Unraveling the Molecular Mechanism of Lignin Accumulation in Stipule Thorns of Zanthoxylum bungeanum: Insights from Transcriptomic and Targeted Metabolomic Analysis

Zanthoxylum bungeanum (Zb), an economically important tree, is widely cultivated in China. However, its abundant and intricate thorns pose challenges in management and harvesting, thereby reducing its economic benefits. Although the origin and formation mechanism of stipule thorns in Zb remain unclear, it is hypothesized that thorn hardening may be associated with lignin synthesis and accumulation. In this study, we utilized histologic, transcriptomic, and metabolomic analysis methods with stipule thorns at five distinct developmental stages (25 days, 40 days, 55 days, 70 days, and 80 days after flowering) to investigate the mechanisms underlying lignin accumulation and synthesis. Our findings revealed that guaiacyl and syringyl lignin were present in the stipule thorns of Zb. Lignification occurs from the top to bottom and from the outside to inside. Through a weighted gene co-expression network analysis and construction of a gene regulation network, we identified 20 genes significantly involved in lignin synthesis and metabolism including 10 structural genes and 9 transcription factors such as MYB, bHLH, WRKY, and NAC. Notably, our target gene prediction results of hub genes indicated that four NAC genes play a critical role in lignin synthesis. Furthermore, we predicted a possible NAC-MYB model gene-regulatory network. This research provides novel insights into the synthesis of lignin in Zb, while offering a molecular foundation for breeding varieties of thornless or soft-thorned Zb.