Transcript expression profiling for adventitious roots of Panax ginseng Meyer

•Transcriptome generated from MeJA elicited in in-vitro grown adventitious roots.•De novo transcriptome assembly achieved for 22 public and in house libraries.•Candidates for putative ginsenoside pathway were predicted validated by qRT-PCR.

Panax ginseng Meyer is one of the major medicinal plants in oriental countries belonging to the Araliaceae family which are the primary source for ginsenosides. However, very few genes were characterized for ginsenoside pathway, due to the limited genome information. Through this study, we obtained a comprehensive transcriptome from adventitious roots, which were treated with methyl jasmonic acids for different time points (control, 2 h, 6 h, 12 h, and 24 h) and sequenced by RNA 454 pyrosequencing technology. Reference transcriptome 39,304,529 (0.04 GB) was obtained from 5,724,987,880 bases (5.7 GB) of 22 libraries by de novo assembly and 35,266 (58.5%) transcripts were annotated with biological schemas (GO and KEGG). The digital gene expression patterns were obtained from in vitro grown adventitious root sequences which mapped to reference, from that, 3813 (6.3%) unique transcripts were involved in ≥ 2 fold up and downregulations. Finally, candidates for ginsenoside pathway genes were predicted from observed expression patterns. Among them, 30 transcription factors, 20 cytochromes, and 11 glycosyl transferases were predicted as ginsenoside candidates. These data can remarkably expand the existing transcriptome resources of Panax, especially to predict existence of gene networks in P. ginseng. The entity of the data provides a valuable platform to reveal more on secondary metabolism and abiotic stresses from P. ginseng in vitro grown adventitious roots.