We determined a draft sequence of an estimated 1.4 billion bp genome of Hevea brasiliensis (Para rubber tree), a euphorbiaceous tree for producing latex. We optimized assembling and scaffolding of reads by HiSeq 2000 and PacBio RS II derived from Hevea brasiliensis PB260 clone. An optimized scaffolds comprised of ca. 50 k scaffolds covering 90% of the gene-rich regions of the genome, and has N50 of 120 kb and maximum scaffold size of 1.2 Mb, containing 227 Mb (14.7%) of unknown nucleotides (N’s), in total. We also revealed the planted Hevea clones have ten thousands of nucleotide differences, rich in genetic diversity. To develop set of DNA markers for elite tree selection utilizing the whole genome information of a rubber tree, we established a technology to identify representative clones of Hevea. The markers developed were a useful tool to enabling an efficient investigation for many samples from the plantation of Hevea. With use of the DNA markers, we started a field survey to find out representative trees for breeding to enhance the productivity of natural rubber.
