Transcriptomic analysis uncovers the red leaf coloration mechanism in Euonymus sacrosancta Koidz

Abstract Two leaf color variants red-leaf (R-type) and common-leaf (G-type) of Euonymus sacrosancta Koidz., were employed as experimental materials to elucidate the molecular mechanisms underlying chromatic transition. Physiological profiling identified anthocyanins and flavonoids as the predominant pigments responsible for the red foliar phenotype, which exhibited reduced chlorophyll and carotenoid accumulation but elevated soluble sugars and proteins. Comparative transcriptomic analysis revealed that differentially expressed genes (DEGs) between R-type and G-type were significantly enriched in flavonoid biosynthesis and carotenoid metabolism pathways. The up-regulation of 22 key genes of anthocyanin synthesis (e.g., CHS , CHI , LAR , LDOX and UFGT ) in R-type may lead to the phenotype of red leaves through the increase of anthocyanin accumulation. The downregulated expression of 13 carotenoid synthesis-related genes (e.g., PSY , PDS and VDE ) and 6 carotenoid degradation genes (e.g., ABA2 , CYP707A and NCED ) may lead to lower carotenoid content in R-type compared to G-type. Combined with weighted gene co-expression network analysis (WGCNA), five candidate genes ( EsLAR , EsLDOX , EsPDS , EsCYP707A and EsABA2 ) were screened from two modules highly correlated with anthocyanin content in E . sacrosancta leaves. These genes may play key regulatory roles in leaf coloration and could serve as candidate genetic resources for leaf color improvement in E. sacrosancta . Additionally, transcription factors such as C2H2s, C3Hs, and WRKYs were identified as potential regulators in the formation of R-type in E. sacrosancta . This study provides the first systematic elucidation of the transcriptional regulatory network governing red-leaf formation in E . sacrosancta , establishing a critical theoretical foundation for molecular breeding in ornamental plants.