International Journal of Molecular Evolution and Biodiversity 2024, Vol.14, No.5, 219-228 http://ecoevopublisher.com/index.php/ijmeb 224 The study identified several MADS-box genes closely related to floral organ development, such as EuAP3 and EuAG, which showed significant expression differences during the development of male flower buds, suggesting their important regulatory roles in the formation of male reproductive organs. Through gene function annotation, key enzyme genes related to α-linolenic acid synthesis, such as FAD7, were identified. The expression levels of these genes were significantly higher in fruits and leaves than those in other tissues, indicating that these are the main sites for the synthesis and accumulation of α-linolenic acid. The study not only provides new perspectives for the evolutionary analysis of Eucommia ulmoides but also deepens the understanding of its sex differentiation and α-linolenic acid accumulation mechanisms, laying a solid foundation for subsequent genetic improvements and cultivar development. It will accelerate the development of superior Eucommia ulmoides varieties, enhancing its value in both medicinal and economic fields. 6.2 Divergence inrbcLgene The rbcL gene, which encodes the large subunit of ribulose-1,5-bisphosphate carboxylase/oxygenase (RuBisCO), is a critical component of the photosynthetic machinery in plants. In the chloroplast genome of Eucommia ulmoides, the rbcL gene has been identified as one of the regions exhibiting significant divergence. Comparative analysis with other species, such as those in the Helianthus genus, has shown that the rbcL gene can experience positive selection, particularly during transitions between annual and perennial life cycles (Azarin et al., 2021). This suggests that the rbcLgene in E. ulmoides may also be subject to evolutionary pressures that could influence its function and efficiency in photosynthesis (Bernabeu and Rosselló, 2021). 6.3 Inversions and repeats in the chloroplast genome Inversions and repeats are common structural variations in chloroplast genomes that can lead to genome size variation and affect genome stability. In the chloroplast genome of Eucommia ulmoides, DNA repeat variations have been identified as a significant factor contributing to genome size differences between individuals (Wang et al., 2018; Abdullah et al., 2020). These variations can result in heterogeneous sequence divergence patterns, with a notable number of SNPs and indels distributed across different regions of the genome. Similar patterns have been observed in other plant species, such as the Helianthus genus, where SSRs in non-coding regions contribute to genome size variation (Azarin et al., 2021; Turudić et al., 2022). 7 Environmental and Evolutionary Factors Influencing Divergence 7.1 Impact of environmental changes on genome divergence Environmental changes play a significant role in the divergence of the chloroplast genome in Eucommia ulmoides. The heterogeneous sequence divergence patterns observed in different regions of the E. ulmoides chloroplast genomes suggest that environmental pressures may influence the mutation rates and types in specific genomic regions. For instance, the majority of SNPs were found in gene regions, while indels were more common in intergenic spacers, indicating that different environmental factors might affect these regions differently (Wang et al., 2018; Zhang et al., 2020; Sugimoto et al., 2020). Additionally, the study of chloroplast genomes in other species, such as Ulva, has shown that environmental pressures could drive the compactness of genome organization and decrease overall GC content, which might also be applicable to E. ulmoides (Liu et al., 2023). 7.2 Co-evolution with other organelles The co-evolution of chloroplasts with other organelles, particularly mitochondria, has been a crucial factor in the divergence of the chloroplast genome. Both chloroplasts and mitochondria originated from endosymbiotic events, and their genomes have undergone significant reduction and specialization over time. The episodic influx of prokaryotic genes into the eukaryotic lineage during major evolutionary transitions, such as the origin of chloroplasts and mitochondria, has contributed to the divergence of these organelles (Ku et al., 2015; Calderon and Strand, 2021). In land plants, despite sharing the same cell lineage and being dependent on the same nucleus for most of their gene products, chloroplast and mitochondrial genomes exhibit remarkably different tempos and patterns of evolutionary change, highlighting the complex interplay between these organelles (Tyszka et al., 2023).
RkJQdWJsaXNoZXIy MjQ4ODYzNA==