Journal of Tea Science Research, 2024, Vol.14, No.2, 79-91 http://hortherbpublisher.com/index.php/jtsr 79 Systematic Review Open Access Unlocking the Tea Genome: Advances in High-Quality Sequencing and Annotation Xi Chen1, Yichen Zhao2 1 Guizhou Institute of Pratacultural / Plant Conservation & Breeding Technology Center, Guizhou Academy of Agricultural Sciences, Guiyang, 550006, Guizhou, China 2 Key Laboratory of Plant Resources Conservation and Germplasm Innovation in Mountainous Region (Ministry of Education), College of Tea Sciences, Guizhou University, Guiyang, 550025, Guizhou, China Corresponding author: yczhao@gzu.edu.cn Journal of Tea Science Research, 2024, Vol.14, No.2 doi: 10.5376/jtsr.2024.14.0008 Received: 18 Jan., 2024 Accepted: 20 Feb., 2024 Published: 02 Mar., 2024 Copyright © 2024 Chen and Zhao, 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., and Zhao Y.C., 2024, Unlocking the tea genome: advances in high-quality sequencing and annotation, Journal of Tea Science Research, 14(2): 79-91 (doi: 10.5376/jtsr.2024.14.0008) Abstract This study explores the latest advancements in high-quality sequencing and annotation of the tea plant genome, revealing its genetic diversity, regulatory mechanisms, and biotechnological applications. Through comprehensive genomic analysis, significant discoveries have been made, including the assembly of the complex tea plant genome, key genes regulating the synthesis of bioactive compounds (such as catechins and caffeine), and epigenetic regulatory mechanisms influencing tea plant phenotypes and environmental adaptability. Comparative genomics studies have elucidated the relationships between tea cultivars and their wild relatives, enhancing the understanding of genetic variation and adaptive traits. These findings highlight the potential of tea genomics in precision breeding, which can be used to develop climate-resistant cultivars, improve tea quality, and diversify market products. The advancements in high-quality sequencing and annotation of the tea plant genome have significantly improved our understanding of the genetic and metabolic bases of tea quality. These discoveries provide valuable resources for future research and breeding programs aimed at improving tea plant varieties and expanding the diversity of tea flavors. Keywords Tea plant genome; High-quality sequencing; Annotation; Genetic diversity; Biotechnological applications; Precision breeding 1 Introduction Tea (Camellia sinensis) is one of the most widely consumed beverages globally, cherished not only for its unique flavors but also for its numerous health benefits. The economic, cultural, and medicinal significance of tea has driven extensive research into its genetic makeup. Understanding the tea genome is crucial as it provides insights into the genetic basis of key quality traits of tea, such as flavor, aroma, and health-promoting compounds (Shi et al., 2011; Xia et al., 2017; Wei et al., 2018). Simultaneously, it aids in the identification of genes responsible for stress resistance and adaptation, which is vital for improving tea crop resilience in the face of climate change (Xia et al., 2020a; Kong et al., 2022). Furthermore, comprehensive genomic knowledge facilitates advanced breeding programs aimed at developing superior tea varieties with enhanced traits (Zhang et al., 2021a). The journey of tea genome sequencing has seen significant milestones over the past years. Early efforts were marked by the draft genome sequence of Camellia sinensis var. sinensis, which provided initial insights into the evolution of the tea genome and its quality traits (Wei et al., 2018). Subsequent studies focused on high-quality genome assemblies, such as the haplotype-resolved genome assembly of the Oolong tea cultivar Tieguanyin, which shed light on the evolutionary history and genetic diversity of tea plants (Zhang et al., 2021a). The reference genome of Camellia sinensis var. sinensis, consisting of 15 pseudo-chromosomes, further elucidated the roles of LTR retrotransposons in genome size expansion and gene diversification (Xia et al., 2020a). Additionally, transcriptome profiling using advanced sequencing technologies has revealed candidate genes for major metabolic pathways, enhancing our understanding of tea-specific compounds (Shi et al., 2011; Wang et al., 2020).
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