Identification of terpenoid backbone biosynthetic pathway genes in Ajowan (Trachyspermum ammi L.) by RNA-Seq

RNA-seq can facilitate and accelerate the identification of key genes involved in the synthesis of the plant secondary metabolites. The fruits of the medicinal plant Ajowan (Trachyspermum ammi) contain 2-9 % essential oil which the monoterpenes thymol, γ-terpenine and para-cymene, are the major constituents. In the present study transcriptome analysis of Ajowan via RNA-seq by Illumina high-throughput technique was done. 42260830 high-quality clean reads were assembled into 68051 unigenes with the average length of 859.4 and N50 of 1257 bp. In order to identify unigenes involved in terpenoid backbone biosynthetic pathway, the sequences were uploaded on the KAAS database. On the basis of results, 30 genes in the pathway were identified including all the genes in two terpenoid backbone pathway (MEP and MVA) from the beginning of the pathway to IPP production. Enzymes involved in MEP pathway that were present in our dataset included 1-deoxy-D-xylulose-5-phosphate synthase (DXS), 1-deoxy-D-xylulose-5-phosphate reductoisomerase (DXR), 2-C-methyl-D-erythritol 4-phosphate cytidylyltransferase(ispD), 4-diphosphocytidyl-2-C-methyl-D-erythritol kinase (ispE), 2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase (ispF), 4-hydroxy-3-methylbut-2-enyl diphosphate synthase (gcpE), 4-hydroxy-3-methylbut-2-en-1-yl diphosphate reductase (ispH), isopentenyl-diphosphate delta isomerase, isoprene synthase (ispS), and geranyl-diphosphate synthase (GPS). Likewise, MEV pathway genes included acetyl-CoA acetyltransferase, HMG-CoA synthase, HMG-CoA reductase (HMGCR), phosphomevalonate kinase and mevalonate diphosphate decarboxylase. Identification of genes involved in biosynthetic pathways of terpenoid backbone will aid in future studies of the genes characterization, over-expression and metabolite engineering.