De novo hybrid assembly of the rubber tree genome reveals evidence of paleotetraploidy in Hevea species

Abstract

Para rubber tree (Hevea brasiliensis) is an important economic species as it is the sole commercial producer of high-quality natural rubber. Here, we report a de novo hybrid assembly of BPM24 accession, which exhibits resistance to major fungal pathogens in Southeast Asia. Deep-coverage 454/Illumina short-read and Pacific Biosciences (PacBio) long-read sequence data were acquired to generate a preliminary draft, which was subsequently scaffolded using a long-range “Chicago” technique to obtain a final assembly of 1.26 Gb (N50 = 96.8 kb). The assembled genome contains 69.2% repetitive sequences and has a GC content of 34.31%. Using a high-density SNP-based genetic map, we were able to anchor 28.9% of the genome assembly (363 Mb) associated with over two thirds of the predicted protein-coding genes into rubber tree’s 18 linkage groups. These genetically anchored sequences allowed comparative analyses of the intragenomic homeologous synteny, providing the first concrete evidence to demonstrate the presence of paleotetraploidy in Hevea species. Additionally, the degree of macrosynteny conservation observed between rubber tree and cassava strongly supports the hypothesis that the paleotetraploidization event took place prior to the divergence of the Hevea and Manihot species.

The Tung Tree (Vernicia Fordii) Genome Provides A Resource for Understanding Genome Evolution and Oil Improvement

“…More than 85% NBS genes were clustered in groups, and clusters were most abundant on chromosomes 2, 9, and 3 (Figure S24). Enrichment of NBS genes in these corresponding genomic regions indicated that resistance gene evolution might involve tandem duplication and divergence of linked gene families, as described in other plant genomes such as rubber tree [23] and pear [24]. RNA-seq data showed that the 88 tung tree NBS genes displayed differential expression patterns in roots after F. oxysporum infection (Figure 5B; File S5).…”

The complete chloroplast genome of Hevea camargoana

“…Hevea camargoana is a tropical plant that produces natural latex, native to the Amazon Basin and belongs to the family Euphorbiaceae. It is a close relative of H. brasiliensis, which is the primary commercial source for high-quality natural rubber (Rahman et al 2013) and accounts for more than 98% of the total production worldwide (Pootakham et al 2017). The genus Hevea contains 11 species (Gonçalves et al 1990), most of which are diploid with 36 chromosomes (Lau et al 2016).…”

HeveaDB: a genetic resource database for rubber tree genomic study

“…Recent progress in next-generation sequencing technique greatly promoted the genomic study in rubber tree [4][5][6][7][8][9][10][11][12][13]. At current stage, 4 versions of draft genome in rubber trees were compiled [14][15][16][17] and more than 100 NGS transcriptomic data were produced [18][19][20][21][22][23][24][25]. However, these data are still deposited in NCBI and other public database in raw format, which hindered the NGS data utilization for the scientists in rubber tree community.…”