Genomics and Applied Biology 2024, Vol.15, No.5, 235-244 http://bioscipublisher.com/index.php/gab 242 9 Concluding Remarks The study on the chloroplast genome structure of Eucommia ulmoides has yielded several significant insights. The chloroplast genome of E. ulmoides was found to be highly consistent in structure, with variations in genome size attributed to DNA repeat variations. The genome exhibited a typical quadripartite structure, including a LSC region, a SSC region, and two IR regions. The study identified 135 genes within the chloroplast genome, including 89 protein-coding genes, 38 tRNA genes, and 8 rRNA genes. Additionally, the research revealed heterogeneous sequence divergence patterns, with most SNPs located in gene regions and most indels in intergenic spacers. Phylogenetic analysis confirmed the sister relationship between E. ulmoides and Aucuba japonica. The findings from this study have several implications for future research. The identification of 71 polymorphic cpDNA fragments and the development of eight polymorphic cpSSR loci provide valuable molecular markers for subsequent population genetics studies of E. ulmoides. These markers can be instrumental in conservation genomics, aiding in the preservation of this endangered species. Furthermore, the comprehensive chloroplast genome data can facilitate comparative genomic studies, enhancing our understanding of the evolutionary relationships within the Garryales order. Future research could also explore the functional genomics of the identified genes, particularly those involved in the biosynthesis of medicinal compounds, to improve the industrial and medicinal applications of E. ulmoides. The characterization of the chloroplast genome in Eucommia ulmoides is a significant milestone in the genomic study of this medicinally and industrially important species. The detailed genomic information not only enhances our understanding of the genetic structure and evolutionary history of E. ulmoides but also provides essential tools for its conservation and improvement. The insights gained from this study underscore the importance of chloroplast genome research in uncovering the genetic basis of key traits and in supporting the sustainable utilization of E. ulmoides in various applications. As we continue to explore the genetic intricacies of this species, the knowledge generated will undoubtedly contribute to its preservation and the optimization of its valuable properties. Acknowledgments The authors extend sincere thanks to two anonymous peer reviewers for their feedback on the manuscript. Funding This research was funded by a grant from the National Natural Science Foundation of China [31870285, 30660146], Guizhou Academy of Agricultural Sciences Talent Special Project (No. 2023-02 and 2024-02), National High Tech nology Research and Development Program of China (“863” Program) grant number 2013AA102605-05, Talent Base for Germplasm Resources Utilization and Innovation of Characteristic Plant in Guizhou (RCJD2018-14). Conflict of Interest Disclosure The authors affirm that this research was conducted without any commercial or financial relationships that could be construed as a potential conflict of interest. References Bayly M., Rigault P., Spokevicius A., Ladiges P., Ades P., Anderson C., Bossinger G., Merchant A., Udovicic F., Woodrow I., and Tibbits J., 2013, Chloroplast genome analysis of Australian eucalypts--Eucalyptus, Corymbia, Angophora, Allosyncarpia and Stockwellia (Myrtaceae), Molecular Phylogenetics and Evolution, 69(3): 704-716. https://doi.org/10.1016/j.ympev.2013.07.006 Cronn R., Liston A., Parks M., GeRNAndt D., Shen R., and Mockler T., 2008, Multiplex sequencing of plant chloroplast genomes using Solexa sequencing-by-synthesis technology. Nucleic acids research, 36(19): e122. https://doi.org/10.1093/nar/gkn502
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