Ampelopsis megalophylla is an important species used in Chinese folk medicine. Flavonoids, the most important active components of plants, greatly determine the quality of A. megalophylla. However, biosynthesis of flavonoids at the molecular and genetic levels in A. megalophylla is not well understood. In this study, we performed chemical analysis and transcriptome analysis of A. megalophylla in different seasons (i.e., May, August, and October). Accumulation of flavonoids was higher in May than in the other two months. Genes involved in the flavonoid biosynthesis pathway, such as chalcone synthase, anthocyanidin synthase, flavanone 3-hydroxylase, flavonoid-3′,5′-hydroxylase, caffeoyl-CoA O-methyltransferase, dihydroflavonol 4-reductase, 4-coumarate-CoA ligase, phenylalanine ammonia-lyase, cinnamate 4-hydroxylase, flavonoid 3′-monooxygenase, shikimate O-hydroxycinnamoyltransferase, and leucoanthocyanidin reductase, were identified based on transcriptome data. Fifty ATP binding cassette (ABC) transporter, nine SNARE, forty-nine GST, and eighty-four glycosyltransferases unigenes related to flavonoid transport and biomodification were also found. Moreover, seventy-eight cytochrome P450s and multiple transcription factors (five MYB, two bHLH, and three WD40 family genes) may be associated with the regulation of the flavonoid biosynthesis process. These results provide insights into the molecular processes of flavonoid biosynthesis in A. megalophylla and offer a significant resource for the application of genetic engineering in developing varieties with improved quality.

Artemisia argyi Levl. et Van (A. argyi) is a traditional medicinal plant, which is widely used in health, food and medicine. Thujone is an important cyclic monoterpene derivative in the volatile oil of A. argyi leaves with multiple efficacy. Although the thujone synthetic pathway has been preliminarily analyzed in very few species, genes related to the thujone content in A. argyi leaves remain largely unknown. In this study, we identify candidate genes involved in the synthesis and regulation of thujone content in A. argyi leaves by the comparative transcriptome analysis of two group materials with high and low thujone content. A total of 89 candidate genes related to thujone content are identified including one gene involved in the mevalonate pathway, three genes involved in the methylerythritol phosphate pathway, 19 genes involved in the metabolic process from geranyl pyrophosphate to thujone (four b-terpene synthase, five cytochrome P450, five dehydrogenase, and five reductase-encoding genes) and 66 transcription factor-encoding genes. Taken together, our results provide valuable gene resources for further analyzing the synthetic and regulatory pathway of thujone in A. argyi.