Genome-Wide Identification and Expression Analysis of the PEPC Gene Family in Zanthoxylum armatum Reveals Potential Roles in Environmental Adaptation

Phosphoenolpyruvate carboxylase (PEPC) is a crucial enzyme in plant photosynthesis and stress responses, yet its gene family remained uncharacterized in <i>Zanthoxylum armatum</i>. This study presents the first genome-wide identification and comprehensive analysis of the PEPC gene family in <i>Z. armatum</i>. A total of 12 <i>ZaPEPC</i> genes were identified and classified into plant-type (PTPC) and bacterial-type (BTPC) subfamilies based on phylogenetic analysis. These genes exhibited conserved protein domains but distinct gene structures, with evidence of gene duplication events contributing to family expansion. Promoter analysis revealed an abundance of stress- and hormone-responsive <i>cis</i>-elements, particularly those related to light, abscisic acid (ABA), and methyl jasmonate (MeJA). Expression profiling demonstrated that <i>ZaPEPC</i> genes display environment-specific expression patterns, with <i>ZaPEPC7</i> and <i>ZaPEPC11</i> showing significantly higher expression in high-altitude, high-light environments (Yunnan) compared to other regions (Shandong and Chongqing). Co-expression network analysis further indicated interactions between specific <i>ZaPEPCs</i> and stress-related transcription factors. These findings systematically reveal the molecular characteristics and potential roles of the <i>ZaPEPC</i> gene family in environmental adaptation, providing valuable genetic resources and a theoretical foundation for improving stress tolerance and photosynthetic efficiency in <i>Z. armatum</i> through molecular breeding.