Medicinal Plant Research 2024, Vol.14, No.1, 31-44 http://hortherbpublisher.com/index.php/mpr 38 The medicinal properties of yam are deeply rooted in its traditional uses and are supported by a rich array of bioactive compounds. Advances in genomic research are providing valuable insights into the biosynthetic pathways of these compounds, paving the way for enhanced utilization and conservation of this important medicinal plant. 5 Genomic Analysis Techniques 5.1 Genomic sequencing technologies For medicinal plants, the advancement of genome sequencing projects will drive the application of cutting-edge technologies in medicinal plant research. This progress provides a theoretical basis for elucidating the synthesis and regulation of effective components in medicinal plants, facilitating the screening of plant-derived natural medicines and the study of important secondary metabolite biosynthesis. Currently, research on biosynthetic pathways and regulation of secondary metabolites in medicinal plants remains relatively weak, often employing single-gene research strategies. Genomic studies will promote the application of multi-omics approaches in the study of secondary metabolic pathways and their regulation, providing references for the "batch" discovery of relevant genes in these pathways. This will have a positive impact on the application research of biosynthesis and metabolic engineering of secondary metabolites with significant medicinal value (Chen et al., 2010). The advent of high-throughput sequencing technology represents a significant milestone in genomics research, drastically reducing the cost per base of nucleotide sequencing and providing a new platform and developmental opportunities for genomic research (Chen et al., 2010). The low cost of sequencing enables the sequencing of more species' genomes and decoding of genomic genetic codes, with next-generation high-throughput sequencing technologies increasingly chosen by researchers for whole-genome sequencing studies. Genomic sequencing technologies have significantly advanced our understanding of yam, providing insights into its adaptive evolution and medicinal properties. High-throughput sequencing platforms, such as the Illumina HiSeq 4000, have been employed to sequence the transcriptomes of leaf and rhizome tissues of yam, yielding millions of clean reads and thousands of unigenes (Hou et al., 2020). Additionally, low-coverage whole genome sequencing has been utilized to develop genomic resources for related Dioscoreaspecies, such as D. nipponica, revealing key mutational hotspots and polymorphic nuclear SSRs (Hu et al., 2023). These technologies enable comprehensive genomic surveys, facilitating the identification of genetic variations and the development of molecular markers essential for phylogenetic and population genetic studies (Luo et al., 2023). 5.2 Bioinformatics tools for genome analysis Bioinformatics tools play a crucial role in analyzing the vast amount of genomic data generated from sequencing technologies. In the study of yam, bioinformatics software was used to analyze transcriptome data, identify differentially expressed genes (DEGs), and validate expression patterns through qRT-PCR analysis (Hou et al., 2020). Comparative genomic analyses have also been conducted using tools to align and compare plastome sequences, identify divergent regions, and develop DNA barcodes for species delimitation (Xia et al., 2019; Lu et al., 2023). Furthermore, tools such as Automatic Barcoding Gap Discovery (ABGD), Poisson Tree Processes (PTP), and Generalized Mixed Yule Coalescence (GMYC) analysis have been applied for species delimitation based on variable loci derived from plastid genome sequences (Xia et al., 2019). Completion of whole genome sequencing for various Dioscorea species facilitates the use of bioinformatics tools for electronic cloning, structural and functional analysis of genes, and molecular evolutionary analysis within the Dioscorea genus. Starch is a crucial component of underground tubers in Dioscoreaspecies, with Granule-Bound Starch Synthase (GBSS) playing a key role in controlling amylose synthesis. Using the GBSS gene sequence of Dioscorea polystachya as a probe, electronic cloning methods obtained GBSS gene sequences from four Dioscorea species: Dioscorea alata, Dioscorea rotundata, Dioscorea bulbifera, and Dioscorea zingiberensis. Bioinformatics analysis compared and analyzed the GBSS gene structures, protein structures, and phylogenetic characteristics across these species. Identification and characterization of Dioscoreagene family members based on conserved domains provide insights into their sequence features, gene structure, chromosome localization, gene collinearity, cis-acting elements, interspecies collinearity, and phylogenetic relationships, facilitating comprehensive studies of gene family characteristics and functions in Dioscoreaspecies.
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