Genomics and Applied Biology 2024, Vol.15, No.2, 75-88 http://bioscipublisher.com/index.php/gab 79 relationship within the Garryales order (Wang et al., 2018b). The genome of E. ulmoides has undergone two significant whole-genome duplication events: the core eudicot γ whole-genome triplication event and a more recent whole-genome duplication, approximately 27.3 million years ago (Du et al., 2023). These events have contributed to the complexity and expansion of the E. ulmoides genome, distinguishing it from related species. 4.3 Genomic features and annotations The E. ulmoides genome exhibits several unique features. The expansion of long terminal repeats has played a significant role in its evolution (Li et al., 2020). The genome contains 21 ribonuclease T2 (EURNS) genes, which are involved in RNA cleavage and have been conserved across eukaryotic organisms (Qing et al., 2021). Additionally, the WRKY gene family, consisting of 45 genes, has been identified and is implicated in various biological processes, including stress responses and leaf development (Wang et al., 2018a). The genome also includes genes related to sex differentiation, such as EuAP3 and EuAG, which are crucial for understanding the dioecious nature of the species (Du et al., 2023). Furthermore, the high expression of ω-3 fatty acid desaturase coding gene EU0103017 is linked to the high α-linolenic acid content in E. ulmoides (Du et al., 2023). Overall, the comprehensive genomic data of E. ulmoides not only enhances our understanding of its genome structure and organization but also provides valuable resources for future research and breeding programs aimed at improving its industrial and medicinal applications. Recent advances in genetic research on E. ulmoides have significantly enhanced our understanding of its genome and medicinal properties. High-quality genome sequencing using PacBio and Hi-C technologies has produced a haploid chromosome-scale genome assembly, offering detailed genetic insights (Li et al., 2020). Genome-wide association studies (GWAS) have identified loci linked to the biosynthesis of key metabolites in the leaves, shedding light on the genetic basis of its medicinal properties (Liu et al., 2021). Genetic linkage mapping has pinpointed quantitative trait loci (QTL) for growth traits, aiding marker-assisted selection (Li et al., 2014; Jin et al., 2020). Transcriptome analyses have revealed genes involved in floral development and rubber biosynthesis, enhancing knowledge of its reproductive biology and rubber production (Liu et al., 2016). Comparative genomics, facilitated by tools like Genomicus, has illustrated gene organization, evolutionary relationships, and the mechanisms of gene loss/gain and segmental duplications (Louis et al., 2012). This comparative approach has also provided evolutionary insights into sex differentiation and adaptation mechanisms (Qing et al., 2022). Research on secondary metabolite biosynthesis has focused on compounds like aucubin and chlorogenic acid, crucial for the tree’s medicinal uses (Ye et al., 2019; Du et al., 2023). The selection of comparative species based on phylogenetic relationships and available genomic data has enhanced the understanding of functional genomic elements and evolutionary patterns (Cordone et al., 2021). These genetic and molecular studies offer a comprehensive framework for the conservation and improvement of E. ulmoides for industrial and medicinal applications (Table 2) (Filipski and Kumar, 2005; Li et al., 2020). 5 Evolutionary Insights from Comparative Genomics 5.1 Phylogenetic relationships 5.1.1 Methods for phylogenetic analysis Phylogenetic analysis of E. ulmoides has been conducted using various genomic data, including chloroplast genomes and nuclear genomes. Techniques such as genome skimming, which involves sequencing a subset of the genome to obtain high-coverage data for specific regions, have been employed to generate complete chloroplast genomes (Wang et al., 2018b). Additionally, high-quality de novo assembly using PacBio and Hi-C technologies has provided comprehensive nuclear genome data, facilitating detailed phylogenetic studies (Li et al., 2020). 5.1.2 Phylogenetic position of E. ulmoides E. ulmoides, a member of the order Garryales, has been confirmed to have a sister relationship with Aucuba japonica, based on chloroplast phylogenomic analyses (Wang et al., 2018b). This phylogenetic positioning is further supported by nuclear genomic data, which places E. ulmoides as a sister taxon to lamiids and campanulids, indicating its unique evolutionary lineage within the core eudicots (Wuyun et al., 2017).
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