Transcriptomic and metabolic basis of volatile compound dynamics in apricot fermentation

Abstract Here, we assessed the capacity of Wickerhamomyces anomalus LY13 to produce natural aroma compounds from apricot residue by combining time-resolved GC-MS profiling with RNA-Seq across five fermentation stages (0, 16, 32, 48, and 64 h). Without genetic engineering, W. anomalus LY13 accumulated five aroma-active volatile compounds: 2-phenylethanol (rose-like; 13.59 µg/g), the aldehyde phenylacetaldehyde (honey- and hyacinth-like; 6.13 µg/g), and the ketone 3-hydroxy-2-butanone (buttery; 11.14 µg/g), together with isoamyl alcohol (29.12 µg/g) and 2,3-butanediol (1.28 µg/g). All five volatile compounds showed a general tendency to rise initially and then decline, reaching their peak concentrations at 48 h. This metabolic peak coincided with minimal transcriptional change: only 70 genes were differentially expressed between 32 and 48 h, compared with 1,411 and 1,999 during the two preceding intervals. This indicates that the aroma genes are induced early rather than concurrently with peak metabolite accumulation. Integrating expression and metabolite data identified candidate genes for most aroma pathways—3-hydroxy-2-butanone/2,3-butanediol, phenylalanine-derived (Ehrlich), and higher-alcohol. One step previously had no assigned gene in this species: the reduction of phenylacetaldehyde to 2-phenylethanol (EC 1.1.1.90). Combining KOG annotation with expression–metabolite correlation, we identified a short-chain alcohol dehydrogenase, WICANDRAFT_98376, as a leading candidate. Together, these results resolve the temporal architecture of aroma biosynthesis in W. anomalus and establish a candidate-gene framework that positions apricot-processing waste as a promising feedstock for producing high-value natural aromas.