Integration of transcriptome and targeted metabolome reveals regulatory and structural genes involved in anthocyanin biosynthesis of four Ceiba speciosa germplasms.

Ceiba speciosa has become a common landscape tree species in southern China due to its abundant petal colors and ornamental application values. Until now, there is little knowledge relevant to the molecular mechanisms involved in petal color formation and phenotypical variations in this species. In this study, transcriptome and targeted metabolome were integrated for four types of germplasm resources with different petal colors to identify candidate regulators, structural genes, and anthocyanins that might be involved in the formation of petal colors. Through qualitative and quantitative analyses of anthocyanins, the contents of two cyanidins (Cyanidin-3,5-O-diglucoside and Cyanidin-3-O-glucoside) were both consistent with color trends among four types of cultivars. By using RNA-seq, several structural genes, including six PALs, three F3Hs, one CHI, one 4CL, two CHSs, two DFRs, one ANS, and seven GT1s, were identified to be involved in the pathway of anthocyanin biosynthesis and were differentially expressed and highly correlated with the content of at least one compound. Then, 12 core transcription factors, including seven MYBs (MYB-33, MYB-37, MYB-80, MYB-92, MYB-111, MYB-112, and MYB-121), two C3Hs (C3H-105 and C3H-106), one EIL (EIL-10), one GRAS (GRAS-53), and one G2-like (G2-like-1), were obtained and possibly related to petal color differentiation together with other co-expressed transcription factors. In addition, the expression of numerous members belongs to an MYB-bHLH-WD40 module, and the main transcription factors involved in regulating anthocyanin biosynthesis were also significantly correlated with the content of five important anthocyanins, which have the highest average contents among all the samples. Molecular co-expression networks were constructed to display the relationship among TFs, structural genes, and metabolites. Our study lays the foundation for revealing the molecular mechanism involved in flower color production and variations in C. speciosa.