Medicinal Plant Research 2024, Vol.14, No.1, 31-44 http://hortherbpublisher.com/index.php/mpr 39 5.3 Comparative genomics and phylogenetics Comparative genomics and phylogenetic analyses are essential for understanding the evolutionary relationships and genetic diversity within Dioscorea species. The pan-plastome of D. alata, for instance, was constructed to investigate genetic variations and phylogenetic relationships among different accessions, revealing distinct clades and potential DNA barcodes (Lu et al., 2023). Similarly, the complete chloroplast genomes of various Dioscorea species have been sequenced and compared, identifying highly variable regions and constructing phylogenetic trees to resolve relationships within the genus (Wonok et al., 2023). These studies highlight the importance of comparative genomics in elucidating the evolutionary history and adaptive mechanisms of Dioscorea species, contributing to their conservation and utilization in medicinal and agricultural applications. By integrating genomic sequencing technologies, bioinformatics tools, and comparative genomics, researchers can gain a comprehensive understanding of the genetic basis underlying the adaptive evolution and medicinal properties of yam and related species. This knowledge is crucial for the development of molecular-assisted breeding programs and the sustainable use of these valuable plants in traditional medicine and agriculture. 6 Case Studies 6.1 Identification of key genes involved in adaptation Recent genomic studies have provided significant insights into the adaptive evolution of Dioscorea species. For instance, the study on Dioscorea zingiberensis revealed that tandem duplication coupled with a whole-genome duplication event provided key evolutionary resources for the diosgenin saponin biosynthetic pathway, which is crucial for the plant's adaptation and survival (Li et al., 2022). Furthermore, using chloroplast and mitochondrial DNA sequences, the phylogenetic relationships of Dioscoreaspecies were reconstructed, revealing evolutionary patterns of reproductive traits that play significant roles in species adaptation and diversification (Chen et al., 2022). These findings underscore the importance of specific gene expression patterns and genetic variations in the adaptive evolution of Dioscoreaspecies. Steroidal saponins are not only the main raw materials for synthetic steroids but also have significant medicinal value, now acclaimed as "medicinal gold" in the pharmaceutical industry. However, due to the complex and diverse structures of steroidal compounds, apart from a few steroid hormones that have received widespread attention, little is known about the biosynthetic pathways of other compounds. Preliminary genome sequencing and analysis of Dioscorea nipponica, rich in steroidal saponins, were conducted to evaluate genome size and complexity. This study provides a basis for further research on the genomes of Dioscorea species, including Dioscorea nipponica. Transcriptomic sequencing and chemical component analysis were employed to predict and analyze the biosynthetic pathways of steroidal saponins. Through transcriptome assembly and annotation, genes potentially involved in the biosynthesis of steroidal saponins were identified and analyzed for their expression, revealing 21 candidate genes likely involved in the biosynthesis pathway (Wang Bo, 2015, Peking Union Medical College). 6.2 Genetic research related to the pharmacological effects and biosynthesis of yam Yam is renowned for its medicinal properties, which are attributed to its rich chemical composition, including polysaccharides, stilbenes, diarylheptanoids, steroids, lignans, and terpenoids. These compounds exhibit various biological activities such as anti-oxidation, immune enhancement, and hypoglycemic effects (Ge et al., 2023). Genomic studies on Dioscorea nipponica, a closely related species, have developed extensive genomic resources, including plastome-derived SSRs and polymorphic nuclear SSRs, which can be instrumental in understanding the genetic basis of these medicinal properties (Hu et al., 2023). Furthermore, the pan-plastome analysis of Dioscorea alata has revealed significant genetic variations and potential DNA barcodes that could be utilized for molecular-assisted breeding and industrial utilization of Dioscorea species (Lu et al., 2023). The main component of yam, diosgenin saponin, possesses various beneficial effects including anti-inflammatory, anti-tumor, antiviral, cholesterol-lowering, blood pressure-reducing, molluscicidal, and contraceptive properties. It is used in the treatment of tracheitis and has insecticidal and antifungal effects against dermatophytes. Its
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