Combined Metabolome and Transcriptome Analyses of Young, Mature, and Old Rhizome Tissues of Zingiber officinale Roscoe

Abstract

Ginger (Zingiber officinale Roscoe) is known for its unique pungent taste and useability in traditional Chinese medicine. The main compounds in ginger rhizome can be classified as gingerols, diarylheptanoids, and volatile oils. The composition and concentrations of the bioactive compounds in ginger rhizome might vary according to the age of the rhizome. In this regard, the knowledge on the transcriptomic signatures and accumulation of metabolites in young (Y), mature (M), and old (O) ginger rhizomes is scarce. This study used HiSeq Illumina Sequencing and UPLC-MS/MS analyses to delineate how the expression of key genes changes in Y, M, and O ginger rhizome tissues and how it affects the accumulation of metabolites in key pathways. The transcriptome sequencing identified 238,157 genes of which 13,976, 11,243, and 24,498 were differentially expressed (DEGs) in Y vs. M, M vs. O, and Y vs. O, respectively. These DEGs were significantly enriched in stilbenoid, diarylheptanoid, and gingerol biosynthesis, phenylpropanoid biosynthesis, plant-hormone signal transduction, starch and sucrose metabolism, linoleic acid metabolism, and α-linoleic acid metabolism pathways. The metabolome profiling identified 661 metabolites of which 311, 386, and 296 metabolites were differentially accumulated in Y vs. M, Y vs. O, and M vs. O, respectively. These metabolites were also enriched in the pathways mentioned above. The DEGs and DAMs enrichment showed that the gingerol content is higher in Y rhizome, whereas the Y, M, and O tissues differ in linoleic and α-linoleic acid accumulation. Similarly, the starch and sucrose metabolism pathway is variably regulated in Y, M, and O rhizome tissues. Our results showed that ginger rhizome growth slows down (Y > M > O) probably due to changes in phytohormone signaling. Young ginger rhizome is the most transcriptionally and metabolically active tissue as compared to M and O. The transitioning from Y to M and O affects the gingerol, sugars, linoleic acid, and α-linoleic acid concentrations and related gene expressions.

Dynamic transcriptome profiling provides insights into rhizome enlargement in ginger (Zingiber officinale Rosc.)

“…This indicates that SAURs may affect cell expansion through the synthesis and transport of auxin under the regulation of ARFs, which are conserved in the plant kingdom [43,45], and function in the regulation of rhizome enlargement in ginger. Liu et al found that the expression of genes related to auxin signaling pathway was higher in young ginger tissues and lower in mature and old tissues [46]. The reason for the inconsistent results may be that the rhizome enlargement period we studied was before the maturity period of Liu et al No more auxin is required after the completion of the expansion process, so auxin-related gene expression is reduced in mature and old tissues.…”

“…However, BRs have been shown to play an important role in controlling cell elongation and can induce the expression of SAUR genes [52,53]. In Liu et al's study, most DEGs enriched in plant hormone signals such as ethylene, BRs, JA and SAwere relatively highly expressed in young ginger rhizomes, and played important roles in ginger rhizome growth [46]. In our study, the JA content increased with the development of ginger, which is consistent with the upregulation of all three JA biosynthesis-related JA O-methyltransferase and JAR genes through the S1-S2 and S2-S3 transitions (Fig 1C and S5 Table).…”

Green Synthesis of Gold Nanoparticles by Aqueous Extract of Zingiber officinale: Characterization and Insight into Antimicrobial, Antioxidant, and In Vitro Cytotoxic Activities

“…Herein, the aqueous extract of Z. officinale rhizome was used for the green synthesis of AuNPs. As reported previously, Z. officinale rhizome provides an enriched source for various constituents, such as terpenes, lipids, phenolic compounds, polysaccharides, organic acids, and volatile oils [49,50]. These metabolites were used as biocatalyst to reduce metals and their oxide to produce nanoscale structures, followed by capping and stabilization (mediated by the extracted compounds).…”

Integrated non‐targeted metabolomics and transcriptomics reveals the browning mechanism of scraped ginger (Zingiber officinale Rosc.)

“…Samples were prepared following the protocol described by Liu et al. (2021). Briefly, the samples were ground into a powder and subjected to lyophilization under vacuum.…”