Medicinal Plant Research 2025, Vol.15, No.3, 142-150 http://hortherbpublisher.com/index.php/mpr 145 Figure 2 Growth status and metabolite accumulation patterns of Astragalus membranaceus var. mongholicus at different harvest stages (Adopted from Li et al., 2024) 3.3 Analytical methods and bioinformatics tools A few of the bioinformatics tools to be used for pan-genome analysis include whole-genome aligners (progressiveMauve, Mugsy, progressiveCactus) for multiple genome alignment and locally collinear block detection (Alonge et al., 2019). Compressed hybrid-indexing methods (DHPGIndex) enable large-scale and rapid sequence alignment of big pan-genome datasets (Maarala et al., 2021). Gene clustering and orthology finding tools (OrthoMCL) are utilized for classifying core and dispensable genes. The tools and techniques employed, together with sequencing depth and assembly method, can impose a substantial effect on the ultimate pan-genome and its biological significance (Jayakodi et al., 2021). 4 Construction and Application Progress of the Astragalus Pan-genome 4.1 Germplasm resources and genetic diversity of Astragalus Astragalus has abundant germplasm resources and high genetic diversity, and over 2 500-3 000 species are available in the world with great variation among wild and cultivated populations. With SSR, ISSR, and RAPD markers, studies have detected abundant genetic diversity within and among populations, and most of the genetic variation being between populations but not within them. Core collections produced through molecular markers preserve the majority of allelic diversity and population structure and are a good investment for breeding and conservation (Dong et al., 2024). Genetic diversity in Astragalus plays significant roles in germplasm identification, conservation of resources, and the production of novel varieties with target traits (Liu et al., 2016; Dong, 2024). 4.2 Gene structural variations revealed by the pan-genome Pan-genomic and genomic comparative analyses portrayed the structural divergence in Astragalus as utmost, including chromosomal reorganization, inversions, and repeat-mediated recombination events particularly plastid genomes (Moghaddam et al., 2023). Structural variation and hypervariable loci like a 13-kb inversion within the IR region have been shown to cause genome evolution and diversity. Structural variation is an important molecular markers for phylogeny and species identification studies (Moghaddam et al., 2023).
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