Integrated Genomic and Transcriptomic Analyses Suggest the Potential Involvement of the COBRA Gene Family in Heat, Drought and Combined Stress Responses in Phoebe bournei

The COBRA gene family is crucial for plant cell wall formation and stress adaptation. Although COBRA/COBL genes have been characterized in several plant species, their potential contribution to cell wall-mediated responses in woody plants under combined heat–drought stress remains largely unclear. In this study, eight COBRA genes (PbCOBRA1–PbCOBRA8) were systematically identified in Phoebe bournei, a highly valued timber species, and their potential stress-associated roles were investigated by integrating comparative genomic analysis, tissue expression profiling, transcriptome-based WGCNA, physiological stress indicators, qRT-PCR validation, functional enrichment analysis, and three-dimensional structure prediction. Crucially, Weighted Gene Co-expression Network Analysis (WGCNA) discovered three modules that responded to different pressures, involving a total of four PbCOBRA genes (PbCOBRA1, PbCOBRA4, PbCOBRA6, and PbCOBRA8). PbCOBRA6 and PbCOBRA8, meanwhile, were assigned to the same module, which was uniquely associated with combined stress. With contrasting kME values, these two genes may play different roles within this module. The three-dimensional structure prediction further revealed the structural basis for PbCOBRA function under stress conditions. Taken together, these findings identify PbCOBRA members as promising stress-responsive candidate genes potentially associated with heat, drought, and combined stress responses in P. bournei. This study provides a theoretical basis for future functional validation and offers candidate genes for exploring cell wall-mediated stress adaptation in this valuable woody species.