International Journal of Molecular Evolution and Biodiversity 2024, Vol.14, No.5, 219-228 http://ecoevopublisher.com/index.php/ijmeb 223 5.3 Role of non-coding regions in genome evolution Non-coding regions play a pivotal role in the evolution of the chloroplast genome by acting as sites for adaptive evolution and selective constraint. In E. ulmoides, the high rate of indel mutations in intergenic regions suggests that these regions are under selective pressure, contributing to the overall genetic diversity of the species (Wang et al., 2018). Studies in other organisms, such as Drosophila, have shown that non-coding DNA can evolve under both purifying selection and positive selection, indicating its functional importance (Andolfatto, 2005). The adaptive evolution of non-coding regions is also evident in the integration of foreign DNA sequences, which can drive genome rearrangements and influence the evolutionary trajectory of the chloroplast genome (Liu et al., 2023). Overall, the divergence patterns in non-coding regions are crucial for understanding the mechanisms of genome evolution and the adaptive strategies of E. ulmoides. 6 Case Studies 6.1 Analysis of sex differentiation and divergence patterns in the Eucommia ulmoides genome With the advancement of genomics technology, research on the genome of Eucommia ulmoides has gradually deepened, providing new insights into the mechanisms of sex differentiation and the biosynthesis of important metabolites. Du et al. (2023) successfully constructed a high-quality female Eucommia ulmoides genome using PacBio and Hi-C technologies and reassembled the male genome released in 2018. Comparative analysis of the male and female genomes revealed key genes and molecular mechanisms involved in sex differentiation and α-linolenic acid biosynthesis (Figure 2). Figure 2 Internal anatomical structure and external morphological characteristics of male and female flower buds at different differentiation stages (Adopted from Du et al., 2023) Image caption: The image shows significant changes in the male and female flower buds of Eucommia ulmoides during four stages: inflorescence primordium formation, bract differentiation, pistil and stamen differentiation, and their morphological formation. Notably, during the pistil and stamen differentiation stage, the internal structures of the male and female flower buds begin to exhibit clear differences, with male buds forming stamen clusters and female buds forming pistils. This image illustrates the gradual morphological changes during the sex differentiation process in Eucommia ulmoides flower buds, providing direct morphological evidence for understanding the molecular mechanisms of sex differentiation (Adapted from Du et al., 2023)
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