Transcriptome analysis reveals the genetic basis underlying the biosynthesis of volatile oil, gingerols, and diarylheptanoids in ginger (Zingiber officinale Rosc.)

Abstract

Background: Ginger (Zingiber officinale Rosc.) is a popular flavoring that widely used in Asian, and the volatile oil in ginger rhizomes adds a special fragrance and taste to foods. The bioactive compounds in ginger, such as gingerols, diarylheptanoids, and flavonoids, are of significant value to human health because of their anticancer, anti-oxidant, and anti-inflammatory properties. However, as a non-model plant, knowledge about the genome sequences of ginger is extremely limited, and this limits molecular studies on this plant. In this study, de novo transcriptome sequencing was performed to investigate the expression of genes associated with the biosynthesis of major bioactive compounds in matured ginger rhizome (MG), young ginger rhizome (YG), and fibrous roots of ginger (FR).

Results: A total of 361,876 unigenes were generated by de novo assembly. The expression of genes involved in the pathways responsible for the biosynthesis of major bioactive compounds differed between tissues (MG, YG, and FR). Two pathways that give rise to volatile oil, gingerols, and diarylheptanoids, the "terpenoid backbone biosynthesis" and "stilbenoid, diarylheptanoid and gingerol biosynthesis" pathways, were significantly enriched (adjusted P value < 0.05) for differentially expressed genes (DEGs) (FDR < 0.005) both between the FR and YG libraries, and the FR and MG libraries. Most of the unigenes mapped in these two pathways, including curcumin synthase, phenylpropanoylacetyl-CoA synthase, trans-cinnamate 4-monooxygenase, and 4-hydroxy-3-methylbut-2-en-1-yl diphosphate synthase, were expressed to a significantly higher level (log₂ (fold-change) ≥ 1) in FR than in YG or MG.

Conclusion: This study provides the first insight into the biosynthesis of bioactive compounds in ginger at a molecular level and provides valuable genome resources for future molecular studies on ginger. Moreover, our results establish that bioactive compounds in ginger may predominantly synthesized in the root and then transported to rhizomes, where they accumulate.

Keywords: Bioactive compounds; Fibrous root; Ginger; Rhizome; Transcriptome sequencing.

Fig. 1

Histogram of gene ontology (GO) annotations for unigenes in ginger matured rhizome, young rhizome, and fibrous root libraries. Level two GO terms belonging to three categories, molecular function, biological process, and cellular component are along the x-axis and the number of unigenes assigned to each term is represented along the y-axis. Bars with different colors indicate different libraries

Fig. 2

Pairwise comparisons of unigene expression in ginger matured rhizome, young rhizome, and fibrous root libraries (a) and a Venn diagram of the differentially expressed genes (DEGs) among the three libraries (b)

Fig. 3

Gene ontology (GO) enrichment of differentially expressed genes (DEGs) between ginger matured rhizome, young rhizome, and fibrous root libraries. P values are represented along the x-axis and level two GO terms belonging to three categories, molecular function, biological process, and cellular component are represented along the y-axis. Numbers indicate the number of unigenes assigned to each term

Fig. 4

Differentially expressed genes (DEGs) involved in the “terpenoid backbone biosynthesis” pathway of ginger. The red columns indicate genes expressed at a significantly high level in fibrous roots. The green columns indicate genes expressed at a significantly high level in rhizomes. The red boxes indicate the biosynthesis of the major compounds found in ginger volatile oil. This color-coded map of DEGs corresponds to map00900 in the KEGG database (http://www.genome.jp/dbget-bin/www_bget?pathway:map00900)

Fig. 5

Differentially expressed genes (DEGs) involved in the “stilbenoid, diarylheptanoid and gingerol biosynthesis” pathway. The red columns indicate genes expressed at a significantly high level in fibrous roots; the green columns indicate genes expressed at a significantly high level in rhizomes. This color-coded map of DEGs corresponds to map00945 in the KEGG database (http://www.genome.jp/dbget-bin/www_bget?pathway:map00945)

Fig. 6

Heat map of the expression levels of seven ginger unigenes as determined by the fragments per kilobase of exon per million fragments mapped (FPKM) (a) and qRT-PCR analysis (b)