Comparative Transcriptome Analysis to Identify Candidate Genes Related to Chlorogenic Acid and Flavonoids Biosynthesis in Iridaceae

Abstract

Iris (Iridaceae) is one of the most widely admired ornamental plants. It has been used mainly in medicine due to the high concentration of chlorogenic acid (CGA), flavonoids, isoflavones, lignans, and other compounds in its rhizomes. In iris, the gene functions related to CGA and flavonoids biosynthesis are still unclear. In this study, we compared the I. germanica rhizome with a high accumulation level of CGA but a low accumulation level of flavonoids, and the I. pallida rhizome with a low accumulation level of CGA but a high accumulation level of flavonoids at the transcriptome and metabolome levels. A total of 761 metabolites were detected, including 202 flavonoids and 106 phenolic acids based on metabolome profiling. In total, 135 flavonoids were highly accumulated in I. pallida, including three flavanols, 51 flavonoids, 12 flavonoid carbonosides, 31 flavonols, and 21 isoflavones. Based on single-molecule long-read sequencing technology, 94,461 transcripts were identified in iris. Expression analysis indicated that the high accumulation level of C4H and 4CL in I. germanica were essential for CGA accumulation, while CHS, DFR, ANS, ANR, LAR, and 3GT were essential for flavonoids biosynthesis in I. pallida. Many transcription factors such as transcript_83288 (MYB), transcript_57970 (WRKY), and transcript_77465 (WRKY) act as regulators, playing important roles in these biological processes. Our findings provide new insights into the molecular mechanisms associated with the biosynthesis and regulation of flavonoids and CGA in the iris rhizome, and highlight the usefulness of an integrated approach for understanding this process.