Integrated analyses of metabolome, epigenome and transcriptome under different light intensities reveal dynamic regulation of histone modifications on the secondary metabolism in Camellia sinensis

Camellia sinensis is an industrial crop characterized by specific secondary metabolites, which are beneficial to humans. Previous researches reveal that the secondary metabolism of tea plants is significantly affected by various environmental factors, especially light intensity. However, the epigenetic mechanism involved in the high light-induced secondary metabolite changes is lack of systematic research. In this study, the metabolite landscape by widely targeted metabolome revealed 244 differentially accumulated metabolites in high light, with substantial up-regulated differentially accumulated metabolites accumulated in amino acids and derivatives and alkaloids. The landscape of 9 crucial histone modifications showed the distribution diversity on the genome and complex relationship with gene expression. Integrated analysis of metabolome, epigenome and transcriptome indicated that the dynamics of histone modifications H3K4ac, H3K4me3, H3K9ac, H3K9me2, H3K27ac and H3K27me3 on gene regions were closely related to the expression of enzyme genes in secondary metabolic pathways, leading to metabolite changes in high light. In additionm, H3K27ac and H3K27me3 were identified as key histone modifications, regulating the expression of genes in high light. These results suggest the crucial function of histone modifications in the high light-induced secondary metabolite changes of tea plants.