Abstract:In order to understand the gene information of flavonoids and their synthase in Cymbopogon citratu, the metabolome, transcriptome and qRT-PCR were studied by using young leaves of C. citratu growing in sunlight and shade. The results showed that C. citratus contained 69 flavonoids belonging to 11 kinds. The contents of flavonoids, such as rutin, demethyltorosaflavone, astragalin and glucosylorobol etc., decreased under shade environment. The flavonoid biosynthesis involved 10 kinds of enzymes encoded by 54 genes. The expressions of 4 genes, such as F3'H (c99177.1), decreased significantly under shade environment, while those of 6 genes, such as FSI (c51975.0) etc., were opposite. The up-or down-regulation expression trend of 5 flavonoid synthase genes under light and shading was consistent with the change of FPKM in transcriptome sequencing, however, there was difference in the differential expression multiples between the two methods. Therefore, Shading could decrease the relative content of flavonoid in C. citratus, but the relative expression of synthetase genes was irregular whether up or down regulation.