Supplementary file 1_Research on the epigenetic alterations in Atractylodes macrocephala and the synergistic regulatory mechanism of “soil environment-rhizosphere microbes” on its secondary metabolism.docx

However, existing research has primarily focused on its germplasm resources and medicinal properties, while studies on the interaction mechanisms between secondary metabolism and rhizosphere soil environmental factors remain insufficient.</p>Methods<p>This study investigated four Atractylodes macrocephala of quality grades, systematically compared their secondary metabolic pathways and rhizosphere soil environmental factors based on epigenetic variation assessments, and explored the intrinsic relationships between them using multidimensional statistical methods.</p>Results<p>The results revealed that cultivated Atractylodes macrocephala modulates DNA methylation patterns to adapt to environmental changes, exhibiting rich epigenetic diversity.

Additionally, significant differences are observed in the secondary metabolic pathways of phenylpropanoids, isoflavonoids, and flavonoids. Soil nitrogen nutrition and pH value were identified as key environmental driving forces, with efficient nitrogen transformation and weakly acidic conditions being more favorable for Atractylodes macrocephala cultivation. Rhizosphere fungi serve as key microbial regulators, influencing secondary metabolism through energy pathways (b-oxidation, glycolysis, glyoxylate cycle), cofactor production (ubiquinone, heme), and amino acid and lipid metabolism (nutrient supply, release of phosphatidic acid and ROS).</p>Discussion<p>In contrast, bacteria mainly support soil iron nutrition, pollutant degradation, and pathogen infectivity modulation via virulence actor release.