Medicinal Plant Research 2025, Vol.15, No.3, 142-150 http://hortherbpublisher.com/index.php/mpr 143 Over the past decade, the pan-genome platform, including the core and accessory gene set of a species, has also emerged as an analytical tool of immense utility for defining the entire genetic repertoire and structural variation of a species. Pan-genome analyses of rice, maize, and soybean crops have unraveled extensive-scale genetic diversity linked with agronomic quality, stress resistance, and metabolite diversity. Alternatively, in pharmaceutical factories, pan-genomics is increasingly utilized to investigate genetic diversity underlying secondary metabolite biosynthesis and adaptive adaptation. By integrating multi-omics data into advanced bioinformatics tools, pan-genomics reveals unprecedented opportunities to research the molecular foundation of difference in traits, unveiling novel understandings of plant biology and functional breeding (Liu et al., 2025). This Study gives an overall overview of advances in the genomics of Astragalus and the emerging application of pan-genomics to account for trait diversity. It condenses existing developments in genome sequencing and functional annotation, highlights the theoretical foundations and principles of pan-genomic analysis, and outlines how pan-genome research reveals structural variations, metabolic gene diversity, and adaptation traits in Astragalus. Particular emphasis is given to the genetic basis of variation in traits, and examples are taken from polysaccharide composition, flavonoid accumulation, and stress resistance. The study also mentions the possible advantages of pan-genomics to breeding, germplasm utilization, and precision herbal medicine formulation. Through the adoption of information of multi-omics and computation techniques, the study shows the significance of Astragalus pan-genome research in Medicinal plant improvement and promotion of modernization of traditional Chinese medicine. 2 Advances in Astragalus Genomic Research: A Review 2.1 Overview of Astragalus genome sequencing and annotation Recent years have seen impressive progress in the genomics of Astragalus membranaceus and its closest relatives. High-quality chromosome-scale genome assemblies were achieved with the latest sequencing technologies such as PacBio long reads and Hi-C scaffolding. For example, recently available was a 1.43 Gb genome with 98% of assembly anchored onto nine pseudochromosomes and nearly 30 000 protein-coding genes, offering a solid platform for comparative and functional studies (Fan et al., 2024) (Figure 1). Similarly, a reference-quality genome of Astragalus mongholicus detected 27 868 protein-coding genes and reported the gene families for secondary metabolite biosynthesis to be enriched (Chen et al., 2022). Transcriptome sequencing guided by reference genomes as well as without reference genomes has also made it possible to identify full-length transcripts and isoforms to enhance gene annotation and transcript variant discovery (Li et al., 2017; Kang et al., 2024). 2.2 Genes and metabolic pathways related to medicinal compounds Genomic and transcriptomic studies have revealed key genes and pathways for the biosynthesis of the primary medicinal ingredients of Astragalus, such as triterpenoid saponins (astragalosides), flavonoids (e.g., calycosin), and isoflavonoids. Studies have shown that pathways involve dozens of genes and transcription factors (e.g., MYBs, bHLHs, AP2-EREBPs), with gene family expansion through tandem duplication. For instance, the phenylalanine ammonia-lyase (PAL) gene cluster has high expression in roots and is a key player in the biosynthesis of phenylpropanoid and flavonoids (Liang et al., 2020). Differentially expressed during development and tissues related to the accumulation of bioactive compounds and provides targets for breeding and metabolic engineering (Li et al., 2024; Li et al., 2025). 2.3 Comparative applications of genomic research in medicinal plants Comparative genomics of Astragalus and medicinal plants has revealed evolutionary trends, e.g., the absence of recent whole-genome duplication in Astragalus mongholicus and long terminal repeat retrotransposon activity in genome growth (Bagheri et al., 2022). Studies of chloroplast and mitochondrial genomes have contributed to phylogenetic resolution, species definition, and building molecular markers (Lei et al., 2016; Liu et al., 2020; Tian et al., 2021). These resources allow the study of medicinal property trait diversity, adaptation, and molecular basis of medicinal properties to conserve and improve medicinal plant germplasm (Bagheri et al., 2022; Moghaddam et al., 2023; Li et al., 2024) (Figure 2).
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