Genome-wide identification and analysis of YTH gene family and its response to MeJA and salt treatment in Panax ginseng C. A. Meyer

Abstract YTH domain-containing RNA-binding proteins function as m⁶A readers that specifically bind to m⁶A-modified RNAs. YTH domain-containing proteins participate in various biological processes, such as hormone signaling pathways, regulation of stress responses, RNA stability, and cellular differentiation. Despite these important roles, the characteristics and functions of YTH family genes in ginseng (Panax ginseng), a traditional medicinal herb, particularly regarding their response to MeJA treatment and salt stress on a genome-wide scale, have not yet been studied. In this study, 18 YTH genes were identified based on telomere-to-telomere reference genome of ginseng. These PgYTH genes were grouped into four subgroups by phylogenetic analysis. Moreover, the chromosomal distribution, synteny analysis, gene structures and cis-elements of PgYTH genes, and the motifs of YTH proteins were analyzed. Expression profiling results indicated that the PgYTH genes were tissue-specific and spatiotemporally-specific in 14 different tissues of 4-year-old ginseng, in ginseng roots of four different ages, and among 42 different cultivars of 4-year-old ginseng roots. The expression of the majority of PgYTH genes was downregulated in response to MeJA, an elicitor of the ginsenoside biosynthesis pathway. The expression of PgYTH8-12 was upregulated under salt treatment. Additionally, PgYTH12 was localized to the endoplasmic reticulum. Overall, these results lay the groundwork for future functional investigations of PgYTH genes, advancing our understanding of their role in the regulation of the ginsenoside biosynthesis pathway and stress resistance in ginseng.