International Journal of Molecular Evolution and Biodiversity 2024, Vol.14, No.5, 219-228 http://ecoevopublisher.com/index.php/ijmeb 219 Research Insight Open Access Identification of Divergence Patterns in the Chloroplast Genome of Eucommia ulmoides Tiantian Yan 1, Honglin Wang1,2 , Degang Zhao1,2 1 National-local Joint Engineering Research Center of Karst Region Plant Resources Utilization & Breeding (Guizhou), College of Life Sciences/Institute of Agro- Bioengineering, Guizhou University, Guiyang 550025, China 2 Plant Conservation & Breeding Technology Center, Guizhou Key Laboratory of Agricultural Biotechnology / Guizhou Institute of Pomology Science, Guizhou Academy of Agricultural Sciences, Guiyang, 550006, China Corresponding author: wanghonglinly@163.com; dgzhao@gzu.edu.cn International Journal of Molecular Evolution and Biodiversity, 2024, Vol.14, No.5 doi: 10.5376/ijmeb.2024.15.0023 Received: 09 Aug., 2024 Accepted: 17 Sep., 2024 Published: 25 Sep., 2024 Copyright © 2024 Yan 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: Yan T.T., Wang H.L., and Zhao D.G., 2024, Identification of Divergence Patterns in the Chloroplast Genome of Eucommia ulmoides, International Journal of Molecular Evolution and Biodiversity, 14(5): 219-228 (doi: 10.5376/ijmeb.2024.15.0023) Abstract Eucommia ulmoides is a Tertiary relic plant endemic to China, possessing significant medicinal and industrial value. Due to the scarcity of genomic data, studies on the population genetics and genomics of E. ulmoides remain limited. This study reveals the structural organization and sequence variation of the chloroplast genome of E. ulmoides by comparing complete chloroplast genome sequences. The findings show that most single nucleotide polymorphisms (SNPs) are located in gene regions, while insertions/deletions (indels) are primarily concentrated in intergenic spacers. Additionally, the study explores the phylogenetic relationships between E. ulmoides and related species based on chloroplast genome data. The results indicate that the chloroplast genome of E. ulmoides exhibits significant heterogeneous divergence patterns, with all coding-region SNPs being synonymous mutations, thereby not affecting protein function. This discovery provides important molecular markers for the conservation and breeding programs of E. ulmoides and enhances our understanding of plant evolution and genetic diversity. Future research will further investigate the impact of environmental factors on chloroplast genome variation and expression, promoting the conservation and sustainable utilization of E. ulmoides. Keywords Eucommia ulmoides; Chloroplast genome; Divergence patterns; Single nucleotide polymorphisms (SNPs); Phylogenetic analysis; Genetic diversity 1 Introduction Chloroplast genomes, also known as plastomes, are essential components of plant cells, playing a crucial role in photosynthesis and other metabolic processes. Research on chloroplast genomes has significantly advanced our understanding of plant evolution, phylogenetics, and genetic diversity. Comparative genomic studies have revealed the structural organization, gene content, and evolutionary dynamics of chloroplast genomes across various plant species (Turmel et al., 2009; Fučíková et al., 2016). These studies have also identified mutation hotspots and sequence divergence patterns, which are critical for understanding the evolutionary history and adaptation mechanisms of plants (Wang et al., 2018; Liu et al., 2023). Eucommia ulmoides, commonly known as the hardy rubber tree, is a Tertiary relic plant endemic to China with significant medicinal and industrial value. Despite its importance, the population genetics and genomic studies of E. ulmoides have been limited due to the scarcity of genomic data. Understanding the divergence patterns in the chloroplast genome of E. ulmoides is crucial for several reasons (Qing et al., 2021). It provides insights into the evolutionary history and genetic diversity of this species, which is essential for its conservation and sustainable utilization. Furthermore, identifying polymorphic regions and molecular markers can facilitate population genetics studies and breeding programs aimed at improving the medicinal and industrial traits of E. ulmoides (Wang et al., 2018; Du et al., 2023). Besides, studying the chloroplast genome can shed light on the phylogenetic relationships between E. ulmoides and other related species, enhancing our understanding of plant evolution (Zhong et al., 2022).
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