SRP410267 PRJNA905870 Transcriptomic and Metabolomic Analysis of Anthocyanin and Carotenoid Biosynthesis in Red and Yellow Fruits of Sweet Cherry (Prunus avium L.) during Ripening Diversity of fruit color in sweet cherry (Prunus avium L.) has been attributed to the presence of either anthocyanin or carotenoid. Here, we profiled the anthocyanin and carotenoid metabolites by LC-MS/MS and transcriptome analysis by RNA-seq, to investigate the most different pigments and the underlying regulatory mechanisms of differential expression genes (DEGs) between red and yellow fruits of sweet cherry. Results showed that cyanidin-3-O-rutinoside was the most different pigment between two cultivars, the content of which in red fruit was significantly higher than yellow one during the whole ripening stage (especially in stage 3 and stage 4). Total carotenoid content in the two color types of fruits were close, but the content in yellow fruit showed more stable after harvest. Meanwhile, a total of 26,247 unigenes were compared to public databases using homology searches, there was a total of 12,443 DEGs were identified, with the largest proportion at ripening stage 4 (including 3,409 up-regulated and 3,222 down-regulated). Based on the transcriptome data, the heatmap of selected structural DEGs showed that all of the anthocyanin genes expressed significantly higher levels in red fruits than that in yellow fruits. Two unigenes encoding chalcone synthase (CHS) and UDP glucose-flavonoid 3-O-glucosyltransferase (UFGT) expressed 1134.58 and 1151.24 times higher in red than in yellow fruits at stage 4, respectively. The expressions of carotenoid genes were relatively high at early ripening stage in two cultivars, especially HYB, but then decreased gradually during ripening. Correlation analysis showed that anthocyanin genes in JNH were negatively correlated with that in CY, contrastly, there were some strong correlations were observed between two cultivars in carotenoid genes. Thus, the coloration of sweet cherry was mainly attributed to anthocyanin-related genes. This article provides insights into the biosynthetic pattern of fruit coloration in sweet cherry fruit, which contributes to the knowledge of breeding and orchard managements, and improving the quality of sweet cherry fruit.