Genome-wide identification of CpWRKYs and elucidation of the saline-alkali response mechanism in Codonopsis pilosula roots

Codonopsis pilosula ( Cp ) is a medicinally and economically significant edible plant. WRKY transcription factors (TFs) represent a major transcription factor family in plants and are recognized as key regulators of saline-alkali stress responses. Despite their importance, a systematic genome-wide characterization of the WRKY gene family in Cp remains unreported. This study thus aims to identify and functionally profile WRKY genes in the Cp genome, specifically targeting those linked to saline-alkali stress adaptation. A total of 47 WRKY genes were identified in Cp . These genes were unevenly distributed across eight chromosomes. Phylogenetic and conserved domain analysis divided these genes into seven subfamilies with similar conserved motifs but different gene structures. Collinearity analysis identified 13 duplicated gene pairs, indicating a role of segmental duplication in the expansion of the CpWRKY gene family. Transcriptome analysis revealed that differentially expressed WRKY genes under saline-alkali stress mostly belonged to groups I, IIc, and III. Metabolic analysis found that lipid metabolites were the main differentially accumulated metabolites (DAMs) of saline-alkali stress, and gene co-expression network analysis found that lipid metabolite-related genes were associated with WRKY genes such as Cpi05G005333- I. In this study, we identified and analyzed the WRKY gene family members in Cp for their phylogenetic relationships, physicochemical properties, conserved domain, conserved motifs, gene structures, and expression under saline-alkali stress. Some candidate genes were identified based on potential protein network, the expression and co-expression network analysis under saline-alkali stress. This study provided the first comprehensive characterization of the CpWRKY gene family, and identified candidate members potentially that may be involved in the transcriptional response to saline-alkali stress in Cp .