De novo transcriptome sequencing and analysis of Euphorbia pekinensis Rupr. and identification of genes involved in diterpenoid biosynthesis

Abstract

Euphorbia pekinensis Radixz (EPR) is a commonly used Chinese herbal medicine prepared from the dried roots of E. pekinensis Rupr. It has been revealed in chemical analysis that diterpenoids are the primary component of EPR bestowing toxicity and bioactivity; however, little is known about these bioactive and toxic diterpenoid biosynthesis pathways and diterpene diversity in E. Pekinensis. In this study, we sequenced root, stem, and leaf transcriptomes of E. pekinensis, and conducted de novo assembly using 429 million clean reads with Trinity software. Then, 157,491 unigenes were generated whose N50 contained 1826bp. All of the unigenes were interpreted using Nt, Nr, COGs, SwissProt, GO, and KEGG databases. The expression profiling based on FPKM showed 665 genes up-regulated in roots were enrichment pathways for CYP450s and transcript factors. There are extremely diverse specialised diterpene pathways therein, and most specialised diterpenes are limited to several plant genera, species, or special tissues according to their taxonomy. Using homology, we identified 26 diterpenoid synthase candidates which comprised 25 class I proteins, and only one class II protein, in TPS-a and TPS-c sub-families, among which five class I proteins were highly expressed in root. Additionally, 23 CYP450 enzymes from sub-families of CYP71D and CYP726 were identified, and three were highly expressed in root, for which expression patterns were similar to the aforementioned five class I diTPSs expressed in root and may be involved in macroditerpenoid biosynthesis in EPR. Our results provided a beneficial genomic resource which is able to be used for future functional genomics research on E. pekinensis.