Genomics and Applied Biology 2024, Vol.15, No.5, 235-244 http://bioscipublisher.com/index.php/gab 237 genome, which revealed significant similarities in genome structure and gene content between the two species. Such comparisons help elucidate the evolutionary pathways and divergence events that have shaped the chloroplast genomes of these related species (Figure 1) (Wang et al., 2018; Hu et al., 2023). The phylogenetic relationship between E. ulmoides and Aucuba japonica has been confirmed through chloroplast phylogenomic analyses. It indicated a sisterly relationship between them, suggesting a relatively recent common ancestor. The divergence between these species is marked by specific genomic rearrangements and sequence variations that have occurred over evolutionary time scales. This phylogenetic insight is crucial for understanding the evolutionary history and genetic diversity within the Eucommiaceae family and related groups. 3.3 Evolutionary insights The evolution of chloroplast genomes in the Eucommiaceae family, particularly in Eucommia ulmoides, is characterized by a high degree of structural conservation and functional stability. The presence of synonymous mutations in coding regions and the distribution of indels in intergenic spacers suggested that selective pressures have maintained the integrity of essential genes while allowing for variability in non-coding regions. This pattern of evolution highlights the balance between conservation and adaptation in chloroplast genomes (Green, 2011; Zhu et al., 2020). Genome rearrangements and duplications have played a significant role in the evolution of chloroplast genomes in E. ulmoides and related species. The identification of a new whole-genome duplication event, superimposed on an earlier paleohexaploidization event, underscores the complexity of genomic evolution in this lineage. These duplications have contributed to the expansion of gene families and the diversification of metabolic pathways, such as those involved in rubber and chlorogenic acid biosynthesis. Understanding these genomic rearrangements provides valuable insights into the adaptive strategies and evolutionary dynamics of chloroplast genomes in the Eucommiaceae family (Jin et al., 2020). Figure 1 Collinearity analyses of the MYB gene family inE. ulmoides (Adopted from Hu et al., 2023) Image caption: The Circos plot provides a visual representation of the genomic relationships and collinearity of the MYB gene family in Eucommia ulmoides. It highlights the extensive duplication and distribution of these genes across multiple chromosomes, which likely plays a significant role in the plant's adaptability and functional diversity (Adopted from Hu et al., 2023)
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