Integrated metabolome and transcriptome analysis provides insight into the leaf color change of Cymbidium ensifolium

Cymbidium ensifolium L. is an economically important terrestrial orchid. Leaf color is a key horticultural trait with aesthetic and ornamental significance. However, the molecular basis of leaf color change in C. ensifolium remains to be fully understood. Here, different color leaves of C. ensifolium were collected and classified into two groups, namely, leaf buds that appear red in the juvenile stage (RL) and those that transform green in the mature stage (GL). Significantly higher anthocyanin content was observed in RL than GL. RNA-seq data showed a total of 3955 differentially expressed unigenes (DEUs) were screened, and 381 differentially accumulated metabolites (DAMs) were detected by metabolome analysis in RL vs GL. Further analysis revealed that the anthocyanin biosynthesis pathway (ko00942) is essential for leaf color change. Cyanidin-3-O-glucoside, petunidin-3-O-(6″-O-p-coumaroyl) rutinoside, and peonidin-3-O-glucoside were identified as key anthocyanins affecting leaf color change. Meanwhile, we identified key structural unigenes associated with leaf color change, including CHS, CHI, DFR, F3H, F3′H, and ANS. Correlation analysis revealed 77 DEUs associated with transcription factors to exhibit strong correlations with both DEUs and DAMs involved in anthocyanin biosynthesis. Our study identifies the important metabolic and functional role of the anthocyanin biosynthesis pathway in C. ensifolium leaf color change.