Cynomorium songaricum is a perennial parasitic herb, and its stem is widely used as a traditional Chinese medicine, which largely relies on bioactive compounds (e.g., polysaccharides, flavonoids, and triterpenes). To date, although the optimum harvest time of stems has been demonstrated at the unearthed stage (namely the early flowering stage, EFS), the accumulation mechanism of polysaccharides and flavonoids during growth stages is still limited. In this study, the physiological characteristics (stem fresh weight, contents of soluble sugar and flavonoids, and antioxidant capacity) at four different growth stages (germination stage (GS), vegetative growth stage (VGS), EFS, and flowering stage (FS)) were determined, transcriptomics were analyzed by illumina sequencing, and expression levels of key genes were validated by qRT-PCR at the GS, VGS, and EFS. The results show that the stem biomass, soluble sugar and total flavonoids contents, and antioxidant capacity peaked at EFS compared with GS, VGS, and FS. A total of 6098 and 13,023 differentially expressed genes (DEGs) were observed at VGS and EFS vs. GS, respectively, with 367 genes co-expressed. Based on their biological functions, 109 genes were directly involved in polysaccharide and flavonoid biosynthesis as well as growth and development. The expression levels of key genes involved in polysaccharides (e.g., GLCs, XTHs and PMEs), flavonoids (e.g., 4CLLs, CYPs and UGTs), growth and development (e.g., AC58, TCPs and AP1), hormones biosynthesis and signaling (e.g., YUC8, AIPT and ACO1), and transcription factors (e.g., MYBs, bHLHs and WRKYs) were in accordance with changes of physiological characteristics. The combinational analysis of metabolites with transcriptomics provides insight into the mechanism of polysaccharide and flavonoid biosynthesis in C. songaricum during growth stages.

Cynomorium songaricum is a root holoparasitic herb that is mainly hosted in the roots of Nitraria roborowskii and Nitraria sibirica distributed in the arid desert and saline-alkaline regions. The stem of C. songaricum is widely used as a traditional Chinese medicine and applied in anti-viral, anti-obesity and anti-diabetes, which largely rely on the bioactive components including: polysaccharides, flavonoids and triterpenes. Although the differences in growth characteristics of C. songaricum between N. roborowskii and N. sibirica have been reported, the difference of the two hosts on growth and polysaccharides biosynthesis in C. songaricum as well as regulation mechanism are not limited. Here, the physiological characteristics and transcriptome of C. songaricum host in N. roborowskii (CR) and N. sibirica (CS) were conducted. The results showed that the fresh weight, soluble sugar content and antioxidant capacity on a per stem basis exhibited a 3.3-, 3.0- and 2.1-fold increase in CR compared to CS. A total of 16,921 differentially expressed genes (DEGs) were observed in CR versus CS, with 2573 characterized genes, 1725 up-regulated and 848 down-regulated. Based on biological functions, 50 DEGs were associated with polysaccharides and starch metabolism as well as their transport. The expression levels of the selected 37 genes were validated by qRT-PCR and almost consistent with their Reads Per kb per Million values. These findings would provide useful references for improving the yield and quality of C. songaricum.

Cynomorium songaricum is an important medicinal holoparasitic plant in the arid regions of northwestern China. Its extremely low seed germination rate relies on chemical signals released from the rhizosphere of specific host plants. This study aimed to elucidate the chemical basis of host recognition by C. songaricum by characterizing and comparing the rhizosphere volatile metabolomes of five host plant species. Gas chromatography–mass spectrometry (GC–MS) was used to analyze the rhizosphere volatiles of three Nitraria species (N. roborowskii, N. sibirica, N. tangutorum), Peganum multisectum, and Zygophyllum xanthoxylum. Multivariate statistical analyses, including PCA, HCA, and OPLS-DA, were employed to identify shared and differential metabolites. A total of 116 volatile compounds were identified. Alkanes were the predominant metabolite class (accounting for 46.27–76.47% in each host), and 11 C₁₁–C₁₆ alkanes were shared by all species. Notably, Z. xanthoxylon (belonging to a different family) exhibited a distinct metabolic profile, with a significantly higher proportion of benzene derivatives (35.82%) compared to the other hosts. PCA and cluster analysis revealed family/genus-specific clustering patterns, with Z. xanthoxylon forming a separate cluster. Several differential metabolites unique to Z. xanthoxylon possessed antimicrobial and stress-resistant activities. This study reveals the chemical signatures of C. songaricum host roots. The shared alkanes are proposed as potential background signals for general recognition, though this hypothetical role requires experimental validation. Family/genus-specific compounds might be involved in host selection. The unique chemical profile of Z. xanthoxylon suggests that C. songaricum may employ a flexible recognition strategy, enabling it to parasitize plants across different families. These findings provide fundamental data for understanding the chemical basis of host–parasite interactions in this species.

This study provides the first evidence, from the perspective of intra-organ metabolic division of labour, that Cynomorium songaricum adapts to the heterogeneity of desert habitats through a synergistic strategy of “stem epidermis perceiving the water environment and fleshy stem buffering soil stress.” The research found a significant spatial metabolic division within the organs of C. songaricum : the stem epidermis is enriched in various essential and functional amino acids, including threonine and serine, with their content significantly higher than in the fleshy stem. In contrast, the fleshy stem specifically accumulates proline and cysteine, showing a significant difference. Environmental driving analysis indicates that, although C. songaricum is a holoparasitic root parasite, the metabolic division within its organs is still significantly driven by differential rhizosphere soil-water environmental factors: the amino acid profile of the stem epidermis is sensitive to water environmental factors such as electrical conductivity and carbonate ions, showing a positive correlation; whereas the amino acid composition of the fleshy stem is mainly regulated by soil factors such as water-soluble salts, showing a negative correlation. This suggests that, even while relying on the host for nutrition, the metabolic characteristics of C. songaricum are still influenced by its growth micro-environment. This finding breaks through the research paradigm of treating plants as homogeneous entities, providing new insights into understanding plant ecological adaptability and offering a key scientific basis for the artificial adaptive management and comprehensive utilization of C. songaricum resources.

Only three species of Nitraria fruits are distributed in Qinghai Province, which serve as important berry resources in the desert ecosystem of Qinghai. These fruits are rich in nutrients; however, the differences in nutritional characteristics and quality evaluation among different species and fruit colors have not been systematically clarified. To explore the nutritional quality of Nitraria fruits in Qinghai, this study investigated red and purple fruits of Nitraria roborowskii , N. tangutorum , and N. sibirica . The contents of 17 amino acids and 27 mineral elements were determined, analyzed by multivariate chemometric methods, and compared with existing research results for verification. The results showed that the contents of total amino acids, essential amino acids, nonessential amino acids, and total mineral elements in N. sibirica were significantly higher than those in N. roborowskii and N. tangutorum . Among them, the proportion of essential amino acids in purple fruits of N. sibirica reached 0.22, close to the FAO ideal protein standard, and it was rich in functional mineral elements such as zinc and iron, showing high nutritional value. These results are consistent with the existing research on the nutritional specialization of desert berries. Fruit color exerted differential effects on nutritional components: nonessential amino acids and total amino acids were positively affected in red fruits, while mineral element contents were not significantly influenced by color, which agrees with studies on metabolic competition related to anthocyanin biosynthesis. Synergistic accumulation was observed between amino acids and mineral elements. Species inheritance was the dominant factor determining nutritional quality. Al, Val, Ca, V, and Cr were screened as core signature components, which improved the indicator system for the quality evaluation of Nitraria plants. Comprehensive evaluation demonstrated that N. sibirica possessed the best overall nutritional quality, and red fruits were generally superior to purple fruits, with purple fruits of N. sibirica exhibiting the optimal nutritional quality. The results of this study provide a theoretical basis for the precise development of Nitraria germplasm resources in Qinghai, the breeding of superior genotypes, and the research and development of distinctive functional foods from desert plants.