Genomics and Applied Biology 2024, Vol.15, No.2, 75-88 http://bioscipublisher.com/index.php/gab 80 Table 2 Comprehensive comparative genomics analysis of E. ulmoides with relevant references Aspect Description References Genome Sequencing High-quality genome sequencing using PacBio and Hi-C technologies has enabled the construction of a haploid chromosome-scale genome assembly for E. ulmoides, providing detailed insights into its genetic makeup. Li et al., 2020 Genome-Wide Association Studies (GWAS) GWAS has identified genetic loci associated with the biosynthesis of key metabolites in E. ulmoides leaves, enhancing the understanding of the genetic basis of its medicinal properties. Liu et al., 2021 Genetic Linkage Mapping Genetic linkage maps have been constructed to identify quantitative trait loci (QTL) affecting growth-related traits, aiding in marker-assisted selection and genome studies. Li et al., 2014; Jin et al., 2020 Transcriptome AnalysisTranscriptome analyses have identified genes related to floral development and rubber biosynthesis pathways, contributing to the understanding of the species' reproductive biology and rubber production. Liu et al., 2016 Comparative Genomic Visualization Tools like Genomicus facilitate the visualization of gene organization and evolutionary relationships across eukaryote genomes, revealing gene loss/gain, segmental duplications, and homology relationships. Louis et al., 2012 Evolutionary Insights Comparative genomics provides insights into the evolutionary history, sex differentiation, and adaptation mechanisms of E. ulmoides, highlighting the evolutionary processes shaping its genome. Qing et al., 2022 Secondary Metabolite Biosynthesis Studies have focused on the biosynthesis of secondary metabolites such as aucubin, chlorogenic acid, and polyphenols, which are crucial for the medicinal properties of E. ulmoides. Ye et al., 2019; Du et al., 2023 Selection of Comparative Species The choice of species for comparative analysis is guided by research questions, phylogenetic relationships, and the availability of genomic data, enhancing the understanding of functional genomic elements and evolutionary patterns. Cordone et al., 2021 Applications of Comparative Genomics Comparative genomics aids in identifying conserved protein functions, adaptation mechanisms, and evolutionary history, providing a comprehensive framework for the conservation and improvement of Eu. ulmoides for industrial and medicinal uses. Filipski and Kumar, 2005; Li et al., 2020 5.1.3 Evolution and synteny of the E. ulmoides genome The study of Li et. al. (2020) on E. ulmoides genome evolution reveals significant insights into its genomic structure and history (Figure 2). The phylogenetic analysis confirms E. ulmoides as part of the lamiid lineage, supporting its classification within the Angiosperm Phylogeny Group system. Synteny analysis with grape and coffee genomes highlights a stable 2:1 synteny ratio, suggesting an additional whole-genome duplication event specific to E. ulmoides lineage. This event, superimposed on an earlier paleohexaploidization, significantly shaped its genome. Moreover, the study identifies unique gene families and expanded ones, which likely contribute to the species' environmental adaptability and defense mechanisms. The detailed insertion times for LTR retrotransposons indicate periods of genomic expansion correlating with environmental changes during the Pliocene epoch. Overall, these findings enhance our understanding of the evolutionary processes influencing E. ulmoides and provide a robust framework for future genomic and functional studies. 5.2 Gene family evolution 5.2.1 Expansion and contraction of gene families Comparative genomic studies have revealed significant expansion and contraction of gene families in E. ulmoides. For instance, the WRKY transcription factor family, which plays crucial roles in plant development and stress responses, has been extensively studied. A total of 45 WRKY genes were identified and classified into three groups, with further subdivisions based on phylogenetic analysis (Liu et al., 2021a). Similarly, the RNase T2 gene family, involved in RNA cleavage, has shown segmental duplication as the dominant mode of duplication, indicating evolutionary adaptation (Qing et al., 2021).
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