Integrated Metabolome and Transcriptome Analyses Reveal the Developmental Program of Anthocyanin Pigmentation in Lavender (Lavandula angustifolia Mill.) Flowers

Lavender (Lavandula angustifolia Mill.) owes much of its ornamental and economic value to its violet–purple inflorescences, yet the molecular basis of this coloration remains poorly understood. By integrating untargeted metabolomics, RNA-seq, and phylogenetic analysis with morphological and microscopic observations across floral development, we resolved the developmental program of anthocyanin pigmentation in L. angustifolia ‘Xinxun 2’. Anthocyanin content followed an initiation–peak–plateau trajectory, peaking at full flowering; nevertheless, the corolla continued to shift toward purple–blue at late flowering despite stable pigment levels, indicating that the final hue is not governed by pigment quantity alone. Molecularly, the delphinidin branch (F3′5′H) was the principal determinant of the violet phenotype, and the pathway was temporally partitioned—structural genes peaked at early flowering, whereas the late anthocyanin-modifying gene AOMT was induced at full flowering, and the competing flavan-3-ol branch enzyme ANR was also up-regulated at this stage; two subgroup-6 R2R3-MYB transcription factors (MYB90, MYB114) emerged as candidate activators. These findings provide the first stage-resolved molecular framework for floral pigmentation in lavender and identify full flowering as the optimal pigment-extraction window, offering concrete targets for molecular breeding of novel flower colors.