Transcriptome analysis of terpenoid biosynthetic genes and simple sequence repeat marker screening in Eucommia ulmoides

Trans -polyisoprene rubber is produced in the tissues of leaves, bark, and fruit of Eucommia ulmoides and is considered an important energy source. Transcript profiles of two tissues from E. ulmoides cv. Qinzhong No. 3, leaf and fruit, were analysed using the Illumina HiSeq 2000 system. In total, 104 million clean reads were obtained and assembled into 58,863 unigenes. Through gene functional classification, 28,091 unigenes (47.72%) were annotated and 65 unigenes have been hypothesized to encode proteins involved in terpenoid biosynthesis. In addition, 10,041 unigenes were detected as differentially expressed unigenes, and 29 of them were putatively related to terpenoid biosynthesis. The synthesis of trans -polyisoprene rubbers in E. ulmoides was hypothesised to be dominated by the mevalonate pathway. Farnesyl diphosphate synthase 2 ( FPPS2 ) was considered a key component in the biosynthesis of trans -polyprenyl diphosphate. Rubber elongation factor 3 ( REF3 ) might be involved in stabilising the membrane of rubber particles in E. ulmoides . To date, 351 simple sequence repeats (SSRs) were validated as polymorphisms from eight E. ulmoides plants (two parent plants and six F 1 individuals), and these could act as molecular markers for genetic map density increase and breeding improvement of E. ulmoides .