Genomics and Applied Biology 2024, Vol.15, No.4, 191-199 http://bioscipublisher.com/index.php/gab 195 5.2 Analysis of chloroplast genome variation among selected cultivars The chloroplast genomes of the selected Camellia sinensis cultivars exhibit notable variations in terms of genome size, gene content, and structural features. For instance, the chloroplast genome of 'Wuyi narcissus' (CWN) showed significant differences in structural characteristics and codon usage compared to other cultivars (Li et al., 2021b). Similarly, the chloroplast genome of 'Liupao' (LP) was found to be 157,097 bp in length with a GC content of 37.3% (Liang et al., 2023), while 'Qiancha 1' (QC1) had a genome length of 157,024 bp and the same GC content (Yang et al., 2022). Comparative analysis revealed that the evolutionary dynamics of the chloroplast genome in Camellia sinensis are driven by repeats, insertion-deletions (indels), and substitutions, which are significantly correlated (Li et al., 2021b). For example, the 'Baiye 1' cultivar exhibited a chloroplast genome length of 156 691 bp with specific variations in the large single-copy (LSC) and small single-copy (SSC) regions (Hao et al., 2019b). 5.3 Phylogenetic relationships and their implications for cultivar development Phylogenetic analysis of the selected cultivars provided insights into their evolutionary relationships and potential implications for tea breeding. The 'Wuyi narcissus' (CWN) cultivar, for instance, showed a unique phylogenetic position, indicating distinct evolutionary pressures and domestication origins. The 'Liupao' (LP) cultivar was closely related to C. sinensis var. pabilimba cv. 'Lingyunbaihao' (Liang et al., 2023), while 'Qiancha 1' (QC1) was found to have the closest evolutionary relationship with C. sinensis cultivar 'Anhua' (Yang et al., 2022). The phylogenetic clustering of these cultivars was not always consistent with the current taxonomy of Camellia, suggesting that some classifications may need to be revisited (Li et al., 2021b). For example, the 'Tieguanyin' (TGY) cultivar revealed a relatively independent event of local domestication among three types of cultivars (Chen et al., 2021). 5.4 Discussion of findings in the context of tea breeding and industry practices The findings from this case study have significant implications for tea breeding and industry practices. The observed chloroplast genome variations and phylogenetic relationships highlight the importance of genetic diversity in tea breeding programs. The distinct evolutionary paths and unique genetic features of cultivars like 'Wuyi narcissus' (CWN) and 'Tieguanyin' (TGY) can be leveraged to develop new cultivars with desirable traits such as improved flavor, disease resistance, and environmental adaptability (Chen et al., 2021; Li et al., 2021b). Moreover, the phylogenetic insights suggest that current classification systems may need to be updated to reflect the true genetic relationships among Camellia sinensis cultivars. This could lead to more accurate identification and selection of breeding stock, ultimately enhancing the quality and sustainability of tea production (Li et al., 2021b). 6 Insights from Chloroplast Genome Variation 6.1 Geographic distribution of genetic variants The geographic distribution of genetic variants in the chloroplast genome of Camellia sinensis reveals significant differences between Chinese and Indian tea varieties. Comparative analyses have shown that Chinese tea (Camellia sinensis var. sinensis) and Indian tea (Camellia sinensis var. assamica) exhibit distinct structural characteristics and codon usage patterns in their chloroplast genomes (Figure 2). Additionally, the divergence times between different tea varieties suggest that the Indian Assamica type tea diverged from the common ancestor of the Assamica type teas around 6.2 million years ago, while the Chinese Assamica type tea and the Chinary type tea diverged approximately 0.8 million years ago (Li et al., 2021a). These findings indicate that geographic isolation and different selection pressures have contributed to the genetic differentiation observed in the chloroplast genomes of tea plants. By comparing the chloroplast genomes of the two tea varieties, it reveals the different evolutionary paths in the genome structure between Chinese tea and Indian tea. Additionally, the estimated divergence times indicate that the Indian Assam tea type diverged from a common ancestor approximately 6.2 million years ago, while the Chinese Assam tea type and Chinese tea type diverged around 800,000 years ago, further supporting their distinct evolutionary histories.
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