Comparative transcriptome analysis of three chrysanthemums provides insights into flavonoid and terpenoid biosynthesis

Chrysanthemum indicum var. aromaticum is an important resource plant for breeding excellent aromatic varieties of ornamental and medicinal chrysanthemums. However, the biosynthesis and regulation mechanisms of typically aromatic ingredients in C. indicum var. aromaticum are poorly understood, which restricted the utilization of this plant. Here, the transcriptome of C. indicum var. aromaticum was investigated and comparative analysis was conducted with the other two closely related chrysanthemum taxa C. indicum and C. nankingense. The global transcriptome profiles showed clear difference of gene expression patterns between the three chrysanthemums, of which 52 flavonoid biosynthesis-associated genes, 157 transcription factors, and 24 flavonoid Uridine diphosphate (UDP) -glucuronosyl and -glucosyltransferase genes were significantly differentially expressed. Furthermore, 22 differential expression genes (DEGs) in relation to the terpenoid backbone biosynthesis and 183 DEGs related to terpenoid diversification were identified. Of which, 14 genes involved into TS/CYP gene cluster showed higher expression in CIA than those in CI or CN. These results increased our understanding of flavonoid diversification and aromatic ingredients accumulation in plants, and will also help improve resource conservation and sustainable utilization of the important resource plant C. indicum var. aromaticum.