Targeted Integration of RNA-Seq and Metabolite Data to Elucidate Curcuminoid Biosynthesis in Four Curcuma Species

Abstract

Curcuminoids, namely curcumin and its analogs, are secondary metabolites that act as the primary active constituents of turmeric (Curcuma longa). The contents of these curcuminoids vary among species in the genus Curcuma. For this reason, we compared two wild strains and two cultivars to understand the differences in the synthesis of curcuminoids. Because the fluxes of metabolic reactions depend on the amounts of their substrate and the activity of the catalysts, we analyzed the metabolite concentrations and gene expression of related enzymes. We developed a method based on RNA sequencing (RNA-Seq) analysis that focuses on a specific set of genes to detect expression differences between species in detail. We developed a 'selection-first' method for RNA-Seq analysis in which short reads are mapped to selected enzymes in the target biosynthetic pathways in order to reduce the effect of mapping errors. Using this method, we found that the difference in the contents of curcuminoids among the species, as measured by gas chromatography-mass spectrometry, could be explained by the changes in the expression of genes encoding diketide-CoA synthase, and curcumin synthase at the branching point of the curcuminoid biosynthesis pathway.

Integration of a Decrescent Transcriptome and Metabolomics Dataset of Peucedanum praeruptorum to Investigate the CYP450 and MDR Genes Involved in Coumarins Biosynthesis and Transport

“…Hence, in this study, HPLC coupled with Q-TOF MS was used to identify the metabolites because it is rapid and can provide accurate mass measurements (Ling et al, 2013 ). Merging with transcriptome dataset, it could largely improve the rapidity, accuracy and efficiency of gene discovery (Yamazaki et al, 2013 ; Li et al, 2015 ). However, correlation analysis of the whole transcriptomic and metabolomics seems intertwined and unnecessary because we mainly concern some certain pathways or genes.…”

Associating gene expressions with curcuminoid biosynthesis in turmeric

“…There was no significant change in the CURS3 expression (< 2-fold change) among the cultivars. CURS3 expressions were also found lower in all the turmeric species differing in curcuminoid yield [24]. These results showed that there is a significant variation in DCS and CURSs gene expressions in turmeric rhizome also affected by genotype and growth stages.…”

“…Transcriptomics studies in turmeric have shed light on the identification and validation of multiple curcumin synthases involved in the curcuminoid biosynthetic pathway in turmeric [17,18,21]. More novel type III PKS genes have been identified recently, such as CLPKS9 and CLPKS10 [22], CLPKS1and CLPKS2 [18], and CLPKS11 [23] which may have a potential role in curcuminoid scaffold biosynthesis; however, the difference in the contents of curcuminoids among the species can be explained by the changes in the expression of genes encoding diketide-CoA synthase and multiple curcumin synthases at the branching point of the curcuminoid biosynthesis pathway in turmeric [24]. The variation in curcuminoid content among the various lines and cultivars of C. longa was reported to be caused by hybridization and introgression [25], agro-climatic variation [26], genotype and environment interaction [27], and microenvironment (below soil surface near root zone) and macroenvironment (above soil surface) interaction [28]; however, the effects of tissue-specific gene expressions on curcuminoid biosynthesis are still unknown.…”

An extreme-phenotype genome‐wide association study identifies candidate cannabinoid pathway genes in Cannabis

“…These have included using whole-genome sequencing such as used in Ocimum sanctum (holy basil) 43 or RNA-Seq as used for Brassica juncea (Indian mustard) 44 . More targeted sequencing-based strategies in Nicotiana tabacum (tobacco) 45 and Curcuma longa (turmeric) 46 , have contributed to improving the accuracy with which chemotype can be genetically characterised and predicted. However, the effectiveness of some of these methodologies can be limited in non-model orphan plant species 47 , where the inbred research lines required for linkage-based analysis such mapping-by-sequencing (MBS) 48 may not be available 49 .…”