NEW YORK (GenomeWeb) – An international research team led by investigators at the Chinese Academy of Tropical Agricultural Sciences’ Rubber Research Institute have produced a whole genome sequence of the Para rubber tree (Hevea brasiliensis) and paired-end reads for five other rubber tree species.
The rubber tree is a member of the spurge family (Euphorbiaceae) along with the cassava (Manihot esculenta) and castor oil plant (Ricinus communis), all three of which are economically important. The first draft of rubber tree genome was released by a team from the University of Science in Malaysia in 2013, but its low sequence coverage and lack of large insert libraries limited the success of the genome assembly.
The new, high-quality rubber tree genome — reported this week in Nature Plants by researchers from China, Malaysia, France, and the US — could provide tree growers and other researchers with "a valuable resource for functional genomics and tools for breeding elite Hevea cultivars," the team wrote in their paper.
To start, the investigators collected young leaves from six rubber tree cultivars, including the Para rubber tree. They extracted the DNA from the leaves, sequenced the genome, and assembled it using shotgun sequences produced on the Illumina GA2 and HiSeq2000. The team further improved the genome assembly by adding pooled bacterial artificial chromosome (BAC) sequences from 47,616 BAC clones.
They estimated that the Para genome is 1.46 Gb, a little less than half the size of the human genome (3.2. Gb). The other five cultivars ranged in size from 1.41 Gb to 1.55 Gb. They also found that the Para genome contains a total of 43,792 genes.
The team further performed RNA sequencing on the samples using the Illumina HiSeq2000, and found mechanisms underlying ethylene stimulation of rubber production. In particular, the researchers noted the REF/SRPP gene family was the most highly expressed, and seemed to be responsible for rubber elongation and creating small rubber particle proteins.
This gene family's divergence into specific isoforms responsible for secreting latex in the plant also seemed crucial for rubber biosynthesis. "A mutation event occurred relatively recently whereby SRPP was truncated to give rise to REF,” the researchers wrote. “Deletion of the SRPP C terminus that resulted in REF isoforms appears to have occurred more than once in the rubber tree’s evolutionary history, but the isoforms that prevail in modern Hevea are REF1 and SRPP1."
When compared to 17 other plants that they sequenced, the researchers found that the REF/SRPP family in the rubber tree genome has isoforms with sizes similar to or larger than SRPP1 in the other plants. However, there are no isoforms with similar sizes to REF1, the predominant molecular variant, in any of the other plants sequenced. The investigators believe that expression of REF genes in particular seem to be a critical component in rubber biosynthesis.
They also observed that REF1 seemed to play the most important role in better natural rubber production. "The amount of REF1 protein in the whole latex has been found to be proportional to the rubber content [and] REF1 gene expression was reported to correlate with yield levels of Hevea cultivars," they wrote. Essentially, it seems that higher amounts of REF1 protein and higher REF1 gene expression created higher natural rubber yields.
The paper concluded that "the data from this study, together with other public resources, pave a way for whole genome association studies, germplasm improvement and genetic modification of Hevea to meet increasing global demand for natural rubber."