Objective:Why are different medicinal parts including heads,bodies and tails of Angelicae Sinensis Radix (ASR) distinct in pharmaceutical activities? Here we explored their discrepancy in chemical constituents and transcriptome.Methods:ASR were separated into three medicinal parts:heads (rootstocks with petiole traces of ASR),bodies (taproots of ASR) and tails (lateral lots of ASR),and chemical and transcriptomic analyses were conducted simultaneously.Results:High performance liquid chromatography (HPLC) fingerprint results showed that five widely used active ingredients (ferulic acid,senkyunolide H,senlyunolide A,n-butylphathlide,and ligustilide) were distributed unevenly in the three ASR medicinal parts.Partial least squares-discriminant analysis (PLS-DA)demonstrated that the heads can be differentiated from the two other root parts due to different amounts of the main components.However,the content of ferulic acid (a main quality marker) was significantly higher in tails than in the heads and bodies.The transcriptome analysis found that 25,062,10,148 and 29,504 unigenes were specifically expressed in the heads,bodies and tails,respectively.WGCNA analysis identified 17 co-expression modules,which were constructed from the 19,198 genes in the nine samples of ASR.Additionally,we identified 28 unigenes involved in two phenylpropanoid biosynthesis (PB) pathways about ferulic acid metabolism pathways,of which 17 unigenes (60.7％) in the PB pathway were highly expressed in the tails.The expression levels of PAL,C3H,and CQT transcripts were significantly higher in the tails than in other root parts.RT-qPCR analysis confirmed that PAL,C3H,and CQT genes were predominantly expressed in the tail parts,especially PAL,whose expression was more than doubled as compared with that in other root parts.Conclusion:Chemical and transcriptomic analyses revealed the distribution contents and pivotal transcripts of the ferulic acid biosynthesis-related pathways.The spatial gene expression patt partially explained the discrepancy of integral medicinal activities of three medicinal root parts.