Artemisinin is found in the traditional Chinese herbal plant Artemisia annua and is used for the treatment of malaria.However,little is known about the mechanism of transcriptional regulation in plants after MeJA and light treatment.To investigate the mechanism,Illumina HiSeq? 2000 sequencing platform was employed.We produced 266,687,896 clean reads,assembled into 185,653 unigenes,with an average length of 537 bp and N50 of 703 bp.Among these 185,653 unigenes,59,490 unigenes(32.04%)were annotated based on the information available from the public databases.Differential gene expression analysis revealed a clear difference in gene expression pattern,identifying 41362 differentially expressed unigenes between Light and Dark,36889 differentially expressed unigenes between Light and Light-MeJA-4h,42937 differentially expressed unigenes between Dark and Dark-MeJA-4h,respectively.Transcription factor(TF)analysis identified 53 TF families,with 285 TFs down-regulated in the Dark relative to Light and 96 TFs were up-regulated in the Light-MeJA-4h relative to Light.A total of 9 TFs were identified as candidates for regulating the artemisinin biosynthesis and we validate one of the candidate TFs by dual luciferase(dual-LUC)assay.These data offer an overview of the gene expression pattern after the MeJA and Light treatment and provide essential information for future studies on the molecular mechanisms of controlling artemisinin biosynthesis.