Understanding flower developmental processes is a prerequisite for improving flowering ‘plants’ production. Adonis amurensis is a fascinating spring ephemeral plant that develops its flower organs underground. Nevertheless, knowledge of the molecular mechanisms driving this particular process is scarce. Herein, we examined transcriptional changes during underground flower differentiation in A. amurensis and unveiled key differently regulated genes and pathways. High-throughput RNA sequencing of meristems at different flower developmental stages, including flower primordium (FP), sepal stage (SE), perianth primordium (PE), stamen stage (ST), and pistil stage (PI), identified 303,234 unigenes that showed 44.79% similarity with sequences in Aquilegia coerulea. Correlations, principal component, and differentially expressed genes (DEGs) analyses revealed that few molecular changes occurred during the transition from PE to ST. Many DEGs exhibited stage-specific regulations. Transcription factor (TF) and phytohormone family genes are critical regulators of the floral differentiation process in A. amurensis. The most differentially regulated TFs were MADS, FAR1, MYBs, AP2/ERF, B3, C2H2, and LOBs. We filtered out 186 candidate genes for future functional studies, including 18 flowering/circadian-related, 32 phytohormone-related, and TF family genes. Our findings deepen our understanding of the underground flower differentiation process and offer critical resources to dissect its regulatory network in A. amurensis. These findings establish a foundational platform for researchers dedicated to exploring the unique phenotypic characteristics of this specific flowering modality and delving into the intricate molecular mechanisms underpinning its regulation and expression.

Phellodendri amurensis Cortex is the dried bark of the cork tree (Phellodendron amurense Rupr.) from the Rutaceae family, and possesses traditional efficacy in clearing heat, drying dampness, purging fire, relieving steaming sensations, detoxifying, and healing sores. Clinically, it is commonly used for treating symptoms such as damp-heat diarrhea and dysentery, jaundice with reddish urine, leukorrhea with vaginal itching, painful and difficult urination due to heat strangury, flaccidity and weakness of the lower limbs, bone-steaming and consumptive fever, night sweats and seminal emission, sores, ulcers, swellings, and toxins, eczema, damp sores, and urinary tract infections. Modern pharmacological studies have further revealed its diverse bioactivities, including antioxidant, antibacterial, anti-inflammatory, immunosuppressive, and anticancer effects. To provide an updated and comprehensive review of the research into Phellodendri amurensis Cortex, this study conducted a thorough literature search and analysis based on databases such as SciFinder, Web of Science, and China National Knowledge Infrastructure. The review integrates information on the plant’s botanical characteristics, geographical distribution, traditional applications, chemical components, quality control methods, and pharmacological effects to present a current and holistic overview of its research status. To date, approximately 170 compounds have been isolated and identified from Phellodendri amurensis Cortex, primarily including alkaloids, phenolics, terpenoids, sterols, lignans, flavonoids, and others. Among these, alkaloids exhibit significant antioxidant and anti-inflammatory activities and demonstrate potential pharmacological value in antibacterial, anticancer, hypoglycemic, and multi-organ protective effects. Although substantial foundational research exists, the mechanisms of action and quality control of Phellodendri amurensis Cortex require further in-depth exploration. Future efforts should focus on clarifying its pharmacodynamic material basis, uncovering new targets and pathways, and improving analytical methods for component analysis and quality control to advance the scientific development and rational utilization of this medicinal material.