Cremastra appendiculata has become endangered due to reproductive difficulties. Specifically, vegetative reproduction is almost its only way to reproduce, and, under natural conditions, it cannot grow branches, resulting in an extremely low reproductive coefficient (reproductive percentage). Here, we performed RNA-Seq and a differentially expressed gene (DEG) analysis of the three stages of lateral bud development in C. appendiculata after decapitation—dormancy (D2), transition (TD2), and emergence (TG2)—and the annual axillary bud natural break (G1) to gain insight into the molecular regulatory network of shoot branching in this plant. Additionally, we applied the auxin transport inhibitors N-1-naphthylphthalamic acid (NPA) and 2,3,5-triiodibenzoic acid (TIBA) to a treated pseudobulb string of C. appendiculata to verify the conclusions obtained by the transcriptome. RNA-Seq provided a wealth of valuable information. Successive pairwise comparative transcriptome analyses revealed 5988 genes as DEGs. GO (Gene Ontology) and KEGG (Kyoto encyclopedia of genes and genomes) analyses of DEGs showed significant enrichments in phytohormone biosynthesis and metabolism, regulation of hormone levels, and a hormone-mediated signaling pathway. qRT-PCR validation showed a highly significant correlation (p < 0.01) with the RNA-Seq generated data. High-performance liquid chromatography (HPLC) and qRT-PCR results showed that, after decapitation, the NPA- and TIBA-induced lateral buds germinated due to rapidly decreasing auxin levels, caused by upregulation of the dioxygenase for auxin oxidation gene (DAO). Decreased auxin levels promoted the expression of isopentenyl transferase (IPT) and cytochrome P450 monooxygenase, family 735, subfamily A (CYP735A) genes and inhibited two carotenoid cleavage dioxygenases (CCD7 and CCD8). Zeatin levels significantly increased after the treatments. The increased cytokinin levels promoted the expression of WUSCHEL (WUS) and inhibited expression of BRANCHED1 (BRC1) in the cytokinin signal transduction pathway and initiated lateral bud outgrowth. Our data suggest that our theories concerning the regulation of shoot branching and apical dominance is really similar to those observed in annual plants. Auxin inhibits bud outgrowth and tends to inhibit cytokinin levels. The pseudobulb in the plant behaves in a similar manner to that of a shoot above the ground.

Phytochrome interacting factors (PIFs) serve as crucial regulators in the light signal transduction pathway and also mediate light signals to regulate secondary metabolite synthesis in plants. However, the regulator role of PIFs in secondary metabolites often varies among different plants. Isorhynchophylline (IRN), an iconic secondary metabolite of Uncaria rhynchophylla, holds significant medicinal value. Low light induces the synthesis of IRN in previous research, but PIFs in U. rhynchophylla have not been studied to date. Building on this, we identified a PIF protein, UrPIF3, which possesses the typical conserved domains of the PIFs and is localized in the nucleus. Moreover, the expression level of UrPIF3 is consistently positively correlated with the expression of two key enzyme genes (UrSGD and UrSTR) in the IRN biosynthesis pathway, regardless of whether under low light or restoring light conditions. Yeast one-hybrid and dual-luciferase assays further demonstrated that UrPIF3 can directly upregulate UrSGD. Conversely, silencing UrPIF3 inhibits IRN synthesis, and significantly reduces the expression levels of UrSGD and UrSTR. In summary, our results suggest that under low light conditions, UrPIF3 can directly upregulate UrSGD and indirectly upregulate UrSTR, thereby promoting the synthesis of IRN.

Mulberry (Morus alba L.) is a woody plant primarily cultivated for silkworm breeding, with significant economic and ecological functions. Its nitrogen use efficiency directly affects leaf yield, quality, and environmental adaptability. The main inorganic nitrogen forms available for plant uptake in soil are ammonium nitrogen and nitrate nitrogen, and plant uptake and assimilation of these two nitrogen sources often exhibit species-specific preferences. This review systematically summarizes the research progress on nitrogen uptake preferences in mulberry, confirming that this species generally shows a preferential uptake of nitrate. Specifically, when supplied with nitrate or a mixed nitrogen source dominated by nitrate, mulberry exhibits better performance in growth and development, photosynthetic efficiency, and accumulation of secondary metabolites. This review further discusses the physiological characteristics and underlying regulatory mechanisms responsible for this preference, and analyzes key factors affecting nitrogen uptake preferences, including soil properties, environmental stresses, and microbial interactions. It should be noted that while controlled experiments have yielded important insights, the applicability of these findings under complex field conditions still requires further validation through field trials. Finally, future research directions are prospected, including in-depth dissection of molecular mechanisms, field validation, plant-microbe interactions, and nutritional strategies for stress resistance, aiming to provide a theoretical basis for efficient cultivation and precise nitrogen management of mulberry.

The fragile Karst landscapes of southwest China face persistent challenges of soil degradation and rocky desertification. While sustainable land use such as mulberry plantation can support ecological restoration, the dynamics of soil organic carbon (SOC) and its driving mechanisms across contrasting soil types remain poorly understood, limiting the development of targeted pedogenically aware carbon management strategies. A comparative field study was conducted in central Guizhou, China, over an eight-month mulberry growing season (April to November). We monitored SOC, physicochemical properties, GRSP, and enzyme activities in plantations established on two contrasting limestone-derived soils (Calcisols and Chromic Luvisols). This study aimed to clarify the relationships between SOC and key soil parameters within each soil type and to identify their dominant driving factors. Soil type significantly influenced SOC concentration, dynamics, and its regulatory mechanisms. SOC was significantly higher and exhibited greater seasonal variability in Calcisols (31.51–39.71 g·kg⁻¹) than in Chromic Luvisols (22.50–28.51 g·kg⁻¹), with Calcisols maintaining 1.28–1.57 times the SOC concentration of Chromic Luvisols. Regression analysis revealed that SOC was significantly positively correlated with TN, AN, AK, and GRSP, but significantly negatively correlated with AP. Random forest modeling further identified distinct key correlated factors in each soil type as follows: TN, T-GRSP, and Urease were primary in Calcisols, whereas TN, T-GRSP, and pH dominated in Chromic Luvisols. Partial least squares path modeling confirmed that soil type does not directly associate with SOC but exerts an indirect effect by modulating core biochemical mediators specifically (Alkaline protease, T-GRSP, and TN); The model also indicated that pH and TN exert direct positive effects on SOC accumulation. In Karst mulberry systems, pedogenically distinct soils (Calcisols vs. Chromic Luvisols) shape SOC storage, stability, and regulatory mechanisms through divergent biogeochemical pathways. SOC management should therefore be soil-type-specific, prioritizing nitrogen synergy in Calcisols and pH-mediated stabilization in Chromic Luvisols, rather than applying uniform strategies. This study thereby establishes a mechanistic framework for understanding and managing SOC in heterogeneous Karst landscapes, providing a critical foundation for developing targeted, soil-specific carbon sequestration practices in ecologically vulnerable regions.