Genomics and Applied Biology 2024, Vol.15, No.5, 235-244 http://bioscipublisher.com/index.php/gab 239 5 Case Studies 5.1 Adaptive evolution inEucommia ulmoides Eucommia ulmoides, a Tertiary relic plant endemic to China, has shown significant adaptive evolution in its chloroplast genome. A comprehensive comparison of two complete chloroplast genomes of E. ulmoides revealed heterogeneous sequence divergence patterns across different regions. Notably, most SNPs were located in gene regions, while indels were predominantly found in intergenic spacers. Interestingly, all detected SNPs in coding regions were synonymous mutations, indicating a potential mechanism for maintaining protein function while allowing genetic diversity (Figure 3) (Du et al., 2023). This adaptive evolution is crucial for the conservation and future genetic studies of this endangered species. 5.2 Chloroplast genome variation under different environmental conditions The chloroplast genome of Eucommia ulmoides has been characterized to understand its variation under different environmental conditions. The chloroplast genome, with a length of 163 586 bp, exhibits a typical quadripartite structure, including LSC and SSC regions, separated by two IRs. The genome contains 135 genes, including 89 protein-coding genes, 38 transfer RNA genes, and 8 ribosomal RNA genes. The overall GC content is 38.4%, which is consistent with other chloroplast genomes. Phylogenetic analysis has shown that E. ulmoides clusters closely with Aucuba japonica, suggesting a shared evolutionary history (Zhu et al., 2020). This detailed characterization provides a foundation for studying how environmental factors may influence chloroplast genome variation in E. ulmoides. 5.3 Comparison of case studies with other species Comparing the chloroplast genome of Eucommia ulmoides with other species, several unique features and commonalities emerge. For instance, the chloroplast genome of E. ulmoides shows a high degree of structural consistency and sequence divergence patterns similar to those observed in other plant species. However, the presence of a significant number of synonymous SNPs in E. ulmoides suggests a unique adaptive strategy to maintain protein function while allowing genetic diversity (Wang et al., 2018). Additionally, the phylogenetic relationship between E. ulmoides and Aucuba japonica highlights a close evolutionary link, which is also observed in other species within the Garryales order (Turmel et al., 2009). These comparisons underscore the importance of chloroplast genome studies in understanding the evolutionary dynamics and adaptive mechanisms in different plant species. Figure 3 Landscape of female V1 and male V2 genome (Adopted from Du et al., 2023) Image caption: This Circos plot provides a comprehensive overview of the comparative genomic landscape between Female V1 and Male V2. It highlights both the similarities and differences at the chromosomal level, offering insights into structural variations, evolutionary relationships, and potential functional implications of the observed genomic patterns (Adopted from Du et al., 2023)
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