Phenotypic and RNA-seq profiles identified key pathways and genes involved in gleditsioside biosynthesis in Gleditsia sinensis Lam

Background Gleditsia sinensis Lam (G. sinensis) is one of the important medicinal herb plant species, and its major bioactive compounds are gleditsioside in pods. The essential economic and medicinal value of gleditsioside has been increasingly recognized. Nonetheless, the molecular mechanisms underlying the changes in the content of gleditsioside during the development of G. sinensis are largely unknown. Results In this resrarch, there is a positive relationship between the accumulation of gleditsioside content and the variation of pod length, and we performed a transcriptome-wide analysis involving gleditsioside biosynthesis in the pods of G. sinensis using RNA-seq. 9000 differentially expressed unigenes (DEGs) were found among six development stages of G. sinensis pods. 703 and 162 DEGs participated in terpenoid backbone and triterpenoid biosynthesis pathways, respectively. 99 unigenes were identified, which can encode 17 enzymes, including key enzyme families, such as ENIN, cytochrome P450 (CYP93E1), and UDP-glucosyltransferase in the gleditsioside biosynthesis pathway. Moreover, DEGs encoding crucial enzymes (HMGCR and AGBH) can determine the gleditsioside synthesis during the development of G. sinensis pods. According to the generation of different hormones, 10 pathways have been expanded outward in the gleditsioside synthesis pathway, forming a relationship network together. They shared the same precursor substances (IPP and DMAPP), and the 11 pathways should be inhibitory with the gleditsioside synthesis pathway. In addition, WGCNA analysis was further conducted combined with the phenotype of pods and gleditsioside content. As a result, it was found that Unigene32740 (HMGCS) and CL4789.Contig4 (COL) were involved in the gleditsioside biosynthesis and the pod development, respectively. Conclusions Overall, this study shows an important gene resource for the future functional researches and provides new insights into the fundamental mechanisms of the gleditsioside biosynthesic process in G. sinensis.