Integrating metabolomics and transcriptomics comprehensively reveals the global metabolic differences in three species of Nitraria berries.

Nitraria berry, a traditional Chinese medicine, is harvested when ripe and then dried in the sun as medicine. Three species of Nitraria have attracted more attention in the pharmaceutical field: Nitraria tangutorum Bobr. (NT), Nitraria sibirica Pall. (NS) and Nitraria roborowskii Kom. (NR). However, the differences in chemical composition and the corresponding metabolic mechanisms of the three species of berries has not been reported. This study combined metabolomics and transcriptomics to explore the differences among three species of Nitraria berries. The results indicate that different metabolites (DMs) and different expressed genes (DEGs) are mainly enriched in the biosynthetic pathways of anthocyanins and flavonoids. 4 petunidins and 2 isorhamnetins were significantly accumulated in the NR, while 4 cyanidins and 3 kaempferols were significantly accumulated in the NS and NT. The transcriptomics results show that the biosynthesis of flavonoids (including anthocyanins) in Nitraria berry may be regulated by 10 structure genes, including 5 PAL, 2 4CL, CHI, 2 F3'H. Based on this, a network metabolic map for flavonoids was constructed, and a correlation analysis was performed between major DMs and DEGs. Overall, this study provides the theoretical basis and development suggestions for the comprehensive utilization and in-depth development of Nitraria berries.