To investigate the expression level of the assembled transcripts, we determined the RPKM value for each transcript. According to GO categorization of the resulting 100 most abundant transcripts, stress response-related transcripts were the most highly expressed categories in the adventitious roots (Fig. 3 and Fig. 4). Consistent with our results, stress

proteins have also been reported to be highly expressed in calli of other plant species [44] and [45]. Furthermore, proteomic analysis PD-0332991 chemical structure of ginseng hairy roots revealed that stress response-related proteins are the mostly highly expressed [46]. In normal ginseng plants, stress-responsive proteins are induced to high levels upon exposure to abiotic and biotic stresses [47] and [48]. Therefore, our results strongly suggest that in vitro culture conditions represent a stress on adventitious roots of ginseng plants, with stress response-related transcripts induced to protect cells from harmful conditions. Although MAPK Inhibitor Library research buy two cultivars showed different characteristics in adventitious root culture (Fig. 1), no significant difference of transcriptome profile was found between two cultivars. GO assignments and gene

expression showed almost similar patterns between both cultivars (Fig. 2, Fig. 3, Fig. 4, Fig. 5 and Fig. 6, Table 2 and Table 3). Further comparative transcriptomics will be necessary to identify which gene makes a difference in adventitious root growth. Ten transcripts encoding enzymes involved in ginsenoside biosynthesis were also identified through similarity searches with reported genes. old Most of the ginsenoside biosynthesis transcripts were highly expressed

in both cultivars, including transcripts for dammarenediol synthase or β-amyrin synthase, which catalyze the rate-limiting step for ginsenoside biosynthesis [49] and [50] (Fig. 5). This implies that the content and composition of ginsenosides may not be different between the cultivars under in vitro culture conditions. In addition, 21 transcripts related to UGT proteins were identified in the datasets of both cultivars ( Fig. 6). Among those, three transcripts were closely related to MtUGT73K1, MtUGT71G1, and SvUGT74M1, which function in triterpene saponin biosynthesis. Therefore, these transcripts most likely encode UGTs involved in the last step of ginsenoside biosynthesis in P. ginseng. Simultaneous analysis of metabolite profiles and the transcriptome may promote in-depth understanding of the ginsenoside biosynthesis pathway. Through a comparative analysis of the transcriptomes of adventitious and normal ginseng roots, more than 6,000 transcripts were identified to be unique to adventitious or normal roots, whose functional differences were characterized using GO analysis (Fig. 7).