more extended in Hevea compared to other rubber-producing plants [4,5], probably due to a whole genome duplication shared with cassava (Manihot esculenta), another Euphorbiaceae plant species [6]. Among various clones, REF transcript levels have been shown to be positively correlated with latex yield [7].…”

“…Several de novo genomes of rubber clones, with contrasting latex physiology, are available such as Reyan 7-33-97 [4], RRIM 600 [18], BPM 24 [19]; PB 260 [20,21] and GT 1 [5]. The rubber tree genome is large and complex to assemble because of its high heterozygosity, whole genome duplication and transposable element (TE) content [4,5]. TEs, first described in 1931 by the Nobel Prize winner Barbara McClintock, are also known as "jumping genes".…”

Tobacco rattle virus -induced gene silencing in Hevea brasiliensis

“…Although a large number of genomic data and transcriptome data of rubber tree can be obtained [9][10][11], but few functional genes have been proved in rubber tree [12][13][14][15]. Functional gene analysis is still a major challenge lacking e cient and reliable genetic transformation system [15,16].…”

“…The physiological functions of rubber molecule and latex remain intrigue [7,8]. To date, rubber biosynthesis pathway has been well characterized [8], the whole-genome data and transcriptome database became available in rubber tree [9][10][11], but only a few NR biosynthesis-related genes functions are evaluated by transgenic rubber tree due to low genetic transformation e ciency [12][13][14][15]. The development of an e cient and reliable rubber tree transformation system is still challenging [15,16].…”