Metabolomics and transcriptomics analyses reveal the potential molecular mechanisms of flavonoids and carotenoids in guava pulp with different colors

• Cyndin-3-O-soproposide and its possible copigments were the main factors that contributed to the color difference between the pink and red guava. • Structural genes C4H, CHS, LDOX, and transcription factors MYB and NAC participate in the accumulation of flavonoid metabolites in the red pulp guava. • β-cryptoxanthin myristate, β-cryptoxanthin palmitate, and rubixanthin palmitate were the main carotenoids leading to the yellow pulp of the yellow guava cultivar. PDS, ZEP, CHYB, and transcription factors NAC were involved in the accumulation of these carotenoid components. To understand the forming mechanism of flavonoids and carotenoids in guava pulp with different colors. Based on our previous wide-targeted metabolome analysis, the differences of carotenoids were analyzed by targeted metabolomics, and the molecular mechanism was understood through transcriptomics analysis. The results showed that cyndin-3-O-soproposide and its possible copigments (myricetin, myricitrin, quercetin, quercitrin, etc.) were the main factors that contributed to the color difference between the pink and red guava. The accumulation of these flavonoid components was mainly due to the expression of structural genes C4H, CHS, LDOX, and transcription factors MYB and NAC. β-cryptoxanthin myristate, β-cryptoxanthin palmitate, and rubixanthin palmitate were the main carotenoids leading to the yellow pulp of the yellow cultivar. PDS, ZEP, CHYB, and transcription factors NAC were involved in the accumulation of these carotenoid components. This study provides primary data for further utilization and color regulation of guava. Graphical Abstract .