Genome-Wide Identification of the R2R3-MYB Gene Family in Mango and Multi-Omics Analyses Reveal Genes Involved in Anthocyanin Biosynthesis in Fruit Peels of Different Colors

Mango (Mangifera indica L.) is an economically important tropical fruit, and anthocyanins are key determinants of peel color. Although R2R3-MYB transcription factors (TFs) are well-established regulators of anthocyanin biosynthesis in various plant species, their roles in mango remain largely unexplored. In this study, 370 MiMYB genes were identified in the M. indica genome, including 194 MiR2R3-MYB genes that were unevenly distributed across 20 chromosomes. Phylogenetic analysis classified MiR2R3-MYB genes into 39 subfamilies, while gene structure analysis revealed their conserved organization. Tandem and segmental duplication were the primary drivers of gene family expansion, whereas the ratio of nonsynonymous to synonymous substitutions (Ka/Ks) suggested that these genes had predominantly undergone purifying selection. Transcriptomic analysis of red, yellow, and green mango peels identified differentially expressed MiR2R3-MYB genes and anthocyanin structural genes. Additionally, 143 potential MYB-binding sites were predicted in the promoters of anthocyanin structural genes. Integrated transcriptomic and metabolomic analyses revealed significant correlations between 45 differentially expressed MiR2R3-MYB genes and 36 differentially accumulated anthocyanin metabolites. Based on the number of significantly correlated anthocyanin metabolites, eight candidate genes were selected for validation by reverse transcription quantitative real-time PCR (RT-qPCR). Notably, the MiMYB107 candidate gene showed positive correlations with the largest number of anthocyanin components. Subcellular localization analysis of the MiMYB107-eGFP fusion protein indicated predominant nuclear localization, and Western blotting confirmed MiMYB107 protein expression. This study provides valuable insights into the molecular mechanisms underlying anthocyanin accumulation in mango fruit peels.