LAUSR

Abstract Essential oil content is the major component of Cinnamomum cassia Presl quality. In this research, an analysis of transcriptome and metabolite profiles between Cinnamomum cassia Presl (CK) and Cinnamomum cassia Presl var. macrophyllum Chu (Var) was performed to investigate the molecular mechanisms underlying the difference of active components content in the barks, branches, and leaves. Results revealed that higher contents of flavonoids were present in the barks, branches, and leaves of Var, and higher levels of cinnamaldehyde and coumarine were present in the barks of Var, but lower in the leaves when compared with CK. Transcriptome analysis revealed that genes related to photosynthesis and flavonoid biosynthesis were upregulated in Var relative to CK. Differences in essential oil contents between the two varieties could be attributed to the differential expression of genes related to the two branches of the phenylpropanoid metabolic pathway, i.e., one controls flavonoid metabolism and was highly active in Var, whereas the other regulates the synthesis of cinnamaldehyde and coumarine and was only upregulated in the barks of Var, but downregulated in the leaves. The findings of this study provide insights into the mechanism behind the phenylpropanoid metabolic pathway of Cinnamomum cassia Presl.