Maize Genomics and Genetics 2024, Vol.15, No.3, 123-135 http://cropscipublisher.com/index.php/mgg 128 Another example is the impact of TEs on flowering time in maize. The insertion of a TE in the promoter region of the ZmCCT9 gene has been associated with delayed flowering. This insertion disrupts the normal expression of the gene, leading to changes in the plant's developmental timing. Such variations in flowering time can have significant implications for adaptation to different environmental conditions (Pimpinelli and Piacentini, 2020). TEs have also been implicated in the evolution of disease resistance in maize. The insertion of a TE in the promoter region of the Rp1-Dgene, which confers resistance to rust pathogens, can enhance the gene's expression and provide increased resistance. This example highlights how TEs can contribute to the rapid evolution of traits that are critical for plant survival and fitness (Wells and Feschotte, 2020). Furthermore, TEs can generate novel regulatory elements that drive the expression of nearby genes in new patterns. For instance, the insertion of a TE upstream of the tb1 gene, which controls plant architecture, has been shown to create a new enhancer element. This enhancer drives higher expression of tb1, leading to the characteristic upright growth habit of domesticated maize compared to its wild ancestor, teosinte (Fedoroff, 2012). 5 Transposable Elements and Genome Evolution 5.1 Impact on genome structure and function Transposable elements (TEs) are significant contributors to the structural and functional dynamics of genomes. They can cause chromosome rearrangements, influence genome size, and affect gene content and order. TEs are known to drive centromere function and other aspects of nuclear biology, often acting as agents of genomic novelty (Bennetzen and Wang, 2014). In plants, TEs can lead to drastic changes in genome size and provide new coding and regulatory sequences, which are particularly impactful following polyploidization events. These elements can induce bursts of transposition, leading to increased rates of gene mutations and changes in gene regulation due to their insertion near or within genes (Vicient and Casacuberta, 2017). Additionally, TEs can cause inter-element recombination, resulting in large-scale genome rearrangements and reductions in genome size, a process known as diploidization (Vicient and Casacuberta, 2017). 5.2 Role in gene regulation and expression TEs play a crucial role in the regulation of gene expression. They can provide cis-regulatory sequences that influence the expression of nearby genes. These sequences can act as enhancers, promoters, silencers, and boundary elements, thereby facilitating changes in gene regulatory networks (Sundaram and Wysocka, 2020). TEs can also produce regulatory RNAs, such as miRNAs and long non-coding RNAs (lncRNAs), which are involved in post-transcriptional regulation (Ali et al., 2020). In plants, TEs can influence gene expression through various mechanisms, including the provision of alternative promoters and the alteration of chromatin modifications near genes (Hirsch and Springer, 2017). The production of short interfering RNAs (siRNAs) by TEs is another mechanism through which they regulate gene expression, particularly in polyploid plants where TEs from one parent can affect the TEs of the other parent, leading to complex epigenetic regulation (Gill et al., 2021). 5.3 Contribution to the evolution of new gene functions TEs are not merely passive elements within the genome; they actively contribute to the evolution of new gene functions. They can be co-opted by the host genome to create new genes or modify existing ones. This co-option can lead to the development of novel gene functions and regulatory mechanisms (Bennetzen and Wang, 2014). TEs have been shown to contain functional binding sites for transcription factors, contributing to the evolution of gene regulatory networks (Sundaram et al., 2014). In mammals, TEs have been implicated in morphological evolution by altering gene regulatory networks and genome architecture (Nishihara, 2019). The ability of TEs to provide new regulatory sequences and influence gene expression patterns makes them potent drivers of evolutionary innovation (Sundaram and Wysocka, 2020). The waves of TE invasions over evolutionary time have catalyzed the development of complex gene-regulatory networks, highlighting their role in the adaptive evolution of genomes (Chuong et al., 2016). TEs are pivotal in shaping genome structure and function, regulating gene expression, and driving the evolution of new gene functions. Their ability to induce genomic changes and provide new regulatory elements underscores their importance in the evolutionary dynamics of genomes.
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