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. 2015 Jun 12;15:138.
doi: 10.1186/s12870-015-0527-0.

Comprehensive Analysis of Panax Ginseng Root Transcriptomes

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Free PMC article

Comprehensive Analysis of Panax Ginseng Root Transcriptomes

Murukarthick Jayakodi et al. BMC Plant Biol. .
Free PMC article

Abstract

Background: Korean ginseng (Panax ginseng C.A. Meyer) is a highly effective medicinal plant containing ginsenosides with various pharmacological activities, whose roots are produced commercially for crude drugs.

Results: Here, we used the Illumina platform to generate over 232 million RNA sequencing reads from four root samples, including whole roots from one-year-old plants and three types of root tissue from six-year-old plants (i.e., main root bodies, rhizomes, and lateral roots). Through de novo assembly and reference-assisted selection, we obtained a non-redundant unigene set consisting of 55,949 transcripts with an average length of 1,250 bp. Among transcripts in the unigene set, 94 % were functionally annotated via similarity searches against protein databases. Approximately 28.6 % of the transcripts represent novel gene sequences that have not previously been reported for P. ginseng. Digital expression profiling revealed 364 genes showing differential expression patterns among the four root samples. Additionally, 32 were uniquely expressed in one-year-old roots, while seven were uniquely expressed in six-year-old root tissues. We identified 38 transcripts encoding enzymes involved in ginsenoside biosynthesis pathways and 189 encoding UDP-glycosyltransferases.

Conclusion: Our analysis provides new insights into the role of the root transcriptome in development and secondary metabolite biosynthesis in P. ginseng.

Figures

Fig. 1
Fig. 1
GO annotation of root transcripts in P. ginseng. A total of 41,244 transcripts in the Nr unigene set were assigned to at least one GO term in three categories, i.e., biological process, molecular function, and cellular component
Fig. 2
Fig. 2
KEGG pathway assignments of P. ginseng root transcripts. Among Nr unigene sequences, 5,720 transcripts were assigned to KEGG pathways by KASS analysis. The percentage of the 5,720 transcripts assigned to the indicated pathways is shown
Fig. 3
Fig. 3
Expression profiles of differentially expressed transcripts among root samples. A total of 364 transcripts were identified to be differentially expressed among four root samples (a to d) using the edgeR Bioconductor package based on individual FPKM values of three biological replicates for each root sample. Heatmap shows the hierarchical clustering of average FPKM values obtained from individual FPKM values of three replicates. A indicates one-year-old whole roots, and b, c, and d represent main bodies, lateral roots, and rhizomes of six-year-old root samples, respectively
Fig. 4
Fig. 4
Expression profiles of specifically expressed transcripts in each of four root samples. A total of 39 transcripts were found to be specifically expressed based on the criteria of FPKM value > 3 in one sample and <1 FPKM in the other samples. Heatmap shows the hierarchical clustering of average FPKM values obtained from individual FPKM values of three replicates. a indicates one-year-old whole roots, and b, c, and d represent main bodies, lateral roots, and rhizomes of six-year-old root samples, respectively. Transcript IDs are shown to the right of the heatmap
Fig. 5
Fig. 5
Expression profiles of transcripts encoding enzymes involved in ginsenoside biosynthesis in P. ginseng. Enzymes functioning in each step of the MVA and MEP pathways are indicated by bold letters. The expression patterns of transcripts encoding these enzymes are shown in the heatmap, which was constructed using average FPKM values obtained from individual FPKM values of three replicates. a indicates one-year-old whole roots and b, c, and d represent main bodies, lateral roots, and rhizomes of six-year-old root samples, respectively. The number of transcripts identified is shown in parentheses to the left of heatmap. AACT, acetyl CoA acetyltransferase; Beta-AS, beta-amyrin synthase; CDP-MEK, 4-diphosphocytidyl-2-C-methyl-D-erythritol kinase; DS, dammarenediol II synthase; DXR, 1-deoxy-D-xylulose-5-phosphate reductoisomerase; FPS, farnesyl diphosphate synthase; GPS, geranylgeranyl diphosphate synthase; HMBPPR, 4-hydroxy-3-methylbut-2-enyl diphosphate reductase; HMBPPS, 2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase; HMGR, 3-hydroxy-3-methylglutaryl-coenzymeA reductase; HMGS, hydroxymethyl glutaryl CoA synthase; IDI, isopentenyl-diphosphate delta-isomerase; MECDPS, 2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase; MEP-CT, 2-C-methyl-D-erythritol4-phosphate cytidylyltransferase; MK, mevalonate kinase; MVD, mevalonate diphosphate decarboxylase; PMK, phosphomevalonate kinase; PPDS, protopanaxadiol synthase; PPTS, protopanaxatriol synthase; SE, squalene monooxygenase/epoxidase; SS, squalene synthase

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