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. 2025 May 3;15(1):15507.
doi: 10.1038/s41598-025-00445-0.

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

Yanhong Li #  1   2 , Shengyan Wang #  3 , Qing Zhao  1   2 , Qian Wang  1   2 , Zufan Yang  1   2 , Qiangqiang Jia  4   5
Affiliations

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

Yanhong Li et al. Sci Rep. .

Abstract

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.

Keywords: Nitraria berries; Anthocyanins; Flavonoids; Metabolomics; Transcriptomics.

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Conflict of interest statement

Declarations. Competing interests: The authors declare no competing interests.

Figures

Fig. 1
Fig. 1
Morphological features of (A) N. tangutorum Bor. (NT), (B) N. sibirica. (NS), (C) N. roborowskii. (NR).
Fig. 2
Fig. 2
The PCA score plot compars metabolic profiles of NR, NT and NS (A), the number of up-regulated and down-regulated DMs (B), Metabolic pathway enrichment analysis of DMs across three Nitraria species berries (C). (a) Anthocyanin biosynthesis, (b) Flavone and flavonol biosynthesis, (c) Fatty acid biosynthesis.
Fig. 3
Fig. 3
Content of partial differential metabolite in NR, NT and NS (*p < 0.05, **p < 0.01).
Fig. 4
Fig. 4
The PCA score plot of the transcriptome of NR, NT and NS (A), Volcano plots to filter the DEGs of berries in different species groups (B), The KEGG enrichment analysis and functional classification of DEGs in different species groups (C). KEGG primary classification results of DEGs (a), secondary classification results of DEGs enriched into “metabolic” category (b), tertiary classification results of DEGs enriched into pathways (c).
Fig. 5
Fig. 5
Flavonoid biosynthetic structural genes of DEGs and DMs in different species groups. According to log10(FC): red means up, blue means down.
See this image and copyright information in PMC

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