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Background   Euphorbia fischeriana  is an important medicinal plant found in Northeast China. The plant roots contain many medicinal compounds including 12-deoxyphorbol-13-acetate, commonly known as prostratin that is a phorbol ester from the tigliane diterpene series. Prostratin is a protein kinase C activator and is effective in the treatment of Human Immunodeficiency Virus (HIV) by acting as a latent HIV activator. Latent HIV is currently the biggest limitation for viral eradication. The aim of this study was to sequence, assemble and annotate the  E. fischeriana  transcriptome to better understand the potential biochemical pathways leading to the synthesis of prostratin and other related diterpene compounds.    Results  In this study we conducted a high throughput RNA-seq approach to sequence the root transcriptome of  E. fischeriana . We assembled 18,180 transcripts, of these the majority encoded protein-coding genes and only 17 transcripts corresponded to known RNA genes. Interestingly, we identified 5,956 protein-coding transcripts with high similarity (> = 75%) to  Ricinus communis , a close relative to  E. fischeriana . We also evaluated the conservation of  E. fischeriana  genes against EST datasets from the Euphorbeacea family, which included  R. communis ,  Hevea brasiliensis  and  Euphorbia esula . We identified a core set of 1,145 gene clusters conserved in all four species and 1,487  E. fischeriana  paralogous genes. Furthermore, we screened  E. fischeriana  transcripts against an in-house reference database for genes implicated in the biosynthesis of upstream precursors to prostratin. This identified 24 and 9 candidate transcripts involved in the terpenoid and diterpenoid biosyntehsis pathways, respectively. The majority of the candidate genes in these pathways presented relatively low expression levels except for 1-hydroxy-2-methyl-2-(E)-butenyl 4-diphosphate synthase (HDS) and isopentenyl diphosphate/dimethylallyl diphosphate synthase (IDS), which are required for multiple downstream pathways including synthesis of casbene, a proposed precursor to prostratin.    Conclusion  The resources generated in this study provide new insights into the upstream pathways to the synthesis of prostratin and will likely facilitate functional studies aiming to produce larger quantities of this compound for HIV research and/or treatment of patients.

De novo assembly of Euphorbia fischeriana root transcriptome identifies prostratin pathway related genes