Genomics and Applied Biology 2024, Vol.15, No.4, 191-199 http://bioscipublisher.com/index.php/gab 192 of the chloroplast genome in various Camellia sinensis cultivars ranges from approximately 156,607 to 157,166 base pairs (bp) (Li et al., 2019; Chen et al., 2021; Li et al., 2021b). The genome contains around 130-135 genes, including protein-coding genes, transfer RNAs (tRNAs), and ribosomal RNAs (rRNAs). The overall GC content is consistently around 37.3%, with variations in the LSC, SSC, and IR regions (Park et al., 2019; Chen et al., 2021; Liang et al., 2023). 2.2 Comparison with other chloroplast genomes in the theaceae family When comparing the chloroplast genomes of Camellia sinensis with other species in the Theaceae family, several similarities and differences are observed. The general structure, including the quadripartite arrangement and gene content, is conserved across the family (Li et al., 2018; 2019; Chen et al., 2022). However, variations in the length of the chloroplast genome and the IR regions are noted among different species. For instance, the chloroplast genome of Camellia japonica ranges from 156,971 to 157,126 bp, which is similar to that of Camellia sinensis (Li et al., 2019; Park et al., 2019). Additionally, the presence of simple sequence repeats (SSRs) and divergence hotspots in intergenic spaces and coding sequences contribute to the genetic diversity within the family (Chen et al., 2022). 2.3 Variations observed in different Camellia sinensis varieties Significant variations are observed among different varieties of Camellia sinensis. These include differences in the structure and length of the chloroplast genome, as well as the presence of specific insertions, deletions, and single nucleotide polymorphisms (SNPs) (Park et al., 2019; Li et al., 2021b; Chen et al., 2021). For example, the chloroplast genome of the 'Tieguanyin' cultivar is 157,126 bp in length, while the 'Liupao' cultivar has a genome length of 157,097 bp (Chen et al., 2021; Liang et al., 2023). Additionally, the evolutionary dynamics of the chloroplast genome in Camellia sinensis are influenced by repeat-induced and indel-induced mutations, which contribute to the diversification of the genome (Li et al., 2021b). Phylogenetic analyses reveal that different Camellia sinensis varieties, such as the Chinary type and Assamica type teas, have undergone distinct evolutionary routes and selection pressures. 3 Methods for Analyzing Chloroplast Genome Variation 3.1 Sampling and DNA extraction Sampling for chloroplast genome analysis in Camellia sinensis typically involves collecting fresh leaves from various cultivars and species. The leaves are then subjected to DNA extraction using standard protocols, which often include the use of commercial DNA extraction kits or CTAB (cetyltrimethylammonium bromide) methods to ensure high-quality chloroplast DNA (cpDNA) (Li et al., 2021b; Chen et al., 2022; Lin et al., 2022). 3.2 Sequencing techniques used High-throughput sequencing technologies are predominantly used for sequencing the chloroplast genomes of Camellia sinensis. Illumina sequencing technology is frequently employed due to its high accuracy and throughput, allowing for the generation of comprehensive cpDNA sequences (Li et al., 2019; Lin et al., 2022; Chen et al., 2022). Additionally, some studies have combined PacBio and Illumina sequencing data to enhance the accuracy and completeness of the chloroplast genome assembly (Li et al., 2021b). 3.3 Bioinformatics tools for genome assembly and annotation The raw sequencing data are processed using various bioinformatics tools to assemble and annotate the chloroplast genomes. De novo assembly methods are commonly used, with software such as SPAdes or NOVOPlasty being popular choices for assembling the cpDNA sequences (Li et al., 2019; Lin et al., 2022). Annotation of the assembled genomes is typically performed using tools like GeSeq or DOGMA, which help identify genes, tRNAs, rRNAs, and other functional elements within the chloroplast genome (Dong et al., 2018; Chen et al., 2022). 3.4 Identification of genetic variations (SNPs, Indels, etc.) To identify genetic variations such as single nucleotide polymorphisms (SNPs) and insertions-deletions (indels), comparative genomic analyses are conducted. These analyses involve aligning the chloroplast genomes of
RkJQdWJsaXNoZXIy MjQ4ODYzMg==