Transcriptome–Metabolome Combined Analysis of Central Carbon Metabolites in Anoectochilus roxburghii (Wall.) Lindl. Under Salt Stress

Background: Anoectochilus roxburghii (Wall.) Lindl. is an endangered medicinal herb, and salt stress has been reported to promote the accumulation of bioactive secondary metabolites. Central carbon metabolism plays a key role in carbon allocation in plants; however, the integrated molecular and metabolic responses of A. roxburghii to salt stress remain largely unclear. Method: In this study, an integrated transcriptomic and metabolomic approach was employed to investigate the reprogramming of central carbon metabolism in A. roxburghii under 50, 100, and 200 mM NaCl treatments. Results: Metabolomic analysis revealed a significant accumulation of soluble sugars, which suggests enhanced osmotic adjustment and alteration in energy metabolism. Transcriptomic profiling identified 7019 upregulated and 5192 downregulated DEGs, with pathways related to the TCA cycle, galactose metabolism, and fructose/mannose metabolism predominantly upregulated, while oxidative phosphorylation was suppressed. Integrative transcriptome–metabolome profiling further identified key genes associated with oxaloacetate and fructose-6-phosphate, suggesting a coordinated regulation between central carbon metabolism and polysaccharide biosynthesis. Conclusions: Collectively, these findings demonstrate that salt stress induces coordinated metabolic and transcriptional reprogramming in A. roxburghii, driving carbon flux reallocation from growth-related processes toward osmoprotective metabolism. This provides a mechanistic basis for the enhancement of bioactive compounds under moderate stress and offers insights for improving both salt tolerance and medicinal quality in saline environments.