Medicinal Plant Research 2025, Vol.15, No.5, 206-213 http://hortherbpublisher.com/index.php/mpr 208 2.3 Gene family expansion and evolutionary characteristics Comparative phylogenomic analysis revealed 58 expanded gene families in L. japonicus, particularly those related to specialized metabolism, e.g., diterpenoid biosynthesis. Gene duplication and neofunctionalization events, particularly within the UGT-SCPL gene cluster, have been involved in the special accumulation of leonurine in L. japonicus compared to related taxa (Wang et al., 2024). 2.4 Comparative genomics with other medicinal plants Comparative genomic comparison of L. japonicus and L. sibiricus revealed differences in genome structure and gene content, such as biosynthetic biosynthetic pathways of leonurine. Syntenic and phylogenetic comparison with other medicinal plants and Lamiaceae family members revealed whole-genome duplication histories and evolutionary orientations of biosynthetic gene clusters underpinning the intriguing metabolic potential of L. japonicus (Yang et al., 2022; Chen et al., 2024). 3 Elucidation of Metabolic Pathways of Bioactive Components 3.1 Biosynthetic pathways and key functional enzymes of alkaloids Leonurine and stachydrine are significant alkaloids in L. japonicus. The leonurine biosynthesis was disclosed by multi-omics approaches, and arginine decarboxylase (ADC), uridine diphosphate glucosyltransferase (UGT), and serine carboxypeptidase-like (SCPL) acyltransferase were confirmed to be crucial enzymes. The UGT-SCPL gene cluster, which is developed through gene duplication and neofunctionalization, participates in leonurine accumulation in L. japonicus. Whereas the metabolic pathway of stachydrine is thoroughly explained, its anabolic (biosynthetic) pathway is inadequately reported and a subject of continued study (Li et al., 2023; He et al., 2024; Ou et al., 2025). 3.2 Biosynthesis and regulatory mechanisms of flavonoids Flavonols such as luteolin and luteolin-7-methylether are major pharmacological components of L. japonicus. They inhibit aromatase (CYP19) expression and estrogen biosynthesis by regulating the MAPK/CREB pathway. Transcriptomics analysis revealed that flavonoids regulate gene expression of estrogen biosynthesis and inflammation, which is the molecular basis of their therapeutic activities (Du et al., 2020; Shi et al., 2024). 3.3 Biosynthetic pathways of polysaccharides and their precursors Even though the complete biosynthetic routes of the polysaccharides in L. japonicus are not yet as well described as in the case of alkaloids and flavonoids, genomic resources and transcriptomics now enable identification of candidate genes for the biosynthesis of the polysaccharides. These include glycosyltransferase-coding genes and precursor sugar-producing enzyme-coding genes that are overrepresented in specialized metabolic gene families (Wang et al., 2024). 3.4 Formation and characteristics of unique or enriched metabolites L. japonicus var. tongzi is remarkable due to the accumulation of leonurine, as a consequence of neofunctionalization and gene cluster expansion of the UGT-SCPL genes. Furthermore, labdane diterpenoids and stachydrine analogues are abundant in this taxon, whose localization within glandular trichomes and quantitation in diverse plant sources were recently characterized. These new metabolites explain the plant's pharmacological profile and ecological acclimation (Xiao et al., 2017; Lee et al., 2020; Zhang et al., 2025) (Figure 2). 4 Research Strategies Integrating Genomics and Multi-omics 4.1 Transcriptomic approaches revealing expression patterns Transcriptome profiling by RNA sequencing of various tissues has enabled the identification and annotation of more than 22 000 protein-coding genes in L. japonicus. The research has provided expression profiles of significant genes, including biosynthetic genes for the specialized metabolites diterpenoids and alkaloids. For example, transcriptomics found arginine decarboxylase (ADC), uridine diphosphate glucosyltransferase (UGT), and serine carboxypeptidase-like (SCPL) acyltransferase genes are vital for biosynthesis of leonurine, and also transcription factors playing roles in ecological utilization and medicinals (Li et al., 2023; Chen et al., 2024).
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