Genomics and Applied Biology 2024, Vol.15, No.4, 191-199 http://bioscipublisher.com/index.php/gab 193 different Camellia sinensis cultivars and species to detect variations. Tools like MUMmer and MAFFT are used for sequence alignment, while software such as GATK and SAMtools are employed for variant calling (Lin et al., 2022; Shang et al., 2022). The identified SNPs, indels, and other variations are then analyzed to understand their distribution and potential impact on the chloroplast genome structure and function (Li et al., 2021b; Chen et al., 2022; Shang et al., 2022). 4 Phylogenetic Analysis of Camellia sinensis 4.1 Selection of phylogenetic markers The selection of appropriate phylogenetic markers is crucial for constructing accurate phylogenetic trees. In the case of Camellia sinensis, chloroplast genome sequences have proven to be highly informative. Key markers include long and short sequence repeats, single nucleotide polymorphisms (SNPs), and insertion-deletions (indels) (Li et al., 2021b; Lin et al., 2022). Specific intergenic regions such as trnE/trnT and protein-coding genes with high sequence polymorphism, like those found in the atpH-atpI region, have been identified as potential barcode markers for phylogenetic analysis (Lin et al., 2022). 4.2 Construction of phylogenetic trees Phylogenetic trees for Camellia sinensis have been constructed using complete chloroplast genome sequences. These trees often employ maximum likelihood (ML) methods to infer evolutionary relationships. For instance, the complete chloroplast genome of Camellia sinensis var. sinensis cultivar 'Liupao' was used to determine its close relationship with C. sinensis var. pabilimba cv. 'Lingyunbaihao' (Figure 1) (Liang et al., 2023). Similarly, the phylogenetic analysis of Camellia sinensis var. sinensis cultivar 'FuDingDaBaiCha' showed its close relationship with other cultivars like 'AnHua', 'QianCha 1', and 'BanTianYao' (Qiao et al., 2023). These analyses highlight the utility of chloroplast genomes in resolving phylogenetic relationships within Camellia sinensis. 4.3 Comparative analysis with related species in the theaceae family Comparative genomic analyses have revealed significant insights into the phylogenetic relationships between Camellia sinensis and other species within the Theaceae family. For example, the complete chloroplast genome sequence of Camellia tachangensis showed that it clustered with Camellia gymnogyna and Camellia taliensis, while being distinct fromCamellia sinensis and its varieties (Hao et al., 2019a). Additionally, the phylogenetic analysis of Camellia sinensis cultivar 'Sangmok' indicated its close relationship with Camellia pubicosta (Lee et al., 2020). These comparative studies underscore the genetic diversity and evolutionary relationships within the Theaceae family. 4.4 Implications for evolutionary history and domestication The phylogenetic analyses of Camellia sinensis have significant implications for understanding its evolutionary history and domestication. The divergence times estimated from chloroplast genome data suggest that the Indian Assamica type tea (CIA) diverged from the common ancestor of the Assamica type teas around 6.2 million years ago, while the Chinary type tea (CSS) and Chinese Assamica type tea (CSA) diverged approximately 0.8 million years ago (Li et al., 2021b). These findings support the hypothesis of multiple domestication events for different tea types. Furthermore, the observed differences in structural characteristics and codon usage between Chinese and Indian teas suggest that they may have undergone different selection pressures during their evolution. The phylogenetic clustering results also indicate that the current taxonomy of some Camellia species may need to be revisited (Li et al., 2021b). 5 Case Study: Chloroplast Genome Variation inCamellia sinensis Cultivars 5.1 Selection of representative Camellia sinensis cultivars For this case study, we selected a diverse set of Camellia sinensis cultivars to represent the genetic and geographical diversity within the species. The chosen cultivars include: 'Wuyi narcissus' (CWN): A natural triploid Chinary type tea cultivar (Li et al., 2021b).
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