Long-read transcriptome sequencing for the in-depth understanding of anthocyanin biosynthesis in Jaboticaba

Jaboticaba (<italic>Myrciaria cauliflora</italic>) is a grape-shaped fruit characterized by high concentrations of anthocyanins concentrated within its peel, representing a valuable natural source of functional pigments. Here, we report long-read transcriptome sequencing in Jaboticaba, and 86,758 unigene sequences, 9,732 expressed sequence tag-simple sequence repeats, and 1,127 long non-coding RNA sequences were uncovered. In addition, integrated transcriptomic and metabolomic analysis of pigment accumulation during fruit ripening showed that six anthocyanins accumulated in Jaboticaba fruit, with 47 flavonoid synthesis-related genes, and 12 differentially expressed genes. Compared with green fruits, these candidate genes encoded eight upregulated enzymes particularly expressed in ripening fruits—4CL, PAL, F3H, F3'H, DFR, ANS, LAR, and UFGT—and related to the regulation of phenylpropanoid, flavonoid, and anthocyanin biosynthetic pathways. Furthermore, two R2R3-MYB transcription factors McMYB4-1 and McMYB4-2 might negatively regulate anthocyanin accumulation. The results reveal key regulatory mechanisms governing flavonoid and anthocyanin biosynthetic pathways, thereby offering critical perspectives on plant secondary metabolite production in Jaboticaba.