Draft genome sequence of the rubber tree Hevea brasiliensis

Abstract

Background: Hevea brasiliensis, a member of the Euphorbiaceae family, is the major commercial source of natural rubber (NR). NR is a latex polymer with high elasticity, flexibility, and resilience that has played a critical role in the world economy since 1876.

Results: Here, we report the draft genome sequence of H. brasiliensis. The assembly spans ~1.1 Gb of the estimated 2.15 Gb haploid genome. Overall, ~78% of the genome was identified as repetitive DNA. Gene prediction shows 68,955 gene models, of which 12.7% are unique to Hevea. Most of the key genes associated with rubber biosynthesis, rubberwood formation, disease resistance, and allergenicity have been identified.

Conclusions: The knowledge gained from this genome sequence will aid in the future development of high-yielding clones to keep up with the ever increasing need for natural rubber.

Figure 1

Maximum likelihood phylogeny unveiling the taxonomic position of H. brasiliensis. A phylogenetic tree was constructed using 144 orthologous single-copy gene clusters distributed across 17 species for which the genome sequences are available. The tree was constructed by the Maximum likelihood method using PhyML employing SPR and NNI for best tree improvement features. The analysis revealed the position of H. brasiliensis to be in Malvidae with more relatedness to M. esculenta. Bootstrapping procedures were applied over random 100 replicates and 7 seeds and the values are shown at nodes.

Figure 2

Venn diagrams showing the distribution of unique and shared gene families. OrthoMCL was used to identify gene clusters across 13 plant species (a) as well as between the four sequenced Euphorbiaceae members (b).

Figure 3

Schematic representation of the metabolic pathway leading to natural rubber biosynthesis. Import of sucrose until biosynthesis of rubber involves 12 sub-metabolic pathways represented in the large boxes. The number of enzymes and associated proteins in each individual pathway is shown in small white boxes and the number of orthologs in Hevea in the grey boxes. The detailed pathway is shown in Additional file 2: Figure S2.

Figure 4

Phylogenetic analysis of plant CPTs. The evolutionary history was inferred by the Maximum likelihood method using MEGA5.05 [38]. All positions containing gaps and missing data were eliminated. CPT, cis-prenyltransferase; UPPS, undecaprenyl pyrophosphate synthase; and DHDDS, dehydrodolichyl diphosphate synthase. Bootstrapping values (100 replicates) are shown on branches.