Zanthoxylum bungeanum (Rutaceae), a
popular food
flavoring and traditional Chinese medicine ingredient, is an important
cash crop. Its leaves are rich in flavonoids with multiple bioactivities.
However, the transcriptional sequencing has not been investigated,
and the molecular basis for the flavonoid biosynthesis remains unclear
in this plant. This paper, the key flavonoids (epicatechin, rutin,
hyperoside, trifolin, quercitrin, and afzelin) contents were determined
in the leaves of 10 Z. bungeanum varieties from a
common garden. Results show the leaves of Z. bungeanum mainly contained hyperoside (11.410–21.721 mg/g) and quercitrin
(9.401–18.016 mg/g). The total content of these key components
was the highest in Fengxian Dahongpao (66.012 mg/g) and the lowest
in Fugu (32.223 mg/g). Three varieties (Hancheng stingless, Fugu,
and Fengxian Dahongpao) with significant differences in the total
content of key flavonoids were selected for transcriptome analysis
to obtain flavonoid biosynthesis-related genes. In total, 83 522
unigenes were obtained, 40 668 (48.69%) unigenes were annotated,
and 6656 differentially expressed genes (DEGs) were identified. Comparison
of the other two varieties, Fugu had many differentially expressed
genes indicating the particularity of its variety. Flavonoid-related
DEGs of 22 structural genes, including three PALs, one CYP73A, three
4CLs, six CHSs, one CHI, one F3H, one DFR, two ANSs, one ANR, one
FLS, and two CYP75B1s, as well as nine MYBs were obtained. These structural
genes had different expression patterns in different Z. bungeanum varieties. It is worth noting that the genes expressing the flavonoid
3′5’ hydroxylase are absent in Z. bungeanum. Furthermore, quantitative real-time PCR experiment showed consistent
results in transcriptome analysis. The RNA-Seq data set of this study
sheds lights on the molecular mechanism of flavonoid biosynthesis
in Z. bungeanum, provides valuable information for
the metabolic regulation of flavonoids, and may serve as a guide for
future breeding programs.