## 2 Results and Discussion
### Discussion
Among two kinds of unigenes, some having 70% similarity among them, are under one cluster (CL) initiated with “CL” along with the same number such as “CL1490”, followed by different number of contigs, whereas others start directly with “Unigene” such as “Unigene12975”. \(\blacktriangle\) indicates the unigenes from our current study. The box in red outline indicates one group of genes that are more similar with each other. 71,095 all-unigenes were annotated with five above mentioned main databases (Table S11). Furthermore, the Trinity assembly algorithm designed specifically for assembling of putative transcripts has also given us biologically significant results of high confidence. More recent works obtained similar advantages to the use of the Illumina HiSeq(tm)2000 platform in the assembly of a transcriptome for untreated _P. ginseng_ adventitious roots and _Lentinual eododes_ C91-3 respectively [14,54]. More importantly, stimulation of ginseng synthesis by MeJA is performed by the up-regulation of genes including _SS_, _SE_, and _DDS_ involved in ginseng biosynthesis [37,62]. Although many candidate genes related to ginseng biosynthesis have previously been identified both in untreated and MeJA treated _P. ginseng_, several genes encoding ginseng biosynthetic enzymes such as _MVK_, _GPS_, _\(\beta\)-_AS_ and _DDS_ were not found [10,34]. For example, DDS thought to be a rate-limiting and the first enzyme in the biosynthetic pathway of dammarane-type saponins was absent in the 454 EST dataset of untreated _P. ginseng_ roots [34]. Some recent works have discovered only one unigene from 4-year-old untreated _P. ginseng_[15] and three unigenes from American ginseng roots [17] based on the 454 pyrosequencing method. In another case, only two up-regulated _SS_ candidates were found from the same year-old MeJA-treated _P. ginseng_ hairy roots via the traditional Sanger EST analyses [10]. However, we have obtained 10 up-regulated _SS_ unigenes from our dataset. Moreover, nearly all types of major ginseng biosynthetic enzyme genes were discovered in the transcriptome of our MeJA-treated _P. ginseng_ adventitious roots (mentioned above). Based on comparison, the findings indicate that the information of this study is relatively comprehensive and highlights the immense capacity of both MeJA and Illumina/Solexa technology. On the other hand, only a few ABC transporters have been identified in medicinal plants related to ginsengides and transport of other secondary metabolites. Moreover, several MeJA-induced plant PDRs have been discovered associated with defense reactions against pests, pathogens and herbivores by transporting antimicrobial natural secondary metabolites in cells [63,64,65]. Based on the knowledge that secondary metabolites can be induced by MeJA, the identified 12 potential candidate _PDR_ unigenes from our study through phylogenetic analysis will provide more important functions related to the transport of various substrates including secondary metabolites and their transport in cells. Moreover, the annotated unigenes and associated resources from our work provide valuable information for _P. ginseng_ adventitious roots to investigate specific processes and allow the identification of novel genes related to ginsengides and other secondary metabolites biosynthesis, their accumulation, as well as transport, that are responsive to MeJA treatment.