Maize Genomics and Genetics 2024, Vol.15, No.3, 123-135 http://cropscipublisher.com/index.php/mgg 130 between TE insertion frequency and the expression of nearby genes suggests that TEs tend to insert near lowly expressed, nonessential genes to minimize fitness impacts (Wei et al., 2022). 7.2 Mechanisms of TE suppression and genomic defense To counteract the deleterious effects of TEs, organisms have evolved several defense mechanisms that act at various levels, including epigenetic, transcriptional, and post-transcriptional levels (Castanera et al., 2016; Platt et al., 2018; Romano and Fanti, 2022). One of the primary defense mechanisms involves RNA-mediated silencing, which plays a crucial role in limiting TE proliferation. This system uses small RNAs to target and silence TEs, thereby preventing their mobilization and subsequent genomic instability (Blumenstiel, 2011). Epigenetic mechanisms, such as DNA methylation and histone modifications, are also vital in maintaining TE silencing. For example, in fungi, active cytosine methylation machinery is associated with TE-mediated gene silencing, suggesting that epigenetic defenses are crucial in controlling TE proliferation (Castanera et al., 2016). Additionally, the stress-dependent incapacitation of these defense mechanisms can facilitate adaptive responses to environmental challenges, highlighting the dynamic interplay between TEs and host genomes (Schrader and Schmitz, 2018). The evolutionary arms race between TEs and host genomes is characterized by TEs evolving to escape suppression and host genomes developing compensatory changes to re-establish control. This ongoing conflict drives the rapid evolution of TEs and the recurrent positive selection of genes involved in host defense (Platt et al., 2018; Wei et al., 2022). In plants, epigenetic regulation has been transformed from a process to silence invading TEs and viruses into a key strategy for regulating plant genes, demonstrating the co-option of TE components by the host to create new genes or modify gene regulation (Bennetzen and Wang, 2014). The suppression of TEs is a complex and multifaceted process involving various genomic defense mechanisms that work together to maintain genomic stability and prevent the deleterious effects of TE activity. 8 Comparative Analysis with Other Species 8.1 Comparison of TE activity and impact inZea versus other plants and vertebrates Transposable elements (TEs) are ubiquitous across eukaryotic genomes, playing significant roles in genetic diversity and evolution. In Zea (maize), TEs constitute a substantial portion of the genome, contributing to its large size and complexity. This is comparable to other plant species where TEs also play a crucial role in genome evolution. For instance, in Arabidopsis lyrata, selfing populations exhibit higher TE copy numbers and allele frequencies, suggesting that TEs can proliferate more in certain mating systems (Bonchev and Willi, 2018). Similarly, in polyploid plants, TEs are major drivers of genome size changes and new coding/regulatory sequences, often activated by polyploidization events (Vicient and Casacuberta, 2017). In vertebrates, the impact of TEs varies significantly across lineages. For example, in teleost fish, TEs contribute more to genome size compared to mammals, with DNA transposons being more prevalent in fish genomes (Chalopin et al., 2015). In contrast, mammalian genomes are predominantly shaped by non-long terminal repeat (non-LTR) retrotransposons, with older TE sequences persisting over time (Chalopin et al., 2015). This difference in TE composition and activity between vertebrates and plants highlights the diverse evolutionary pressures and mechanisms influencing TE dynamics. Moreover, the diversity of TEs in vertebrates is notable, with some lineages like ray-finned fishes and amphibians exhibiting higher TE diversity compared to birds and mammals (Sotero-Caio et al., 2017). This is akin to the high diversity and dynamic nature of TEs observed in land plants, where genetic and epigenetic factors modulate TE activity and distribution (Mhiri et al., 2022). The evolutionary impact of TEs in vertebrates includes their role in chromosome structure, gene regulation, and the formation of non-coding RNAs and protein-coding genes, driving lineage-specific innovations. 8.2 Insights from cross-species studies Cross-species studies provide valuable insights into the evolutionary roles of TEs. In Zea, TEs are not only a source of genetic variation but also influence gene expression and genome plasticity. This is similar to the role of
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