transcriptomic analysis of american ginseng seeds during the dormancy release process by rnaseq american ginseng panax quinquefolius l is an important herb that is cultivated in china north american and south korea it is propagated from seed but the seed has deep dormancy characteristics described as morphophysiological dormancy twostage temperature stratification a warm 1520c and cold 2c stratification period of 6 months has been used successfully for seed dormancy release however little is known about the molecular mechanisms of seed dormancy release in the stratification process in this study seed development after pollination and seed development in the dormancy release process were investigated in american ginseng the transcriptome during seed dormancy release was analyzed using rnaseq technology and 78207 unigenes mean length 531 bp were generated based on similarity searches of public databases 54292 of the unigenes 694 were functionally annotated further three digital gene expression dge libraries were sequenced and differences in gene expression at three stages during seed cold stratification were examined the greatest number of differentially expressed genes occurred in the 90dcs versus 180dcs libraries while the lowest number of differentially expressed genes occurred in the 135dcs verus 180dcs libraries go enrichment analysis revealed that 59 29 and 39 go terms were significantly enriched in the biological process molecular function and cell component go categories respectively there were 25190 genes with kegg pathway annotation in the three dge libraries and their enrichment pathways were compared the gene expressions of 30 selected unigenes were validated using quantitative pcr this study is the first to provide the transcriptome sequences for seed dormancy release in american ginseng and demonstrates the successful use of dge profiling data for analyzing transcriptomic variation during dormancy release these data provide a basis for future researches of seed dormancy in morphophysiological dormancy seeds in nonmodel plants