## 1 Introduction  
Ginseng (_P. ginseng_ [PERSON]) is well recognized as the king of herbs and widely used as a source of herbal medicine in eastern Asia and North America [1]. The genus \"panax\" means panacea or cure all and the root is so-called \"ginseng\" because of its man-like shape and thought to represent its three characteristics (body, mind and sprit) [2]. The plant has multiple clinical and pharmacological effects related to cancer, stress, obesity, diabetes and cardiovascular disease [3; 4; 5; 6]. The major pharmacologically active compounds of ginseng are ginsengosides belonging to dammarane and oleanane type triterpene saponins. Dammarane-type consists of two groups based on their structure, _i.e._, the Rb group (protopanaxadiols, including Ra1, Ra2, Rb1,Rb2, Rb3, Rc, Rd, Rg3, Rh2 and others) and the Rg group (protopanaxatriols, including Rg1, Rg2, Re, Rf, Rh1 and others), while oleanane-type ginseng represents only one saponin, Ro [7]. They have been identified in all parts of the plant, including the root, stem, leaf and flower [8]. However, research for years on its highly valued root has largely been conducted due to its important herbal applications since ancient times. The large size (\(\sim\)3.2 Gb) and high complexity of the _P. ginseng_ genome that is reportedly tetraploid (\(2n=4x=48\)) [9] has made it difficult to get a whole genomic sequence for this plant. Some researchers have generated ESTs from untreated and MeJA treated ginseng hairy roots by the traditional Sanger sequencing method to detect genes involved in ginsensosides biosynthesis [10; 11; 12]. Over the last few years, the next-generation sequencing (NGS) technology has emerged as a cutting edge approach for high-throughput sequence determination of model and non-model organisms, especially those with large and complex genomes. Besides, this approach has considerably improved our understanding on the complexity of gene expression profiling, discovery, regulation and networks in plants [13; 14]. In spite of its clear potential, the NGS technology has been applied in a few studies for the transcriptome analysis of _Panax_ species, including _P. ginseng_, _P. notoginseng_ and _P. quinquefolius_[15; 16; 17], where the technology was almost limited to the Roche/454 pyrosequencing platform to identify mainly ginseng biosynthetic genes. More recently, the Illumina/Solexa platform has been introduced in untreated adventitious root transcriptome analysis of two _P. ginseng_ cultivars namely Chunpoong (CP) and Cheongsun (CS) for their gene expression profiling and ginsenoside biosynthetic genes identification [14]. However, gene discovery and candidate genes involved in ginsenosides biosynthesis and their transport in ginseng species are still limited. In recent years, plant genetic engineering research has turned towards modulation of the secondary metabolite biosynthesis pathway, and biotic and abiotic stress and defense-related genes [18; 19]. Secondary metabolites biosynthesis and their regulation is a multilayer network requiring common signal pathways and a variety of key elicitors such as MeJA or salicylic acid [20]. Hence, Jasmonicacid and its derivatives have received much attention as key molecules, particularly in regulating the secondary metabolism in many plant species. Increasing evidence shows that MeJA significantly increases the production of many highly valuable secondary metabolites of pharmaceutical and industrial importance [21]. Various secondary metabolites including ginsenosides synthesized by MeJA in medicinal plants have pharmacological effects in human health and play important roles in the adaptation of plants to a particular environment [10]. Among various elicitors, MeJA has recently been confirmed as an effective elicitor for the induction of ginsenoside contents in cultured cells and adventitious roots of _P. ginseng_[22, 23]. In addition, MeJA significantly up-regulates _PDR_ gene expression related to various secondary metabolites including ginsenosides accumulation and their transport in cells [24, 25].