Journal of Tea Science Research, 2024, Vol.14, No.2, 79-91 http://hortherbpublisher.com/index.php/jtsr 84 Figure 2 CO patterns detected by single sperm sequencing of Fudingdabai (Adopted from Zhang et al., 2020a) Image caption: Bin map of single sperm cell ID "QSC-1", showing allelic frequencies in different segments; b: Distribution of CO resolution, with the histogram representing the number of COs and the black curve indicating the cumulative percentage of CO interval size; c: CO distribution at the gene scale, with dark green boxes representing the normalized gene range; d: Association between COs and genomic features in the tea plant genome, showing that most COs occur in transposable element regions (59.53%) and only 3.72% of COs are located within gene bodies. These results reveal the distribution patterns and influencing factors of COs in tea plants, providing important data for further genetic and breeding research in tea plants (Adapted from Zhang et al., 2020a) 5 Comparative Genomics 5.1 Benefits of comparative studies Comparative genomics offers significant benefits in understanding the genetic and evolutionary relationships among different species. By comparing the genome of the tea plant with the genomes of other species, researchers can identify conserved genomic regions and lineage-specific innovations, elucidating the evolutionary relationships and differentiation patterns among different tea species (e.g., Camellia sinensis var. sinensis and Camellia sinensis var. assamica). Comparative analysis of genomic sequences reveals the genetic variations underlying various agronomic traits, such as leaf morphology, biochemical composition (e.g., catechin profiles), and environmental adaptability. For instance, the high-quality reference genome of Camellia sinensis var. sinensis reveals the critical role of long terminal repeat retrotransposons (LTR-RTs) in genome expansion and gene transcription diversification. Notably, genes associated with tea aroma and stress resistance have undergone significant amplification through recent tandem duplications, forming gene clusters that are crucial for the plant's adaptability and quality traits (Xia et al., 2020a). Additionally, comparative studies can help trace the evolutionary history and domestication processes of tea plants, as evidenced by the phylogenetic analyses of diverse tea plant accessions. Through the high-quality assembly of the Camellia sinensis var. sinensis genome and the resequencing of 81 tea samples from different sources, researchers have identified key genes involved in the evolution and adaptation of the tea genome. Phylogenetic analysis supports the southwest origin of tea plants and reveals the historical spread of cultivated tea in China (Xia et al., 2020a).
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