Genomics and Applied Biology 2024, Vol.15, No.2, 75-88 http://bioscipublisher.com/index.php/gab 81 5.2.2 Functional implications The expansion of specific gene families in E. ulmoides has functional implications for its adaptability and secondary metabolite biosynthesis. For example, the expansion of genes involved in stress responses and secondary metabolite biosynthesis, such as those related to polyisoprene biosynthesis, highlights the species' ability to adapt to environmental stresses and its unique rubber biosynthesis pathway (Wuyun et al., 2017). Additionally, the identification of sex-biased gene expression and putative sex-associated genes provides insights into the genetic mechanisms, underlying sexual dimorphism in this dioecious species (Wang and Zhang, 2017). Figure 2 Evolution and synteny of the E. ulmoides genome (Adopted From Li et. al., 2020) Imagine Caption (Adopted From Li et. al., 2020): a. The insertion times for intact LTR-RTs in the E. ulmoides genome. The insertion times for LTR-RTs were calculated by the formula T = K/2r. T insertion time; r synonymous mutations/site/Mya; K the divergence between the two LTRs. A substitution rate of 8.25 × 10−9 per site per year was used to calculate the insertion times. b. Venn diagram of shared orthologs among the five species. Each number represents a gene family number. c. Phylogenetic tree of 12 species based on orthologs of single-gene families. The number at the root (28,004) represents the number of gene families related to the common ancestor. The value above each branch denotes the number of gene families gained/lost during each round of genome duplication after diversification from the common ancestor. The red number below each branch denotes the speculated divergence time of each node. Bootstrap values for all nodes are above 50%. d. Density distributions of Ks for paralogous genes. The peak values are shown in insets for E. ulmoides and C. canephora. e. Density distributions of Ks for paralogous genes. The peak values are shown in insets for E. ulmoides and S. lycopersicum. f. Schematic representation of syntenic genes among E. ulmoides, V. vinifera and C. canephora. Gray lines in the background indicate the collinear blocks of at least twenty genes within the E. ulmoides genome and other plant genomes, while the red lines highlight the syntenic gene pairs
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