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.

白术的根茎是一种含有多种倍半萜类化合物的中药，具有广泛的生物活性。由于缺乏遗传信息，A. macrocephala的根茎生长和倍半萜生物合成基本未知。本研究对大头蒺藜五种不同组织（根茎、根、茎、叶和芽）的代谢分析和转录组测序进行了。从 15 个测序样本中获得的超过 97.08 Gb 的干净数据被组装到 144,137 个 unigenes 中。转录因子（TF）分析表明，主要在根茎中表达的 14 个转录因子可能参与了根茎生长和倍半萜生物合成的调控。共有 73 个 unigenes 和 287 个 CYP450s 被注释到倍半萜烯的生物合成，并验证了 AmFPPS 催化倍半萜烯的生物合成。通过比较五种组织中参考基因的表达情况，EF-1α是A. macrocephala组织表达模式分析的最佳参考基因。因此，来自这项工作的大量转录组数据提供了A. macrocephala不同组织中的综合转录表达模式，这将为进一步研究根茎生长发育的分子机制以及倍半萜的生物合成和调控提供更有价值的资源。