Identification of terpenoid backbone biosynthetic pathway genes in fruit of Citrullus colocynthis (L.) Schrad. medical plant by RNA sequencing

Nowadays, RNA sequencing is an effective and fast choice to study the transcripts of non-model plant species used to identify gene networks and patterns of gene expression producing secondary metabolites in different plant organs. Terpenoids, flavonoids, and alkaloids are the main compounds in fruits and leaves of Citrullus colocynthis (L.) Schrad. In this study, the transcriptome of C. colocynthis fruit was performed using RNA-Seq technique, Iluumina HiSeq2500 platform. After quality control using FastQC and Trimmomatic software, 21,952,885 high-quality reads were produced and the de novo assembly with the Evidential-gene program resulted in the production of 55,311unigenes with an N50 equal to 927 base pairs. The sequence of assembled unigenes was loaded on the KAAS database. A total of 13,657 unigenes were annotated, matched into 134 biosynthetic pathways. The "terpenoid backbone" biosynthetic pathway with 93 unigenes was one of the most numerous identified pathways among 1,552 unigenes of secondary metabolites biosynthetic pathway. By examining the unigenes associated with the biosynthetic pathway of the terpenoid backbone, 29 gene identifiers (K number) of the pathway were detected, which contained all identified genes of the two main biosynthetic pathways, Mevalonic Acid (MVA) and Methylerythritol Phosphate (MEP) pathways, from the beginning of the path to the production of isoprenyl diphosphate (IPP). Identification of the genes in the biosynthetic pathway of the terpenoid backbone makes it possible to realize the commercial development of the medicinal plant products, providing the basis for further research on the identification of biosynthetic pathways of other specific metabolites, metabolite engineering, molecular breeding, and medical plants breeding.