Comprehensive Genome Identification Analysis of <i>WOX</i> Gene Family and Its Expression in Protopanaxatriol Ginsenosides Under <scp>MeJA</scp> Treatment in Ginseng

Panax ginseng is an important medicinal plant, and its major bioactive components are ginsenosides. The WOX gene family is a plant-specific transcription factor family involved in the regulation of multiple biological processes, including stem cell maintenance, embryonic development, lateral organ development, and organogenesis. In this study, we screened and identified members of the PgWOX gene family using an established ginseng transcriptome and genome database. Subsequently, a comprehensive analysis was performed, including phylogenetic analysis, gene structure characterization, conserved motif identification, cis-acting element prediction, expression pattern analysis, and chromosomal localization analysis. In addition, gene ontology (GO) functional annotation and co-expression network analysis were conducted for PgWOX genes, in which the co-expression correlations between PgWOX genes and the previously published key enzyme genes involved in ginsenoside biosynthesis were investigated. Furthermore, ginseng adventitious roots were treated with methyl jasmonate (MeJA) to study the expression responses of three PgWOX genes that clustered with the known key ginsenoside biosynthesis-related enzyme genes in the co-expression network. The results showed that all three PgWOX genes exhibited distinct expression responses to MeJA. Finally, the contents of five protopanaxatriol-type ginsenosides (Re, Rf, Rg1, Rg2, and Rh1) were determined in ginseng adventitious roots treated with MeJA at various time points, focusing on three PgWOX genes (PgWOX21, PgWOX35, and PgWOX36). The results demonstrated that Re content showed the most significant variation among all detected ginsenosides. This study provides valuable data for subsequent research on members of the WOX gene family in P. ginseng and offers an experimental reference for verifying the functions of these family members in the MeJA signaling pathway.