Transcriptome Analysis Reveals Genetic Basis of Differences in Bioactive Compound Biosynthesis between Rhizome and Aboveground Stem in Ginger (Zingiber officinale Rosc.)

Abstract

Ginger (Zingiber officinale Rosc.) is a valuable food and medicinal plant. Its pharmacological activities are mainly attributed to its secondary metabolites. As a non-model plant, there is a lack of reference sequence information for ginger. Understanding the molecular mechanism of the biosynthesis of active compounds has important practical value for molecular breeding and the medicinal use of ginger. Gingerol constituents differ substantially between the aboveground stem and underground rhizome, with gingerols mainly accumulating in the rhizome. Therefore, de novo transcriptome sequencing was performed compare the expression of genes related to secondary metabolite biosynthesis between the two tissues. We obtained 219 479 unigenes after removing low-mass and linker sequences. The unigenes were assembled using Trinity software and compared with the Swiss-Prot, Nr, and KEGG databases for functional annotation. The differentially expressed genes (DEGs) between ginger rhizome (Rh-M) and stem (St-M) samples met the following criteria: FDR ≤ 0.005 and |log 2-fold change| ≥ 3. In total, there were 1418 DEGs between the two tissues (611 genes upregulated in Rh-M vs. St-M and 807 genes downregulated). 11 of these DEGs upregulated in the rhizome were related to the biosynthesis of pharmacologically active compounds, particularly terpenoids, diarylheptanoids, gingerols, and flavonoids, and to plant hormone signal transduction. We speculate that plant hormone signaling might play roles in regulating the biosynthesis of gingerols and other metabolites in the phenylpropane metabolic pathway in the rhizome. These results provide genome resources and information that will be useful for the molecular breeding in ginger.