Integrated metabolome and transcriptome analysis revealed color formation in purple leaf mustard ( Brassica juncea)

Purple leaf mustard has garnered attention owing to its abundant anthocyanin content. This study investigated the phenolic metabolome and transcriptome of purple variety ZC-Red and green variety ZC-2. Each of the two varieties had three biological replicates, and each replicate consisted of ten leaves from five plants. Phenolic metabolome was analyzed using an ultra-high performance liquid chromatography system and tandem mass spectrometry, and the transcriptome sequencing platform was the Illumina NovaSeq 6000 platform. The green variety ZC-2 was used as the control for differential analysis. All differential metabolites and genes were significant. Findings revealed the accumulation of anthocyanins in ZC-Red, whereas ZC-2 exhibited higher levels of phenolic acids and flavonoids, excluding anthocyanins. This could be attributed to the directional preference of the phenylpropanoid metabolic flow. Transcriptome analysis highlighted the pivotal roles of phenylpropanoid metabolism and photosynthesis in color formation. In ZC-Red, nearly all anthocyanin biosynthesis genes exhibited up-regulation, with multiple genes in late biosynthesis showing increases thousands of times greater than ZC-2. Conversely, the expression of genes associated with photosystem subunits and light-harvesting complexes was down-regulated. Key candidate transcription factors, including MYB113, TT8, WRKY44, and MYB30, were identified as regulators of anthocyanin and photosynthesis. Findings contribute valuable insights into the molecular mechanisms underlying anthocyanin accumulation. Core differential metabolites such as anthocyanins and phenolic acids are of great significance to the utilization of diversified functional compounds and targeted breeding of leaf mustard.