Comparative transcriptomic and metabolomic profiling of forest tea and terrace tea in Sandu, Guizhou, China

Ancient forest tea is locally valued in Guizhou, but the transcriptomic and metabolomic differences associated with forest and terrace tea cultivation systems remain unclear. We conducted an exploratory integrated transcriptomic and untargeted metabolomic comparison across three shoot types (single buds, one-bud-one-leaf, and one-bud-two-leaves). Transcriptomic analysis showed the largest number of DEGs at the one-bud-two-leaves stage, suggesting substantial transcriptional variation under the present sampling conditions. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analyses indicated that phenylpropanoid and flavonoid biosynthesis pathways were over-represented. Untargeted liquid chromatography-mass spectrometry (LC–MS) detected 864 differential metabolite features with Metabolomics Standards Initiative (MSI) Level 2 putative annotations, including 374 features with higher relative abundance in forest tea. The largest number of differential metabolite features occurred at the one-bud-one-leaf stage, and these features were enriched in flavonoid biosynthesis. Variable importance in projection (VIP) ranking prioritized discriminant features from false discovery rate (FDR)-filtered data, including four MSI Level 2 features putatively annotated as polyphenol-related compounds that showed higher relative abundance in forest tea. In addition, the expression of genes encoding phenylalanine ammonia-lyase (PAL), a key enzyme in the phenylpropanoid biosynthesis pathway, differed significantly between forest tea and terrace tea. These results suggest that secondary-metabolism-related pathways are associated with molecular differentiation between forest and terrace tea. Because this study lacked sensory evaluation, targeted metabolite quantification, and functional validation, these findings require future validation. This work provides candidate pathways and metabolite features for future validation of tea quality differences.