Bioscience Methods 2024, Vol.15, No.6, 289-301 http://bioscipublisher.com/index.php/bm 294 5 Comparative Analysis 5.1 Evolutionary divergence Eucommia ulmoides and Hevea brasiliensis have distinct evolutionary paths that have influenced their rubber biosynthesis capabilities. E. ulmoides, a member of the order Garryales, has not undergone whole-genome duplication in the last 125 million years, unlike many other eudicots. This ancient genome triplication is shared among core eudicots but is unique in its lack of further duplications (Wuyun et al., 2017). In contrast, H. brasiliensis, which belongs to the order Malpighiales, has a more recent evolutionary history with significant genome duplications that have contributed to its current genetic makeup (Chow et al., 2007). 5.2 Biochemical pathway divergence The biosynthesis of rubber in E. ulmoides and H. brasiliensis involves different primary pathways for the production of isopentenyl diphosphate (IPP), a key precursor. E. ulmoides predominantly utilizes the methylerythritol-phosphate (MEP) pathway for IPP synthesis, which is mainly active in the leaves and central peels (Li et al., 2020). This pathway is less common in rubber-producing plants and highlights a unique aspect of E. ulmoides' biochemistry. On the other hand, H. brasiliensis primarily relies on the mevalonate (MVA) pathway for IPP production in its latex, although the MEP pathway also contributes to a lesser extent, particularly in relation to carotenoid synthesis (Chow et al., 2011). The farnesyl diphosphate synthases (FPSs) and rubber elongation factors (REFs) play crucial roles in the rubber biosynthesis of both species. In E. ulmoides, the FPS and rubber elongation factor/small rubber particle protein (SRPP) gene families have expanded independently from those in H. brasiliensis, leading to the production of trans-polyisoprene (Wuyun et al., 2017). This is in stark contrast to H. brasiliensis, where the FPSs and REFs are more closely associated with the synthesis of cis-polyisoprene. The latex of H. brasiliensis contains multiple isoforms of REFs and SRPPs, which are highly expressed and play significant roles in rubber particle formation and stability (Chow et al., 2007). 5.3 Regulatory mechanisms The regulatory mechanisms governing rubber biosynthesis in E. ulmoides and H. brasiliensis also exhibit notable differences. In E. ulmoides, the high expression levels and gene number expansion for stress response and secondary metabolite biosynthesis genes suggest a complex regulatory network that enhances its environmental adaptability and rubber production (Wuyun et al., 2017). Conversely, in H. brasiliensis, the regulation of rubber biosynthesis is closely linked to the expression of genes involved in stress responses and defense mechanisms, as evidenced by the high abundance of transcripts related to these functions in latex (Chow et al., 2007). This indicates that while both species have evolved sophisticated regulatory systems to optimize rubber production, the specific pathways and gene families involved differ significantly. 6 Case Studies 6.1 Genetic modification inEucommia ulmoides Genetic modification in Eucommia ulmoides has been a focal point of research due to its unique rubber biosynthesis pathway. The high-quality haploid genome assembly of E. ulmoides has provided significant insights into its genetic structure and potential for genetic engineering. The genome assembly, achieved through PacBio and Hi-C technologies, revealed a more primitive rubber biosynthesis pathway that relies on the methylerythritol-phosphate (MEP) pathway rather than the mevalonate pathway, which is predominant in Hevea brasiliensis (Li et al., 2020) (Figure 2). This discovery opens avenues for genetic modifications aimed at enhancing rubber yield and quality by targeting specific genes involved in the MEP pathway. Additionally, the identification of long non-coding RNAs (lncRNAs) and their regulatory roles in rubber biosynthesis further underscores the potential for genetic interventions. These lncRNAs and transcripts of uncertain coding potential (TUCPs) regulate key genes involved in the biosynthesis process, suggesting that genetic modifications could be directed to optimize these regulatory networks (Liu et al., 2018).
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