Genomics and Applied Biology 2024, Vol.15, No.4, 191-199 http://bioscipublisher.com/index.php/gab 191 Research Insight Open Access Research on Chloroplast Genome Variation and Phylogenetic Relationships in Camellia sinensis Lian Chen, Chuchu Liu Institute of Life Science, Jiyang College of Zhejiang A&F University, Zhuji, 311800, China Corresponding author: chuchu.liu@jicat.org Genomics and Applied Biology, 2024, Vol.15, No.4 doi: 10.5376/gab.2024.15.0021 Received: 12 Jun., 2024 Accepted: 21 Jul., 2024 Published: 02 Aug., 2024 Copyright © 2024 Chen and Liu, 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 L., and Liu C.C., 2024, Research on chloroplast genome variation and phylogenetic relationships in Camellia sinensis, Genomics and Applied Biology, 15(4): 191-199 (doi: 10.5376/gab.2024.15.0021) Abstract This study explores the chloroplast genome variation and phylogenetic relationships in Camellia sinensis. As a globally important economic crop, understanding the genome structure of tea is crucial for its breeding and improvement. Research on the chloroplast genome provides key insights into species evolution, especially regarding the classification and domestication of tea varieties. By collecting samples from representative Camellia sinensis cultivars and utilizing high-throughput sequencing techniques and bioinformatics tools, this study analyzes genetic variations in the chloroplast genome, such as SNPs and indels, and constructs phylogenetic trees to demonstrate the relationships between different cultivars. The results reveal that chloroplast genome variation correlates with the geographic distribution and phenotypic traits of tea, making it a potential marker for tea breeding and conservation. This research not only enhances our understanding of the chloroplast genome in Camellia sinensis but also provides valuable references for the genetic improvement and development of the tea industry. Keywords Camellia sinensis; Chloroplast genome; Genetic variation; Phylogeny; Tea breeding 1 Introduction Camellia sinensis is one of the most important economic crops globally, serving as the primary source of tea. It is widely cultivated in countries such as China, India, Japan, and Sri Lanka. Due to differences in cultivation practices, processing methods, and genetic backgrounds, various tea types have emerged, including green, black, oolong, and white tea (Li et al., 2021a; Yang et al., 2022; Liang et al., 2023). The cultivation, processing, and trade of Camellia sinensis not only sustain the global tea industry but also support the livelihoods of millions, making the study of its genetic background crucial for tea breeding and industry development. The chloroplast genome plays a central role in essential biological functions in plants, such as photosynthesis and the synthesis of fatty acids and amino acids (Li et al., 2021a; Lin et al., 2022). Studying the chloroplast genome not only helps reveal the evolutionary history of plants but also provides insights into the genetic diversity and domestication process of tea plants through comparative analyses of genome structure and sequence polymorphisms (Hao et al., 2019a). Additionally, chloroplast genome data have significant applications in developing molecular markers, improving tea cultivars, and conserving the genetic resources of tea plants. This study compiles and analyzes the complete chloroplast genome sequences of various Camellia sinensis cultivars and related species, focusing on structural differences such as repeat sequences, insertions-deletions (indels), and single nucleotide polymorphisms (SNPs). It also explores the phylogenetic relationships among different tea cultivars based on chloroplast genome data, shedding light on key nodes in the evolutionary history of tea plants. These findings will enhance the understanding of the impact of chloroplast genome variation on the classification, domestication, and breeding of tea, providing a scientific basis for future genetic improvement and industry development. 2 Chloroplast Genome Structure inCamellia sinensis 2.1 General structure and features of the chloroplast genome The chloroplast genome of Camellia sinensis exhibits a typical quadripartite structure, which includes a large single-copy (LSC) region, a small single-copy (SSC) region, and a pair of inverted repeats (IRs). The total length
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