Comprehensive Genome Identification of the PHD Gene Family in Panax ginseng and Expression Analysis of PgPHD Genes in Response to MeJA

Plant homeodomain (PHD) finger proteins are important histone modification readers that play broad roles in the epigenetic regulation of plant development and stress responses. However, the PHD finger gene family has not been systematically identified in Panax ginseng, and its association with ginsenoside biosynthesis remains unclear. In this study, we identified 63 PgPHD genes, corresponding to 163 transcripts, from the P. ginseng transcriptome using a combination of HMMER-based domain and BLAST-based homology searches (BLAST+ 2.16.0). Phylogenetic analysis classified these genes into 15 groups. Promoter cis-element prediction, co-expression network construction, and methyl jasmonate (MeJA) induction experiments were further performed to explore the possible regulatory associations of PgPHD genes. The PgPHD genes were distributed across all 24 chromosomes, and 18 segmentally duplicated gene pairs suggested that whole-genome duplication drove the expansion of this gene family. A total of 308 MeJA-responsive cis-elements were identified in the promoter regions, making them one of the most prevalent functional categories. Co-expression network analysis based on 42 landraces identified five candidate genes significantly associated with key enzyme genes involved in ginsenoside biosynthesis, among which PgPHD31-09 showed a significant expression correlation with nine key enzyme genes. qRT-PCR analysis showed that PgPHD31-09 was significantly upregulated in response to MeJA treatment, and its expression pattern was similar to that of several key enzyme-encoding genes related to ginsenoside biosynthesis. This study provides the first systematic analysis of the evolutionary and expression characteristics of the PHD gene family in P. ginseng, identifying PgPHD31-09 as a candidate gene potentially associated with MeJA responsiveness and ginsenoside biosynthesis.