Bioscience Methods 2024, Vol.15, No.6, 289-301 http://bioscipublisher.com/index.php/bm 290 ulmoides genome, offering new insights into its rubber biosynthesis mechanisms and evolutionary history (Li et al., 2020). The unique properties of E. ulmoides rubber (EUR) have garnered increasing attention for its potential applications in various fields, including environment, agriculture, engineering, and biomedical engineering (Wei et al., 2021). Eucommia ulmoides is a typical dioecious tree species whose metabolomics and transcriptomics have been well analyzed (Li et al., 2024). Natural rubber consists of polyisoprene, including trans-polyisoprene (TPI) and cis-polyisoprene (CPI). Eucommia rubber, found in the leaves, bark, fruit peel, and roots of Eucommia, is a high-quality natural rubber resource that accumulates trans-polyisoprene (Ma et al., 2024). It possesses excellent abrasion resistance and aging resistance (Wang et al., 2021) and serves as an efficient reinforcing agent (Liu et al., 2022). Eucommia rubber can be developed into functional materials with electromagnetic shielding or shape-memory properties (Qi et al., 2023). This study explores the differences and similarities in the biosynthetic mechanisms of Eucommia ulmoides to reveal the genetic and biochemical factors influencing various rubber production processes. The research focuses on the roles of the MVA and MEP pathways in IPP synthesis and the expression of key genes involved in rubber biosynthesis. This study will provide valuable insights into the molecular basis of rubber biosynthesis in Eucommia ulmoides and Hevea brasiliensis. Understanding these pathways may offer a theoretical foundation for developing genetically engineered plants with improved rubber production, thereby enhancing rubber yield and quality. Additionally, the findings may provide new perspectives on the evolutionary adaptations of these species and their potential applications in various industrial and medical fields. 2 Genomic Insights into Rubber Biosynthesis 2.1 Eucommia ulmoides genome The Eucommia ulmoides genome has been successfully assembled to a high-quality haploid chromosome-scale, marking a significant milestone in genomic research for tree species. This assembly was achieved using PacBio and Hi-C technologies, resulting in a scaffold N50 of 53.15 MB, a 28-fold increase from previous assemblies. The repetitive sequence content also saw a substantial increase, and the number of gaps decreased dramatically, enhancing the overall quality and contiguity of the genome sequence. This high-quality assembly is pivotal for advancing studies on genome structure, evolution, gene mapping, and functional genomics, and it holds promise for improvingE. ulmoides for industrial and medical applications through genetic engineering (Li et al., 2020). The genome of E. ulmoides has provided valuable insights into its rubber biosynthesis pathways. Unlike Hevea brasiliensis, which relies on the mevalonate pathway, E. ulmoides predominantly uses the methylerythritol-phosphate (MEP) pathway to synthesize isoprenyl diphosphate. This pathway is mainly active in trans-polyisoprene-containing leaves and central peels. Additionally, the genome revealed that enzymes involved in chlorogenic acid biosynthesis are preferentially expressed in leaves rather than in bark, indicating tissue-specific metabolic activities (Wuyun et al., 2017; Li et al., 2020). The E. ulmoides genome has undergone significant evolutionary events, including a new whole-genome duplication superimposed on an earlier γ paleohexaploidization event. Furthermore, an ancient genome triplication shared by core eudicots was identified, but no further whole-genome duplications have occurred in the last approximately 125 million years. These duplication and triplication events have contributed to the expansion of gene families involved in stress responses and secondary metabolite biosynthesis, enhancing the environmental adaptability of E. ulmoides (Wuyun et al., 2017; Li et al., 2020). 2.2 Hevea brasiliensis Genome The genome of Hevea brasiliensis, the primary commercial source of natural rubber, has been sequenced and assembled, covering approximately 1.1 Gb of the estimated 2.15 Gb haploid genome. This draft genome sequence has identified around 68,955 gene models, with 12.7% being unique to Hevea. The comprehensive genome analysis has provided crucial insights into the genetic basis of rubber biosynthesis, rubberwood formation, disease resistance, and allergenicity. This genomic information is essential for developing high-yielding clones to meet the growing demand for natural rubber (Rahman et al., 2013).
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