International Journal of Molecular Evolution and Biodiversity 2024, Vol.14, No.5, 219-228 http://ecoevopublisher.com/index.php/ijmeb 220 This study comprehensively analyzed the divergence patterns within the chloroplast genome of E. ulmoides. By comparing complete chloroplast genome sequences, it uncovered the structural organization and sequence variation of the chloroplast genome, including single nucleotide polymorphisms (SNPs), insertions/deletions (indels), and other polymorphic regions that can serve as molecular markers for population genetics studies. Additionally, it explored the phylogenetic relationships between E. ulmoides and related species based on chloroplast genome data. This study not only supports conservation genomics and breeding programs for E. ulmoides but also deepens the understanding of plant evolution and genetic diversity. The findings provide valuable genomic resources and new insights into the evolutionary dynamics of the E. ulmoides chloroplast genome. 2 Structure of the Chloroplast Genome inEucommia ulmoides 2.1 General characteristics of the chloroplast genome The chloroplast genome of Eucommia ulmoides exhibits a typical quadripartite structure, which includes a large single-copy (LSC) region, a small single-copy (SSC) region, and two inverted repeat (IR) regions. The complete chloroplast genome length of E. ulmoides is approximately 163 586 base pairs (bp) (Zhu e al., 2020). The overall GC content of the chloroplast genome is 38.4%, with the LSC region being 86 773 bp, the SSC region 14 167 bp, and the IR regions each 31 323 bp. This structure is consistent with the general organization observed in many angiosperms. 2.2 Gene content and organization The chloroplast genome of E. ulmoides contains a total of 135 genes, which include 89 protein-coding genes, 38 transfer RNA (tRNA) genes, and 8 ribosomal RNA (rRNA) genes (Zhu e al., 2020). The gene content and order are highly conserved, with no significant variations observed among different samples of E. ulmoides (Wang et al., 2018). The majority of the SNPs detected in the chloroplast genome are located in the gene regions, while most of the indels were found in the intergenic spacers. Additionally, all the putative coding-region-located SNPs identified were synonymous mutations, indicating a high level of conservation in the protein-coding regions. 2.3 Comparison with other plant species When compared to other plant species, the chloroplast genome of E. ulmoides shows a high degree of structural similarity. For instance, the chloroplast genomes of various eucalypt species also exhibit a conserved gene content and order, with minimal length mutations in protein-coding genes (Bayly et al., 2013; Li et al., 2021). Similarly, the chloroplast genomes of green algae such as Pyramimonas and Monomastix display significant structural conservation, although they exhibit more variability in gene content and order compared to E. ulmoides (Figure 1) (Turmel et al., 2009; Liu et al., 2023). In terms of phylogenetic relationships, E. ulmoides is closely related to Aucuba japonica, as confirmed by chloroplast phylogenomic analyses. This relationship is consistent with the findings from other studies that have examined the chloroplast genomes of related species within the Garryales order. The conservation of the chloroplast genome structure and gene content across different species highlights the evolutionary stability of this organelle and its importance in plant biology. Overall, the chloroplast genome of E. ulmoides provides valuable insights into the genetic and evolutionary characteristics of this species, and it serves as a crucial resource for further studies on conservation genomics and population genetics (Wang et al., 2018; Zhu e al., 2020; Du et al., 2023). 3 Methods for Identifying Divergence Patterns 3.1 Data collection and sequence alignment To identify divergence patterns in the chloroplast genome of Eucommia ulmoides, complete chloroplast genome sequences was first collected. One complete chloroplast genome was generated using the genome skimming approach, and it was compared to another available chloroplast genome of E. ulmoides (Wang et al., 2018; Zhu et al., 2020). The sequences were aligned using standard bioinformatics tools to ensure accurate comparison of genomic regions. This alignment process is crucial for identifying SNPs and indels across the genomes.
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