Background: Cerasus humilis is a unique dwarf shrub and fruit color is an important trait in the species. In this study, we evaluated the transcriptomic and metabolomic profiles of the plant at different developmental stages to elucidate the mechanism underlying color formation.Results: In a metabolomics analysis, 16 anthocyanin components were identified at different developmental stages, and high levels of cyanidin O-syringic acid and pelargonidin 3-O-beta-d-glucoside (callistephin chloride) were correlated with the reddening of the fruit peel. Additionally, transcriptome analysis showed that most anthocyanin biosynthetic genes and two MYB transcription factors were significantly up-regulated. qRT-PCR results for these differentially expressed genes were generally consistent with the high-throughput sequencing. A co-expression analysis revealed that ANS and UFGT play keys role in pigmentation. Conclusions: These findings provide insight into the mechanisms underlying anthocyanin accumulation and coloration during fruit peel development, providing a basis for the breeding of anthocyanin-rich C. humilis cultivars.
