Journal of Tea Science Research, 2024, Vol.14, No.2, 79-91 http://hortherbpublisher.com/index.php/jtsr 83 Wei et al. (2018) used Illumina and PacBio sequencing technologies to obtain high-quality tea genome sequences. The results showed that the tea genome underwent two whole-genome duplications (WGD), occurring approximately 30-40 million years ago and 90-100 million years ago. Genome duplication and subsequent gene amplification significantly affected the copy number of secondary metabolite genes, particularly those crucial for tea quality, including catechins, theanine, and caffeine synthesis genes. Through transcriptome and phytochemical data analysis, key gene families related to unique tea metabolites were found to have undergone expansion and transcriptional differentiation. This genome sequence aids in the in-depth understanding of tea genome evolution and metabolic pathways, promoting the improvement of tea breeding. Another study successfully assembled the genome of a wild tea tree, DASZ, at a chromosome scale, which helped clarify the pedigree and selection history of tea varieties and identified key genes involved in flavonoid biosynthesis (Zhang et al., 2020). Additionally, the genome of rooibos (Aspalathus linearis), an important medicinal plant used for tea production, was assembled using various long-read sequencing approaches, demonstrating the effectiveness of these techniques in generating contiguous and accurate genome assemblies (Mgwatyu et al., 2022). 4 Annotation and Functional Analysis 4.1 Importance of accurate annotation Accurate annotation of the tea genome is crucial for understanding the genetic basis of important traits and for facilitating breeding programs. Annotation helps in identifying gene functions, regulatory elements, and structural variations, which are essential for functional genomics studies. For instance, the identification and characterization of unigene derived microsatellite (UGMS) markers in tea have provided insights into the genetic diversity and heterozygosity of tea populations, which are vital for genetic mapping and marker-assisted selection (Ou et al., 2019). Moreover, accurate annotation aids in the identification of gene family members critical for the biosynthesis of key tea metabolites, such as catechins and theanine, which contribute to tea quality and its health benefits (Wei et al., 2018). 4.2 Methods of gene annotation Gene annotation in tea involves several methods, including the use of high-throughput sequencing technologies and bioinformatics tools. The draft genome sequence of Camellia sinensis var. sinensis was assembled using both Illumina and PacBio sequencing technologies, which provided a high-quality genome assembly with 33,932 high-confidence predictions of encoded proteins (Wei et al., 2018). Additionally, functional annotation of unigenes containing SSRs was performed through gene ontology (GO) characterization, revealing significant sequence similarity with known proteins in Arabidopsis thaliana (Ou et al., 2019). Single sperm sequencing has also been employed to phase the genome of tea, aiding in the construction of high-resolution genetic and recombination maps (Zhang et al., 2020a). 4.3 Insights from functional genomics Functional genomics studies have provided valuable insights into the regulation of gene expression and the evolution of the tea genome. For example, By sequencing the genomes of 135 single sperm cells, researchers successfully phased the genome of the 'Fudingdabai' tea plant and constructed a high-resolution genetic map, revealing the distribution patterns and interference mechanisms of crossover sites (Figure 2). The study found that crossover locations were often at the 5' and 3' ends of genes and were distributed relatively randomly. Additionally, the researchers developed a method to infer kinship among tea germplasm, detecting complex kinship and genetic markers, which are crucial for understanding genetic diversity and breeding strategies (Zhang et al., 2020a). Furthermore, the draft genome sequence of Camellia sinensis var. sinensis highlighted the impact of whole-genome duplications and subsequent paralogous duplications on the amplification of secondary metabolite genes, which are crucial for tea quality (Wei et al., 2018). These studies provide a theoretical basis for future research to explore the genetic and epigenetic factors underpinning the regulation of gene expression in tea.
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