Multi-omics integration uncovers mechanisms of chromium tolerance in Cosmos sulphureus

Chromium (Cr) is a highly toxic, mobile heavy metal pollutant that is easily taken up by plants, whereas the Cr tolerance and molecular mechanisms underlying Cr stress responses in C. sulphureus remain poorly elucidated. In this study, we comprehensively investigated phenotypic, physiological, transcriptomic, and metabolomic alterations to uncover the potential molecular mechanisms governing Cr tolerance in C. sulphureus. Phenotypic and photosynthetic physiology results showed that seedlings exposed to low concentrations of Cr exhibited normal leaf and root growth, accompanied by significantly increased chlorophyll content and root vitality; while high Cr exposure exerted the opposite inhibitory effects. Additionally, high Cr stress markedly elevated Cr accumulation and decreased enrichment coefficient in seedlings, with roots displaying a more prominent increase than other tissues. Physiological assessments indicated that the accumulation of reactive oxygen species (ROS), malondialdehyde (MDA) levels, and antioxidant capacity exhibited distinct tissue-specific differences and concentration-dependent variations under Cr stress. Transcriptomic analysis identified 16259 differentially expressed genes (DEGs) under low Cr stress and 19946 DEGs under high Cr stress. Metabolomic profiling detected 1524 differentially accumulated metabolites (DAMs) under low Cr stress and 1591 DAMs under high Cr stress. The integrated transcriptome and metabolome analysis indicates that flavonoid biosynthesis and glutathione metabolism may be potential regulatory pathways mediating Cr stress responses. Collectively, our findings demonstrate that roots serve as the primary tissue for Cr accumulation in C. sulphureus. By coordinating with other plant tissues, they modulate oxidative stress homeostasis, transcriptional reprogramming and metabolic remodeling to mount systematic defenses against Cr toxicity.