Developmental-envelope screening and genome-annotation audit prioritize chemical authenticity candidates in commercial Rubus chingii fruit

Commercial dried Rubus chingii (Chinese raspberry) fruit is traded by producing region, but unknown harvest maturity can generate compositional ranges that resemble provenance differences. We characterised nine producing-location groups using HS-SPME-GC–MS, LC-MS/MS, amino-acid analysis, electronic-nose sensing and report-derived electronic-tongue outputs, and then applied two sequential evidence gates: developmental-envelope screening of chemical candidates and species-specific annotation auditing of chemistry-linked gene families. The resource contained 124 volatile rows, 318 putatively annotated LC-MS/MS rows, 17 quantified amino acids and 14 electronic-nose channels. In an independent public dataset of 24 fresh-fruit samples (six per stage), 20 of 21 metabolites were stage-resolved and all 11 cross-dataset overlaps were stage-sensitive. The observed four-stage envelope covered the complete nine-location range for eight overlaps. Gallic acid and ellagic acid retained positive range excess in 8/9 and 9/9 leave-one-location-out analyses and exceeded the 95th percentile in all three moderate drying scenarios, defining Tier 1 validation candidates. Kaempferol 3-O-glucoside was retained in 9/9 analyses but exceeded that scenario threshold in 1/3 settings, defining Tier 2. Whole-proteome screening identified 178 PF00201 UGT candidates, recovered all 172 previously catalogued RchUGTs and added six profile-defined candidates; 32 TPS candidates had motif support. Comparative analysis in R. idaeus and R. occidentalis independently supported re-curation of the LG03.2235 boundary, whereas LG02.1599 remained consistent with a single homologous model. This two-gate workflow converts missing maturity metadata and incomplete genome labels into explicit validation priorities without presenting the candidates as established origin markers, causal regulators or enzyme assignments.