Genome-Wide Characterization of the ALKBH Gene Family Reveals a Potential Role of PgALKBH10 in Multiple Abiotic Stress Responses in Panax ginseng C. A. Mey.

Background/Objectives: N6-methyladenosine (m6A) is a prevalent RNA modification that significantly influences various biological processes. AlkB homologs (ALKBHs) belong to the family of specific demethylases and, by regulating m6A methylation, are known to be involved in the modulation of plant stress responses. However, the ALKBH gene family has not been systematically characterized in ginseng. Methods: A genome-wide identification and characterization of the ALKBH gene family in ginseng were performed using a telomere-to-telomere reference genome. Phylogenetic relationships, gene structures, conserved motifs, 3D structures, chromosomal distribution, syntenic relationships, cis-acting regulatory elements, protein-protein interaction (PPI) networks, and expression profiles were analyzed. Transcriptome datasets covering multiple tissues, developmental stages, cultivars, and abiotic stress treatments were examined. Candidate stress-responsive genes were further validated by qRT-PCR. Results: A total of 17 PgALKBH genes were identified and classified into seven subfamilies. Structural analyses revealed conserved motifs, exon–intron organization, and 3D structures among members within the same subfamily. Chromosomal localization and synteny analyses suggested that the PgALKBH family has been evolutionarily conserved between ginseng and Arabidopsis and has primarily undergone purifying selection during its expansion. Promoter analysis identified abundant light-, hormone-, and stress-responsive cis-elements. Expression profiling revealed distinct tissue- and developmental stage-specific patterns. The PPI analysis suggested that PgALKBH proteins, especially PgALKBH10, may play a central role in m6A-mediated RNA regulation in ginseng. Transcriptome and qRT-PCR analyses further showed that PgALKBH genes respond differentially to drought, cold, and salt stresses. Notably, PgALKBH10 was induced under all three stress conditions. Conclusions: This study provides a comprehensive characterization of the ALKBH gene family in ginseng and identifies PgALKBH10 as a promising candidate involved in multiple abiotic stress responses. These findings establish a foundation for elucidating the roles of RNA m6A demethylation in ginseng and provide valuable genetic resources for developing stress-tolerant ginseng cultivars.