Transcriptome and Metabolome Analyses Reveal the Mechanism of Color Differences in Pomegranate (Punica granatum L.) Red and White Petals

Pomegranate (<i>Punica granatum</i> L.) is an important economic tree, possessing both edible and ornamental value. Flower color is an important ornamental trait of pomegranate, but the color formation pattern and related molecular mechanisms of pomegranate petals are still unclear. In this study, we conducted physiological, transcriptomic, and metabolomic studies on the petals of Tunisia and White pomegranate varieties during the blooming stage. The results showed that compared to White petals, the contents of anthocyanin, carotenoid, and sucrose in Tunisia petals were significantly increased, while the flavonoid content was significantly decreased. Through RNA-seq, 23 DEGs were identified in the anthocyanin synthesis, and 3 DEGs were identified in the carotenoid synthesis. Transcription factor genes such as <i>MYB</i>, <i>bHLH</i>, <i>WRKY</i>, and <i>MADS</i> were identified as key candidates for regulating anthocyanin metabolism. Metabolomic analysis revealed that eight DEMs are associated with anthocyanin synthesis and three DEMs are associated with carotenoid synthesis. In addition, caffeic acid and its derivatives were significantly upregulated in Tunisia petals. In summary, we propose the following hypothesis: the accumulation of anthocyanins and carotenoids is the reason for the red color of Tunisian petals, and the upregulation of structural genes, including <i>PAL</i>, <i>C4H</i>, <i>4CL</i>, <i>CHS</i>, <i>CHI</i>, <i>F3H</i>, <i>F3'H</i>, <i>DFR</i>, <i>ANS</i>, <i>PSY</i>, and <i>LCYB</i>, leads to an increase in their content. Transcription factor genes such as <i>MYB</i>, <i>bHLH</i>, <i>bZIP</i>, <i>MADS</i>, and <i>WRKY</i> may also play a positive role in anthocyanin accumulation. The research results provide a basis for the theory of pomegranate petal color formation.