Integrated transcriptome and metabolome provide insight into phenolics and soluble sugar variation in the different varieties of Gastrodia elata Blume from different areas in China.

Gastrodia elata Blume is known for its "medicinal food homology", its chemical components include phenols, glycosides and polysaccharides. In China, the Anhui, Hubei, Guizhou, and Yunnan provinces are the primary G. elata-producing areas, among which Gastrodia elata Bl. f. elata (GR), Gastrodia elata Bl. f. glauca S. Chow (GB), and Gastrodia elata Bl. f. glauca S. Chow and Gastrodia elata Bl. f. elata (GR×GB) are essential varieties. This research employed metabolomics and Ultra Performance Liquid Chromatography (UPLC) to quantify 19 soluble sugars and six phenolic compounds in G. elata from various origins and varieties. Transcriptome sequencing was performed on 24 G. elata samples to identify differentially expressed genes (DEGs). Key enzyme genes involved in the phenolic biosynthesis pathways were further analyzed through phylogenetic analysis, structural modeling and molecular docking. Sucrose, glucose, D-fructose, and D-xylose were identified as the major soluble sugar components in G. elata. The phenolic content of the same variety exhibited significant regional differences. In the GR, the largest number of differentially expressed genes (DEGs) was identified in the AH-GR vs. GZ-GR comparison (4,866). In addition, 96 genes encoded 11 key enzymes in the phenolic biosynthesis pathways. In the phenolic synthesis pathway, we identified several alcohol dehydrogenase (ADH) and glucosyltransferase (GT) genes at the downstream level that potentially contribute to the variation in phenolic metabolism. Phylogenetic, structural modeling, and molecular docking analyses suggested that six GTs catalyze the production of gastrodin from p-hydroxybenzyl alcohol. This study provides a fundamental theoretical basis and data support for the selective breeding of G. elata varieties and aids in elucidating the regulatory mechanisms of phenolic active compounds.