Genomics and Applied Biology 2024, Vol.15, No.5, 235-244 http://bioscipublisher.com/index.php/gab 236 explores the phylogenetic relationships between E. ulmoides and related species, aiding in the understanding of its evolutionary history. These findings not only enhance the genomic resources of E. ulmoides but also offer valuable insights for its conservation and utilization in medicinal and industrial applications. By leveraging detailed chloroplast genome data, this research establishes a foundation for future studies on the genetic diversity and evolutionary dynamics of this important medicinal plant. 2 Characterization of Eucommia ulmoides Chloroplast Genome 2.1 Genome size and content The chloroplast genome of Eucommia ulmoides, a significant traditional medicinal plant in China, has been thoroughly analyzed and reported to be 163 586 base pairs (bp) in length. This genome exhibits the typical quadripartite structure, comprising a LSC region of 86 773 bp, a SSC region of 14 167 bp, and two IR regions, each 31 323 bp in length. The overall GC content of the chloroplast genome is 38.4%, with the remaining nucleotides being adenine (A) and thymine (T) at 30.8% each, and cytosine (C) and guanine (G) at 19.2% each (Zhu et al., 2020). 2.2 Gene organization and coding regions The chloroplast genome of E. ulmoides contains a total of 135 genes. These include 89 protein-coding genes, 38 transfer RNA (tRNA) genes, and 8 ribosomal RNA (rRNA) genes. This gene composition is consistent with other angiosperm chloroplast genomes, which typically feature a similar number of genes and organization. The presence of these genes supports the essential functions of the chloroplast, including photosynthesis and various biosynthetic pathways (Zhu et al., 2020; Li et al., 2021). 2.3 Repetitive sequences and inverted repeats Repetitive sequences play a crucial role in the structural variation and evolution of chloroplast genomes. In the case of E. ulmoides, the chloroplast genome contains several simple sequence repeats (SSRs), which are predominantly composed of single nucleotides (A) n and (T) n, reflecting an A/T bias. These SSRs are mostly 10~12 bp in length. Additionally, the IR regions in the E. ulmoides chloroplast genome are significant, each being 31 323 bp long. These IR regions contribute to the stability of the chloroplast genome and are involved in the regulation of gene expression (Wang et al., 2018; Zhu et al., 2020; Li et al., 2021). The detailed characterization of the chloroplast genome of E. ulmoides provides valuable insights into its genetic structure and evolutionary relationships, which are essential for further studies on its conservation and utilization in medicinal and industrial applications. 3 Comparative Genomics 3.1 Intraspecific comparisons The chloroplast genomes of Eucommia ulmoides exhibit notable consistency in their overall structure. However, variations in genome size have been observed, which are primarily attributed to differences in DNA repeat sequences. A comprehensive comparison of two E. ulmoides chloroplast genomes revealed that the structure remains highly conserved, but sequence divergence patterns vary across different regions. Specifically, most SNPs are located in gene regions, while indels are predominantly found in intergenic spacers. Additionally, all detected coding-region SNPs were synonymous mutations, indicating a high level of functional conservation (Yang et al., 2020). The chloroplast genome of E. ulmoides is characterized by a typical quadripartite structure, consisting of a LSC region, a SSC region, and two IR regions. The genome size is approximately 163 586 bp, with a GC content of 38.4%. This structure includes 135 genes, comprising 89 protein-coding genes, 38 tRNA genes, and 8 rRNA genes. Despite the overall structural consistency, variations in genome size are influenced by the presence of DNA repeats and other sequence elements (Zhu et al., 2020). 3.2 Interspecific comparisons Phylogenetic analyses have shown that Eucommia ulmoides shared a close evolutionary relationship with Aucuba japonica, both belonging to the order Garryales. This relationship is supported by chloroplast comparative
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