Integrated metabolomic and transcriptomic profiling reveals the tissue-specific flavonoid compositions and their biosynthesis pathways inZiziphora bungeana

Background Ziziphora bungeanaJuz. is a folk medicine from the Xinjiang Uygur Autonomous Region. The herb or the aerial parts of it have been used to medicinally treat cardiovascular diseases. Flavonoids are the main pharmacologically active ingredients inZ.bungeana. Identification of the tissue-specific distribution of flavonoids inZ.bungeanais crucial for effective and sustainable medicinal use of the plant. Furthermore, understanding of the biosynthesis pathways of these flavonoids inZ.bungeanais of great biological significance. Methods The flavonoids from different tissues ofZ. bungeanawere identified using liquid chromatography-tandem mass spectrometry (LC-MS/MS). The full-length transcriptome ofZ. bungeanawas determined using a strategy based on a combination of Illumina and PacBio sequencing techniques. The functions of differentially expressed unigenes were predicted using bioinformatics methods and further investigated by real-time quantitative PCR and phylogenetic relationship analysis. Results Among the 12 major flavonoid components identified fromZ. bungeanaextracts, linarin was the most abundant component. Nine flavonoids were identified as characteristic components of specific tissues. Transcriptome profiling and bioinformatic analysis revealed that 18 genes were putatively involved in flavonoid biosynthesis. The gene expression and phylogenetic analysis results indicated thatZbPALs,Zb4CL3,ZbCHS1, andZbCHI1may be involved in the biosynthesis of the main flavonoid intermediate.ZbFNSII,ZbANS, andZbFLSmay be involved in the biosynthesis of flavones, anthocyanins, and flavonols, respectively. A map of the biosynthesis pathways of the 12 major flavonoids inZ. bungeanais proposed. Conclusions The chemical constituent analysis revealed the compositions of 9 characteristic flavonoids in different tissues ofZ. bungeana. Linarin can be hydrolysed into acacetin to exert a pharmaceutical role. Apigenin-7-O-rutinoside is hypothesised to be the precursor of linarin inZ. bungeana. There was greater content of linarin in the aerial parts of the plant than in the whole herb, which provides a theoretical basis for using the aerial parts ofZ. bungeanafor medicine. These results provide a valuable reference for further research on the flavonoid biosynthesis pathways ofZ. bungeanaand will be significant for the effective utilisation and ecological protection ofZ. bungeana.