Medicinal Plant Research 2024, Vol.14, No.1, 31-44 http://hortherbpublisher.com/index.php/mpr 32 2 Genomic Features of Yam 2.1 Genome sequencing and assembly The genome sequencing and assembly of yam have been pivotal in understanding its genetic makeup and potential for medicinal applications. High-quality genome sequencing has been performed on related Dioscorea species, such as Dioscorea zingiberensis (Figure 1), Dioscorea rotundata (Ma et al., 2018; Li et al., 2022), which provides insights into the biosynthesis and evolution of important metabolites like diosgenin saponins (Ma et al., 2018; Li et al., 2022). These studies reveal that the genome of Dioscorea species is complex, with significant gene duplication events that have contributed to the evolution of their unique metabolic pathways. The assembly of these genomes has been anchored on multiple chromosomes, providing a comprehensive framework for further genetic and functional studies. Figure 1 Genome assembly characterization and genome evolution of D. zingiberensis (Adopted from Li et al., 2022) Image caption: (a) Circos view of the D. zingiberensis genome. (i) TE density distributions in each linkage group. (ii) Gene density: numbers of genes in 1-Mb non-overlapping windows. (iii) Gene expression levels: gene expression levels of each gene in leaves, stems, and rhizomes of D. zingiberensis. The distribution of TE density shows a peak in the middle, while that of gene density shows two peaks, with one at each end. (b) Phylogenetic tree showing the divergence times and evolution of gene family sizes for 13 plant species. The value at each node represents the divergence time in millions of years ago (Mya) relative to the present. Expansion: number of gene families expanded (green); Contraction: number of gene families contracted (red); Total: total number of gene families (black). (c) WGD events detected in D. zingiberensis. Frequency plot of Ks distributions of paralogs identified fromD. zingiberensis, D. rotundata, andA. officinalis (Adopted from Li et al., 2022)
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