Integrated Transcriptomics and Metabolomics Analysis Reveals IbCCoAOMT7 Negatively Regulating Anthocyanin Accumulation in Sweetpotato Storage Roots

Anthocyanins dictate the nutritional quality of purple-fleshed sweetpotato (PFSP), yet how the lignin pathway influences anthocyanin biosynthesis and phenylpropanoid metabolic flux allocation remains largely elusive. Through integrated transcriptomic and metabolomic analyses of a purple-fleshed sweetpotato cultivar (XZ13) and its natural mutant (XZ13M), we revealed that diminished anthocyanin accumulation correlated strongly with systemic transcriptional repression of the phenylpropanoid pathway. We subsequently identified a crucial methyltransferase gene, IbCCoAOMT7, with dual nucleocytoplasmic localization. Its overexpression in its storage roots was directly associated with reduced anthocyanin accumulation and increased lignin content. Further investigations suggested that IbCCoAOMT7 was putatively involved in modulating metabolic flux toward lignin biosynthesis that downregulates the transcriptional activity of core anthocyanin biosynthetic genes. Collectively, our study highlights that IbCCoAOMT7 represents a promising candidate gene that influences the balance between the lignin and anthocyanin pathways. These findings propose a tentative regulatory model, possibly involving substrate availability and transcriptional feedback inhibition, providing precise genetic targets for breeding anthocyanin-enriched sweetpotato.