Differential transcriptome analysis of genes associated with the rhizome growth and sesquiterpene biosynthesis in Atractylodes macrocephala

[Display omitted] •Atractylodes III mainly accumulated in the underground parts of Atractylodes macrocephala.•Transcriptome sequencing of five different tissues of A. macrocephala were performed.•EF-1α was the best reference gene for tissue expression pattern analysis in A. macrocephala.•14 transcription factors predominantly expressed in the rhizomes of A. macrocephala.•AmFPPS was verified to catalyze the biosynthesis of sesquiterpene in A. macrocephala. The rhizome of Atractylodes macrocephala is a kind of traditional Chinese medicine containing a variety of sesquiterpenoids and has a wide range of bioactivities. Due to the lack of genetic information, the rhizome growth and sesquiterpene biosynthesis in A. macrocephala are basically unknown. In this study, the metabolic analysis and transcriptome sequencing of five different tissues (rhizomes, roots, stems, leaves and buds) of A. macrocephala were performed. Over 97.08 Gb clean data obtained from fifteen sequencing samples were assembled into 144,137 unigenes. Transcription factor (TF) analysis revealed that 14 TFs predominantly expressed in the rhizomes might be involved in the regulation of rhizome growth and sesquiterpene biosynthesis. A total of 73 unigenes and 287 CYP450s were annotated to sesquiterpene biosynthesis, and AmFPPS was verified to catalyze the biosynthesis of sesquiterpene. EF-1α was the best reference gene for tissue expression pattern analysis in A. macrocephala by comparing the expression of reference genes in five tissues. Thus, extensive transcriptome data from this work offered a comprehensive transcriptional expression pattern in different tissues of A. macrocephala, which will provide a more valuable resource for further research on molecular mechanisms of the growth and development of rhizome, and the biosynthesis and regulation sesquiterpenes.