Anthocyanin and chlorophyll accumulation by targeted metabolomic and transcriptomic analysis involved in pigment accumulation during fruit maturation in Liriope spicata

Liriope spicata is extensively distributed in China, often cultivated under forest or in semi-shade as a traditional Chinese herbal medicine material, and has attracted widespread global interest due to its high ornamental value. To obtain a better understanding of the differential metabolites between pigmented fruit and the color change from light green to black during development and ripening, we used a targeted metabolomic- and transcriptomic-based approach to investigate the anthocyanin and chlorophyll biosynthesis mechanism. A total of 9 cyanidin derivatives, 8 delphinidin derivatives, 5 malvidin derivatives, 9 pelargonidin derivatives, 6 petunidin derivatives, 4 petunidin derivatives, and 8 flavonoid derivatives were identified in L. spicata fruit at five development stages. Transcriptional factors MYB, bZIP, and WRKY were upregulated, which activated the expression of structural genes. The weighted gene correlation network analysis (WGCNA) of anthocyanins, chlorophyll, and associated genes revealed a regulatory system involved in the pigmentation of light green to black L. spicata fruit. Three phenylalanine deaminase genes (PALs) and a stay green gene (SGR) are involved in anthocyanin and chlorophyll biosynthesis, respectively. In the correlation analysis of anthocyanin components, it was suggested that PAL genes were closely related to different anthocyanins accumulated, moreover, the anthocyanin content and PAL activity show a positive correlation at different stages of fruit maturation. These findings provide new insights into molecular mechanisms of anthocyanin and chlorophyll biosynthesis and regulation of pigmentation changes in fruit. Therefore, this will facilitate the breeding of cultivars with high levels of anthocyanin in L. spicata which enhanced ornamental value and research on potential tinctorial and functional raw material.