Transcriptome-wide identification and systematic analysis of the Retrotransposon genes and their roles in ginsenoside biosynthesis in Panax ginseng.

backgroundPanax ginseng, a valuable medicinal herb, owes its medicinal and economic importance to ginsenosides, its primary active components. Ginsenoside biosynthesis involves complex processes, including catalytic enzymes and transcription factors. Retrotransposons, key elements of the ginseng genome, also play a role in phenotype formation that cannot be ignored. However, research has primarily focused on their roles in genome structure and evolution, while their basic characteristics and impact on ginsenoside biosynthesis remain largely unexplored.

results1,301 Retrotransposon genes were identified in ginseng transcriptome using bioinformatics methods, and a systematic analysis was conducted on their gene structures, phylogenetic relationships, and expression patterns. Phylogenetic analysis revealed phenomenon of horizontal transfer of retrotransposons in ginseng. Further, expression analysis revealed spatiotemporal specificity in retrotransposons expression, with the highest levels observed in 25-year-old ginseng. About one-third of the sequences showed elevated expression in the leaves. Subsequently, an association analysis between retrotransposon genotypes, genes expression and other related factors with ginsenosides contents, identifying 30 Retrotransposon genes highly significantly associated to ginsenosides biosynthesis. Methyl Jasmonate (MeJA)-induced transcriptome analysis identified 15 of 30 genes significantly responsive to MeJA regulation, five of which were strongly linked to ginsenosides contents variation. MeJA-treated ginseng seedlings were analyzed for these five genes expression levels using quantitative real-time PCR, while ginsenosides contents were detected via high-performance liquid chromatography (HPLC). The results demonstrated that these five genes not only responded to MeJA treatment but were also closely associated with changes in ginsenoside content. These findings confirm the analysis’s accuracy and validate the regulatory roles of these genes in ginsenosides biosynthesis in ginseng.

conclusionsRetrotransposons in ginseng were identified and analyzed to enhance understanding of their fundamental features. A series of correlation analyses revealed 30 sequences linked to ginsenoside biosynthesis. Functional validation of these sequences was performed using two types of ginseng materials treated with MeJA, which confirmed the functions of 5 sequences, demonstrating their close association with ginsenoside biosynthesis and their involvement in regulatory network controlling its synthesis. This study provides a valuable reference for the research on retrotransposons in medicinal plants and offers insights for future studies on the regulatory relationships between retrotransposons and phenotypes. CLINICAL TRIAL: The materials utilized in this study were derived from the plant species Panax ginseng. And the specific content is the identification and analysis of the Retrotransposon genes in ginseng and the study of its function. This study does not include any components related to clinical trials.