Genomics and Applied Biology 2024, Vol.15, No.5, 235-244 http://bioscipublisher.com/index.php/gab 235 Research Insight Open Access Characterization of Chloroplast Genome Structure inEucommia ulmoides Xi Chen1, Siyi Tian2, Degang Zhao1,2 1 Plant Conservation & Breeding Technology Center, Guizhou Key Laboratory of Agricultural Biotechnology/Guizhou Institute of Pratacultural, Guizhou Academy of Agricultural Sciences, Guiyang, 550006, China; 2 National-local Joint Engineering Research Center of Karst Region Plant ResourcesUtilization & Breeding (Guizhou), College of Life Sciences/Institute of Agro- Bioengineering, Guizhou University, Guiyang, 550025, China Corresponding author: dgzhao@gzu.edu.cn Genomics and Applied Biology, 2024, Vol.15, No.5 doi: 10.5376/gab.2024.15.0025 Received: 25 Jul., 2024 Accepted: 02 Sep., 2024 Published: 16 Sep., 2024 Copyright © 2024 Chen et al., This is an open access article published under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. Preferred citation for this article: Chen X., Tian S.Y., and Zhao D.G., 2024, Characterization of chloroplast genome structure in Eucommia ulmoides, Genomics and Applied Biology, 15(5): 235-244 (doi: 10.5376/gab.2024.15.0025) Abstract Eucommia ulmoides, a significant medicinal and industrial plant endemic to China, has been the subject of various genomic studies due to its unique properties and evolutionary significance. This study focuses on the characterization of the chloroplast genome structure of E. ulmoides. The complete chloroplast genome of E. ulmoides was sequenced and analyzed, revealing a typical quadripartite structure with a total length of 163 586 bp, including a large single-copy region, a small single-copy region, and two inverted repeat regions. The genome contains 135 genes, comprising 89 protein-coding genes, 38 transfer RNAgenes, and 8 ribosomal RNA genes. Comparative genomic analysis indicated high structural consistency and size variation due to DNA repeat variations. Phylogenetic analysis confirmed the close relationship between E. ulmoides and Aucuba japonica. This comprehensive characterization provides valuable insights into the genetic makeup and evolutionary history of E. ulmoides, facilitating future conservation and utilization efforts. Keywords Eucommia ulmoides; Chloroplast genome; Phylogenetic analysis; Genomic structure; Conservation genomics 1 Introduction Chloroplasts are essential organelles in plants, algae, and cyanobacteria, primarily responsible for photosynthesis, which converts light energy into chemical energy stored in organic compounds. Besides, chloroplasts are involved in the biosynthesis of fatty acids, amino acids, hormones, vitamins, nucleotides, and secondary metabolites (Dobrogojski et al., 2020). The chloroplast genome, or plastome, is highly conserved in terms of gene order and content, making it a valuable tool for phylogenetic studies and evolutionary inferences. The nonrecombinant and uniparentally inherited nature of chloroplast genomes further enhances their utility in evolutionary studies, as they retain signatures of their age better than nuclear genomes (Provan et al., 2000; Ravi et al., 2008). The increasing availability of complete chloroplast genome sequences has facilitated detailed comparative analyses, revealing dynamic patterns of evolution and aiding in the resolution of phylogenetic relationships among plant species (Bayly et al., 2013; Zhou et al., 2021). Eucommia ulmoides, commonly known as the hardy rubber tree, is a significant traditional medicinal plant in China, widely used for orthopedic treatments (Zhu et al., 2020). It is the sole species of the family Eucommiaceae and is considered a Tertiary relic plant endemic to China (Rogers et al., 2007). Despite its medicinal and industrial importance, the population genetics of E. ulmoides has been underexplored due to limited genomic data (Wang et al., 2017). Recent studies have begun to address this gap by generating and analyzing the complete chloroplast genome of E. ulmoides, providing insights into its genomic structure and evolutionary relationships (Wang et al., 2017; Zhu et al., 2020). The chloroplast genome of E. ulmoides exhibits a typical quadripartite structure, with a large single-copy (LSC) region, a small single-copy (SSC) region, and two inverted repeat (IR) regions (Zhu et al., 2020). Comparative analyses have shown that the chloroplast genome of E. ulmoides is highly consistent in structure, with variations primarily resulting from DNA repeat variations (Wang et al., 2017). This study provides a comprehensive characterization of the chloroplast genome structure of E. ulmoides. By analyzing the complete chloroplast genome, it clarifies genomic features such as genome size, gene content, and repetitive sequences, and identifies potential molecular markers for population genetics research. Additionally, it
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