## 2 Results and Discussion
### Discussion  
Transcriptome sequencing is one of the most effective tools for gene identification. Understanding the transcriptome analysis is essential to know which genes are expressed at various developmental stages or physiological conditions of a cell. Plant genomics, especially for non-model species, is always hard due to its large and complex genome, high levels of ploidy and large proportions of repeat sequences. Instead of the whole genome sequencing, transcriptome sequencing is a better alternative for rapid and efficient access to genetic information [48]. High-throughput Illumina/Solexa sequencing technology has recently been an efficient, fast, inexpensive and reliable tool for transcriptome characterization and gene discovery in non-model organisms as well. Previously, a number of ESTs were generated from leaves, seeds, rhizomes and roots of _P. ginseng_ by the Sanger sequencing technology [11, 12, 49, 50]. However, deep EST sequencing using this traditional method is highly expensive, labor intensive and time-consuming. Therefore, with the development of large scale genomics, the Sanger method could not meet the needs of the development. However, over the past few years, the NGS technologies have overcome the current limitations of the Sanger method and at the same time, the NGS platform has become the prime approach for high-throughput gene discovery on a genome-wide scale both for model and non-model organisms. These technologies can produce a large number of quality reads with high sampling rates of cDNA libraries providing a complete view of transcriptomes. Thus, plant genomics in recent years has developed rapidly with the application of various NGS technologies with respect to costs, efficiency and speed compared with that of the traditional Sanger method. Hence, over the past several years, these technologies have made a revolution in genomics and provided a rapid and economic way to sequence extremely large amounts of genetic material [51, 52]. Among NGS technologies, the Illumina/Solexa platform has been one of the most useful and widely used technologies due to its fast, inexpensive, accurate, efficient and reliable transcriptome characterization, gene discovery and various functional studies in many organisms [53]. Using this technology, comprehensive sequencing resources have been successfully constructed from non-model plants including _P. ginseng_[14], _Lentinula edodes_[54] and _Auriculara polytricha_[55]. However, transcriptome assembly was highly challenging including mis-assembled contigs [56]. Recently, \"Trinity\", [26] a novel assembly method has been introduced most notably through an expand capability for transcriptome _de novo_ assembly using relatively short reads. The results from this study suggested that short reads from Illumina/Solexa sequencing can effectively be assembled through \"Trinity\" giving the advantage of a high assurance and reliable assembly of putative unigenes, including potential and valuable splice variant information. Therefore, _de novo_ sequencing and assembly of transcriptomes or genomes has effectively been utilized for model [57, 58] and non-model organisms [59, 60, 61]. Despite the commercial and medicinal values of _P. ginseng_, NGS-based MeJA-elicited transcriptome information on this species in public databases was scarce prior to our study. In our work, Illumina/Solexa sequencing technology was applied to perform this work. Compared to the Sanger method, this technology provides a large amount of genetic resources in a fast, efficient and economic way. Through this program, we obtained about 55 millions raw reads separately from Pg-Con and Pg-MeJA and subsequently 53 millions clean reads from each sample. Finally, all of these clean reads assembled into  
Figure 9: Phylogenetic analysis of 12 potential _PDR_ unigenes of our dataset and other plant _PDRs_.