BackgroundThe rhizome of Ligusticum chuanxiong is a well-known traditional Chinese medicine. The major bioactive compounds found in Ligusticum chuanxiong are Ferulic Acid with 4- hydroxyl -3- methoxybenzene acrylic acid. However, the epigenetic mechanisms and biosynthetic pathways of active metabolites based on the transcriptomic analysis of Ligusticum chuanxiong rhizome have remained unclear. To clarify the key genes in rhizome formation and active metabolite synthesis pathways of Rhizome of Ligusticum chuanxiong, we focus on the change between the investigate the rhizome and leaf of Ligusticum chuanxiong through transcriptomic analysis.MethodsThe RNA extracted from rhizomes and leaves of Ligusticum chuanxiong were sequenced using the Illumina platform, yielding 295,725 unique transcripts with N50 of 778 bp. The transcripts against annotation databases including GO (Gene Ontology) and KEGG (Kyoto Encyclopedia of Genes and Genomes) to identify differentially expressed genes (DEGs).Resultsystematic analysis of transcriptome profiles revealed that a total of 1707 differentially expressed unigenes were found in the two tissues, among which 1246 were down-regulated and 462 were up-regulated. Remarkably, some DEGs are enriched in the biosynthetic pathway of phenylalanine ammonia lyase, one of the key enzymes in the pathway of ferulic acid synthesis.ConclusionsThrough the transcriptome analysis, we have identified the regulatory mechanisms and epigenetic influences in the secondary metabolic biosynthetic pathway of Ligusticum chuanxiong. Among them, DEGs analysis revealed ferulic acid and other secondary metabolites are some of the major products in the biosynthetic pathway of Ligusticum chuanxiong.