Genomics and Applied Biology 2024, Vol.15, No.2, 75-88 http://bioscipublisher.com/index.php/gab 77 2.2 Economic and medicinal importance E. ulmoides holds substantial economic and medicinal value. It is widely utilized in traditional Chinese medicine for its pharmacological properties, including anti-inflammatory, anti-hypertensive, and anti-oxidative effects. The tree is also a source of gutta-percha, a form of rubber used in various industrial applications. The biosynthesis of secondary metabolites such as aucubin, chlorogenic acid, and polyphenols in its leaves further enhances its medicinal importance (Li et al., 2020; Liu et al., 2021b; Du et al., 2023). Additionally, the tree is employed in landscaping, wind sheltering, and sand fixation, contributing to its ecological significance (Jin et al., 2020). 2.3 Previous studies onE. ulmoides Several studies have been conducted to understand the genetic and molecular basis of E. ulmoides. A genetic linkage map was constructed to identify quantitative trait loci (QTL), affecting growth-related traits, providing a tool for marker-assisted selection and genomic studies (Li et al., 2014; Jin et al., 2020). Genome-wide association studies have revealed genetic loci associated with the biosynthesis of key leaf metabolites, offering insights into the genetic mechanisms underlying these traits (Liu et al., 2021b). High-quality genome assemblies have been developed, shedding light on the evolutionary history, sex differentiation, and rubber biosynthesis pathways of these species (Li et al., 2020; Du et al., 2023). Transcriptome analyses have identified genes related to floral development, further contributing to the understanding of the species' reproductive biology (Liu et al., 2016). These studies collectively provide a comprehensive understanding of the genetic and molecular framework of E. ulmoides, facilitating its conservation and improvement for industrial and medicinal applications. 3 Comparative Genomics: Concepts and Methods 3.1 Definition and scope of comparative genomics Comparative genomics is a field of biological research in which the genomic features of different organisms are compared. This comparison can involve the entire genome or specific parts of the genome, such as genes, regulatory sequences, and non-coding regions. The primary goal is to understand the structure, function, and evolutionary relationships of genomes. Comparative genomics provides insights into the genetic basis of phenotypic differences and similarities among species, and it can reveal the evolutionary processes that shape genomes over time (Filipski and Kumar, 2005; Cordone et al., 2021). 3.2 Techniques and tools for comparative genomic analysis 3.2.1 Sequencing technologies Advancements in sequencing technologies have been pivotal in the field of comparative genomics. High-throughput sequencing methods, such as PacBio and Illumina sequencing, have enabled the generation of high-quality genome assemblies. For instance, the high-quality haploid chromosome-scale genome assembly of E. ulmoides was achieved using PacBio and Hi-C technologies, significantly improving the assembly quality and providing new insights into the species' evolution and rubber biosynthesis (Li et al., 2020). These technologies allow for the detailed comparison of genomic sequences across different species, facilitating the identification of conserved and divergent genomic regions. 3.2.2 Bioinformatics tools and databases Bioinformatics tools and databases are essential for analyzing and interpreting the vast amounts of data generated by sequencing technologies. Tools such as Genomicus provide a platform for comparative genomic visualization, allowing researchers to explore gene organization and evolutionary relationships across more than 150 eukaryote genomes (Louis et al., 2012). These tools can reveal differential gene loss and gain, segmental or genome duplications, and the evolution of loci through homology relationships. Additionally, databases and software for differential expression analysis, such as those used in the study of chlorogenic acid biosynthesis in E. ulmoides, help identify key genes and regulatory elements involved in specific biological pathways (Ye et al., 2019). 3.3 Data sources and selection criteria The selection of appropriate data sources is crucial for effective comparative genomic analysis. High-quality genome assemblies, such as the one generated for E. ulmoides, provide a robust foundation for comparative
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