Genomics and Applied Biology 2024, Vol.15, No.2, 75-88 http://bioscipublisher.com/index.php/gab 85 to the mevalonate pathway used by Hevea brasiliensis, opens up new avenues for enhancing rubber production through genetic modifications (Li et al., 2020). Additionally, the identification of genes regulating sex differentiation and α-linolenic acid biosynthesis provides opportunities to improve the quality and consistency of E. ulmoides products for medicinal and industrial use (Du et al., 2023). These advancements underscore the potential of comparative genomics to drive innovation in the utilization of E. ulmoides for various applications. 9 Challenges and Future Directions 9.1 Technical and methodological challenges The field of comparative genomics, particularly in non-model organisms like E. ulmoides, faces several technical and methodological challenges. One significant challenge is the generation of high-quality genome assemblies. Although recent advancements have been made, such as the high-quality haploid chromosome-scale genome assembly using PacBio and Hi-C technologies (Li et al., 2020), the complexity of plant genomes, including high levels of repetitive sequences and polyploidy, continues to pose difficulties. Additionally, the identification and annotation of sex-biased genes and sex-associated genes through comparative transcriptome analyses have revealed the complexity of genetic mechanisms underlying sexual dimorphism in E. ulmoides (Wang and Zhang, 2017). Another challenge is the accurate detection and interpretation of sequence divergence and mutation hotspots, as seen in the chloroplast genome of E. ulmoides, which requires comprehensive genome-scale comparisons (Wang et al., 2018b). 9.2 Future prospects in comparative genomics research Future research in comparative genomics of E. ulmoides holds promising prospects. The development of high-density genetic maps using genotyping-by-sequencing (GBS) and SNP markers has laid a solid foundation for chromosome assembly and the localization of growth-trait QTLs (Liu et al., 2022). This advancement will facilitate the investigation of genetic mechanisms underlying important traits and improve breeding efforts. Moreover, the identification of candidate genes related to chlorogenic acid biosynthesis through comparative transcriptome analysis provides valuable genomic resources for genetic improvements (Ye et al., 2019). The integration of these genomic resources with phenotypic data, such as the phenotypic variation in leaf, fruit, and seed traits, will enhance our understanding of the relationship between genetic diversity and phenotypic traits (Wang et al., 2023). 9.3 Integrative approaches combining multi-omics data To overcome the challenges and fully realize the future prospects in comparative genomics research, integrative approaches that combine multi-omics data are essential. The integration of genomics, transcriptomics, and epigenomics data can provide a comprehensive understanding of the genetic and epigenetic regulation of important traits. For instance, the study of the RNase T2 gene family in E. ulmoides, which involved the analysis of gene structure, chromosomal location, and expression patterns, highlights the importance of combining different types of omics data (Qing et al., 2021). Additionally, the use of molecular markers and QTL analysis for growth traits, as demonstrated in the updated genetic linkage map of E. ulmoides, underscores the need for integrative approaches to elucidate the genetic mechanisms underlying complex traits (Jin et al., 2020). By leveraging multi-omics data, researchers can gain deeper insights into the evolutionary history and genetic improvement of E. ulmoides. 10 Concluding Remarks The comparative genomics studies of E. ulmoides have provided significant insights into its evolutionary history and genetic makeup. The high-quality haploid genome assembly revealed a new whole-genome duplication event and highlighted the primitive rubber biosynthesis pathway unique to E. ulmoides, which relies on the methylerythritol-phosphate pathway rather than the mevalonate pathway. Additionally, the construction of genetic linkage maps and QTL analyses have identified numerous quantitative trait loci associated with growth traits, providing valuable tools for marker-assisted selection and genetic improvement. The chromosome-level genome assembly has also shed light on sex differentiation mechanisms and the biosynthesis of α-linolenic acid, with key genes identified for these processes. Furthermore, chloroplast genome studies have revealed heterogeneous divergence and mutation hotspots, contributing to our understanding of the genetic diversity and evolutionary relationships within the species.
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