Comparative analysis of the transcriptomes and primary metabolite profiles of adventitious roots of five Panax ginseng cultivars

Abstract

BackgroundVarious Panax ginseng cultivars exhibit a range of diversity for morphological and physiological traits. However, there are few studies on diversity of metabolic profiles and genetic background to understand the complex metabolic pathway in ginseng.MethodsTo understand the complex metabolic pathway and related genes in ginseng, we tried to conduct integrated analysis of primary metabolite profiles and related gene expression using five ginseng cultivars showing different morphology. We investigated primary metabolite profiles via gas chromatography–mass spectrometry (GC-MS) and analyzed transcriptomes by Illumina sequencing using adventitious roots grown under the same conditions to elucidate the differences in metabolism underlying such genetic diversity.ResultsGC-MS analysis revealed that primary metabolite profiling allowed us to classify the five cultivars into three independent groups and the grouping was also explained by eight major primary metabolites as biomarkers. We selected three cultivars (Chunpoong, Cheongsun, and Sunhyang) to represent each group and analyzed their transcriptomes. We inspected 100 unigenes involved in seven primary metabolite biosynthesis pathways and found that 21 unigenes encoding 15 enzymes were differentially expressed among the three cultivars. Integrated analysis of transcriptomes and metabolomes revealed that the ginseng cultivars differ in primary metabolites as well as in the putative genes involved in the complex process of primary metabolic pathways.ConclusionOur data derived from this integrated analysis provide insights into the underlying complexity of genes and metabolites that co-regulate flux through these pathways in ginseng.

Identification of candidate UDP-glycosyltransferases involved in protopanaxadiol-type ginsenoside biosynthesis in Panax ginseng

“…Mass spectrometry (MS) ion markers were extracted from liquid chromatography–mass spectrometry (LC-MS) raw data using Mzmine2 2.30 software 40 . Mass ion detection was performed with the noise level set to 2000, and based on the detected mass list, peak lists were built with criteria as follows: minimum time span of 0.02 min, minimum height of 3000, and m/z tolerance of 0.006 Da (or 10.0 ppm).…”

Comparative transcriptome analyses on terpenoids metabolism in field- and mountain-cultivated ginseng roots

“…Since Kim et al [19] reported the first transcriptome from the leaf of ginseng, comparative transcriptome analyses have also been widely conducted on different ginseng roots, such as roots of two Korean ginseng cultivars (i.e., cultivars Cheonryang and Yunpoong ) and American ginseng ( P. quinquefolius , Voucher no. MPS002310) [20], adventitious roots from five Korean ginseng cultivars (i.e., cultivars Chunpoong , Cheongsun , Sunhyang , Goopong , and Sunun ) [21], or four parts of the root of the Korean ginseng cultivar Chunpoong (i.e., whole root, main root body, rhizome, and lateral root) [22], providing new insights into the primary and secondary metabolisms of ginseng root. Specific to comparative transcriptome analyses of FCG and MCG roots, several key genes in terpenoids biosynthesis have been reported.…”

Comparative de novo transcriptomics and untargeted metabolomic analyses elucidate complicated mechanisms regulating celery (Apium graveolens L.) responses to selenium stimuli

“…Metabolites are the end products of cellular biological processes, and their levels can be used as indicators of plant responses to genetic and environmental changes [38]. The combination of transcriptomic and metabolic data is useful for identifying genes that may be involved in metabolic networks [39]. Se-induced genes were identified in several species using RNA-seq [40,41], but the genes related to Se uptake, accumulation and tolerance in celery remain unclear.…”