Temporal Partitioning of Carotenoid, Flavonoid and Anthocyanin Biosynthesis Underlies the Ontogenetic Petal Color Transition in Weigela japonica

Background: Ontogenetic flower color change is a prevalent adaptive phenomenon in plants, yet the temporal orchestration of multiple pigment pathways during rapid developmental transitions remains poorly understood. This study aims to elucidate the metabolic and transcriptional basis of the petal basal marking color transition in Weigela japonica from yellow through yellow-orange to purple-red within a 4-day blooming period. Methods: Metabolomic analysis of flavonoids, anthocyanins, and carotenoids was conducted using UPLC-MS/MS across four developmental stages (S0–S3). Differentially accumulated metabolites were screened based on VIP > 1, |Log2FC| ≥ 1, and p < 0.05. Transcriptome sequencing was performed using the NovaSeq 6000 platform, and differentially expressed genes were identified using DESeq2. Weighted gene co-expression network analysis (WGCNA) was employed to identify hub genes associated with pigment accumulation. Key structural genes were validated by qRT-PCR. Results: Metabolomics revealed distinct stage-specific pigment accumulation: carotenoids peaked during the yellow-orange stage (S2), while anthocyanins and flavonoids surged in the final purple-red stage (S3). KEGG enrichment indicated that carotenoid metabolism operates as a discrete module, anthocyanin biosynthesis as a terminal-specific route, and flavonoid metabolism as an intermediary hub bridging the two pathways. Transcriptome analysis identified stage-specific gene expression patterns: PAL and C4H were active at S0–S1, CHS/CHI/F3H peaked at S1-S2, and DFR/ANS were maximally expressed at S2–S3. Carotenoid genes (PSY, LCY, ZDS) showed synchronous expression during the yellow-orange phase. WGCNA identified MYB44, bHLH92, and ERF3 as hub genes strongly correlated with the S3 anthocyanin surge. Conclusions: These findings suggest a sequential activation model in W. japonica, in which temporally partitioned pigment metabolism and stepwise transcriptional regulation converge to orchestrate rapid ontogenetic color change. The study provides a framework for understanding developmental color transitions in ornamental plants, though causal regulatory relationships remain to be functionally validated.