Genomics and Applied Biology 2024, Vol.15, No.2, 75-88 http://bioscipublisher.com/index.php/gab 84 7.2 Comparative analysis of secondary metabolite biosynthesis Secondary metabolites in E. ulmoides, such as chlorogenic acid, aucubin, and various glycosides, are of significant interest due to their pharmacological activities. Comparative transcriptome analyses have identified key genes involved in the biosynthesis of CGA, including PALs, 4CL, and several transcription factors like ERF2 and WRKY (Ye et al., 2019). The uridine diphosphate glycosyltransferases (UGTs) family also plays a crucial role in the biosynthesis of glycosides, catalyzing glycosyl-transferring reactions essential for the formation of pharmacologically active compounds (Ouyang et al., 2021). Furthermore, the WRKY transcription factors, which are involved in multiple biological processes, have been shown to regulate the expression of genes related to secondary metabolite biosynthesis (Liu et al., 2021a). 7.3 Insights into unique functional traits E. ulmoides exhibits several unique functional traits that distinguish it from other species. The high-quality de novo assembly of its haploid genome has revealed a new whole-genome duplication event and the expansion of long terminal repeats, contributing to its evolutionary history and functional diversity (Li et al., 2020). The identification of 21 ribonuclease T2 (RNase T2) genes, which are involved in RNA cleavage and stress responses, highlights the plant's adaptation mechanisms (Qing et al., 2021). Additionally, the construction of a high-density genetic map and the identification of quantitative trait loci (QTLs) associated with growth traits provide insights into the genetic basis of its growth and development (Jin et al., 2020; Liu et al., 2022). These findings underscore the potential of E. ulmoides for genetic improvement and its application in various industries. 8 Applications and Implications of Comparative Genomics 8.1 Conservation genetics and biodiversity Comparative genomics has significant implications for conservation genetics and biodiversity. By comparing the genomic data of E. ulmoides with other species, researchers can identify genetic variations and evolutionary patterns that are crucial for the conservation of this endangered species. For instance, the study of the chloroplast genome of E. ulmoides revealed heterogeneous sequence divergence patterns and identified potential molecular markers for population genetics studies, which are essential for conservation efforts (Wang et al., 2018b). Additionally, the high level of genetic diversity observed within E. ulmoides populations, despite a genetic bottleneck in one population, underscores the importance of maintaining genetic variation for the species' long-term survival (Zhang et al., 2013). Comparative genomic approaches can also help in understanding the processes that influence the diversity of E. ulmoides, thereby aiding in the development of effective conservation strategies (Grueber, 2015). 8.2 Genetic improvement and breeding The insights gained from comparative genomics are invaluable for the genetic improvement and breeding of E. ulmoides. High-density genetic maps and QTL analyses have identified numerous markers and candidate genes associated with growth traits, which can be utilized in marker-assisted selection to enhance breeding programs (Li et al., 2014; Jin et al., 2020; Liu et al., 2022). For example, the construction of a high-density genetic map using SNP markers has provided a solid foundation for chromosome assembly and the localization of growth-trait QTLs, advancing forestry breeding efforts in E. ulmoides (Liu et al., 2022). Moreover, the identification of key genes involved in chlorogenic acid biosynthesis through comparative transcriptome analysis offers potential targets for genetic engineering to improve the medicinal value of E. ulmoides (Ye et al., 2019). The integration of these genomic resources can significantly accelerate the breeding of superior varieties with desired traits. 8.3 Medicinal and industrial applications Comparative genomics also plays a crucial role in enhancing the medicinal and industrial applications of E. ulmoides. The high-quality genome assembly of E. ulmoides has provided new insights into rubber biosynthesis and the biosynthesis pathways of other valuable compounds such as chlorogenic acid and α-linolenic acid (Li et al., 2020; Du et al., 2023). Understanding these biosynthetic pathways at the genomic level allows for the optimization of metabolic engineering strategies to increase the yield of these compounds. For instance, the discovery that E. ulmoides relies on the methylerythritol-phosphate pathway for rubber biosynthesis, as opposed
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