Sclerified endocarp formation represents a defining developmental feature in Cornus officinalis drupes. We systematically investigated cytological dynamics and lignin metabolism to define the mechanistic basis of endocarp sclerification during Cornus officinalis fruit development. Results demonstrated that endocarp sclerification coincided with a significant increase in lignin content. Stone cell density exhibited developmental variation (239–529 piece·mg-1; mean: 400 piece·mg-1), while the microscopic characteristic index of stone cells progressively increased and stabilized at fruit maturity. Critically, the activities of pivotal lignin biosynthesis enzymes (PAL, CCR, CAD, POD) peaked during early fruit development and subsequently declined with progressive lignin accumulation—a trend corroborated by transcriptomic profiling. RNA-Seq analyses revealed stage-specific expression of lignin biosynthesis genes: PAL, C4H, CSE, POD, CAD, and CCR were highly expressed in young fruit but downregulated during later development. Conversely, COMT and F5H expression peaked at ripening, aligning with maximal lignin deposition and indicating their direct regulation of terminal lignin synthesis steps. Collectively, these findings demonstrate that Cornus officinalis endocarp hardening arises from synergistic stone cell differentiation and lignification, with phenylpropanoid metabolism initiated at juvenility and ripening-stage lignin deposition governed primarily by COMT and F5H.

The mature flesh of Cornus officinalis exhibits a vibrant red color, attributed to its rich anthocyanin content, imparting significant edible and medicinal value. Vibrant colors not only enhance the visual allure of medicinal materials but also maintain a close association with their intrinsic quality. However, the intricate process of pigment formation governing the anthocyanin accumulation in the pericarp of Cornus officinalis remains poorly understood. In this study, we conducted the comprehensive sampling and analysis of pericarp tissues at three distinct developmental stages, employing morphological-structure observation and metabolomic and transcriptomic techniques. Our findings reveal a substantial increase in the anthocyanin accumulation during the transition to the red stage of Cornus officinalis fruit maturation. Metabolomic profiling identified the highest expression levels of Cyanidin-3-O-glucoside and Pelargonidin-3-O-rutinoside during the mature stage, suggesting their association with the red coloration of the fruit. Through RNA sequencing, we identified 25,740 differentially expressed genes (DEGs), including 41 DEGs associated with anthocyanin biosynthesis. The correlation between the DEG expression levels and anthocyanin content was explored, further elucidating the regulatory network. Additionally, we validated the pivotal role of the candidate gene BZ1 in the synthesis of Cyanidin-3-O-glucoside through qRT-PCR, confirming its crucial impact on anthocyanin accumulation. This study provides preliminary insights into anthocyanin accumulation in Cornus officinalis, laying the foundation for the future development of new cultivars with enhanced anthocyanin contents.

This study investigated the interactive effects of different light conditions and weed control methods on the medicinal compound composition and rhizosphere bacterial community structure of Epimedium sagittatum. A completely randomized block design was employed, incorporating four treatments: full light with manual weeding (LN), shade with manual weeding (SN), full light with weed-control fabric mulch (LG), and shade with mulch (SG). Active compound levels in two-year-old plants were quantified using HPLC, and rhizobacterial diversity was assessed via high-throughput sequencing. The results indicated that the SG treatment significantly enhanced the photosynthetic efficiency and yielded the highest levels of epimedin C and total active compounds. In contrast, the SN treatment fostered a beneficial rhizosphere environment—characterized by increased pH, ammonium nitrogen (NH₄⁺-N), bacterial diversity, and the abundance of Flavobacterium—which supported the highest production of epimedin B and icariin. Redundancy analysis confirmed that these microbial shifts were primarily driven by soil pH, nitrate nitrogen (NO₃⁻-N), and shading. Furthermore, while stochastic processes governed bacterial community assembly, deterministic selection intensified across the treatments from LN to SG. Collectively, our findings demonstrate that light and mulching can be strategically tailored to manipulate the plant–soil-microbe system, thereby enabling precise modulation of the medicinal quality of E. sagittatum.