Ginger and turmeric expressed sequence tags identify signature genes for rhizome identity and development and the biosynthesis of curcuminoids, gingerols and terpenoids

Abstract

BackgroundGinger (Zingiber officinale) and turmeric (Curcuma longa) accumulate important pharmacologically active metabolites at high levels in their rhizomes. Despite their importance, relatively little is known regarding gene expression in the rhizomes of ginger and turmeric.ResultsIn order to identify rhizome-enriched genes and genes encoding specialized metabolism enzymes and pathway regulators, we evaluated an assembled collection of expressed sequence tags (ESTs) from eight different ginger and turmeric tissues. Comparisons to publicly available sorghum rhizome ESTs revealed a total of 777 gene transcripts expressed in ginger/turmeric and sorghum rhizomes but apparently absent from other tissues. The list of rhizome-specific transcripts was enriched for genes associated with regulation of tissue growth, development, and transcription. In particular, transcripts for ethylene response factors and AUX/IAA proteins appeared to accumulate in patterns mirroring results from previous studies regarding rhizome growth responses to exogenous applications of auxin and ethylene. Thus, these genes may play important roles in defining rhizome growth and development. Additional associations were made for ginger and turmeric rhizome-enriched MADS box transcription factors, their putative rhizome-enriched homologs in sorghum, and rhizomatous QTLs in rice. Additionally, analysis of both primary and specialized metabolism genes indicates that ginger and turmeric rhizomes are primarily devoted to the utilization of leaf supplied sucrose for the production and/or storage of specialized metabolites associated with the phenylpropanoid pathway and putative type III polyketide synthase gene products. This finding reinforces earlier hypotheses predicting roles of this enzyme class in the production of curcuminoids and gingerols.ConclusionA significant set of genes were found to be exclusively or preferentially expressed in the rhizome of ginger and turmeric. Specific transcription factors and other regulatory genes were found that were common to the two species and that are excellent candidates for involvement in rhizome growth, differentiation and development. Large classes of enzymes involved in specialized metabolism were also found to have apparent tissue-specific expression, suggesting that gene expression itself may play an important role in regulating metabolite production in these plants.

Comparative transcriptome of rhizome and leaf in Ligusticum Chuanxiong

“…Except MADS-box gene, this was the first report that BDP, LOB, ROP, WOX4, ULT1, KNOX, LHW, CLE, and C3CH4 genes expressed highly in rhizome (Jang et al 2006;Koo et al 2013). To date, although whether the above genes were involved with the rhizome formation and development have not been identified by transgenic evidence, those highly expressing level in rhizome indicated that they might play essential role in the rhizome formation and development.…”

Senescence, dormancy and tillering in perennial C4 grasses

“…Within this experiment, the authors found that rhizome formation was a key but not the only factor that controlled winter survival, again providing indirect evidence that many aspects of dormancy and winter-survival can be separated. More recently, other researchers have begun the task of dissecting the genes and co-expressed gene sets that might control rhizomatousness in monocots [85][86][87][88][89]. These studies have identified transcripts for several genes including transcription factors that are selectively enriched in rhizomes relative to shoots.…”

Biosynthesis of geranial, a potent aroma compound in ginger rhizome (<i>Zingiber officinale</i>): Molecular cloning and characterization of geraniol dehydrogenase

“…In addition, we referred to the Aromatic Rhizome EST database in the University of Arizona (http://www.agcol. arizona.edu/cgi-bin/pave/GT/index.cgi, (Koo et al 2013)), because this database was opened before we constructed our own database from cv. Kintoki.…”

“…Our previous report showed that NADP + -dependent ADH activity for geraniol was involved in production of citral, whereas geraniol oxidase showed no activity (Sekiwa- Iijima et al 2001). Therefore, we screened candidate GeDH cDNA using the EST database established by the University of Arizona (Koo et al 2013) and our domestic sequence collections constructed for Z. officinale cv. Kintoki using next-generation sequencing technology.…”