Triticeae Genomics and Genetics, 2024, Vol.15, No.1, 31-43 http://cropscipublisher.com/index.php/lgg 36 4.2 Regulatory element creation TEs are instrumental in the creation of new regulatory elements within the Triticeae genomes. These elements can introduce novel promoters, enhancers, and other regulatory sequences that influence gene expression and regulation. In wheat, for example, TEs have been found to contribute significantly to the regulatory evolution by embedding themselves in transcription factor binding sites, thus affecting the transcriptional regulatory network (Zhang et al., 2021). This phenomenon is not unique to Triticeae; in humans, TEs have been shown to contribute to the evolution of regulatory networks by providing binding sites for transcription factors and creating new enhancers (Glinsky, 2018; Ali et al., 2021). The exaptation of TE sequences into functional regulatory elements is a common theme across different species, highlighting their role in driving regulatory innovations (Joly-Lopez and Bureau, 2018). This insertion can result in the modification of gene expression patterns, potentially providing adaptive advantages in response to environmental changes. 4.3 Contribution to adaptation TEs significantly contribute to the adaptability of Triticeae species by inducing genetic variations that can be beneficial under specific environmental conditions. The activation of TEs can lead to the generation of genetic diversity, which is essential for adaptation to new or changing environments. For example, the activity of TEs in the fungal wheat pathogen Zymoseptoria tritici has been linked to chromosomal rearrangements and the creation of new gene regulatory networks, aiding in the pathogen's adaptation and survival (Lorrain et al., 2021). Similarly, the reactivation of TEs in wheat can result in structural changes that enhance the plant's ability to respond to biotic and abiotic stresses (Oggenfuss and Croll, 2023). 5 Case Studies inTriticeae Genome 5.1Wheat (Triticum aestivum) Wheat, as a primary staple crop, has undergone extensive genomic studies to understand the role of transposable elements (TEs) in its genome evolution (Figure 3). The wheat genome is hexaploid, comprising three subgenomes (A, B, and D): which adds complexity to its study. Recent research has highlighted that TEs have massively proliferated in these subgenomes, contributing to the genome's size and structural diversity. No significant TE bursts were observed after polyploidization events, indicating a steady state of TE activity (Wicker et al., 2018). Wicker et al. (2018) revealed the variability and similarities of transposable elements (TEs) in the three subgenomes (AA, BB, DD) of wheat. Sequence alignment of the homologous regions of chromosomes 3A, 3B, and 3D demonstrated highly conserved genes but inconsistent positions of TEs, suggesting independent insertions (Figure 3a). In the hexaploid wheat genome, the distribution ratios of the 20 most abundant TE families varied across the A, B, and D subgenomes (Figure 3b): reflecting the diversity of each subgenome. K-mer analysis further revealed the proportions of repetitive sequences at different frequencies, with the D genome showing the highest proportion of 60-mer repetitive sequences, while the B genome had the lowest, indicating a possible higher abundance of repetitive sequences in the D genome that could impact its genomic structure and function (Figure 3c). The distribution of 20-mer frequencies on physical chromosomes confirmed the characteristic of fewer repetitive sequences in the B genome (Figure 3d). These findings highlight the complex insertion patterns of TEs in the wheat genome and the significant differences between subgenomes, which are crucial for understanding the structural and functional diversity of the wheat genome. Recent advances have shed light on the dynamic nature of TEs in wheat. The presence of high-copy transposons, such as miniature inverted-repeat transposable elements (MITEs): has been shown to significantly influence the wheat genome. Miniature inverted-repeat transposable elements (MITEs) are particularly abundant in wheat, with the Stowaway superfamily accounting for about 80% of the MITE insertions. These elements are distributed across the seven homologous chromosomes of wild emmer and bread wheat, with a significant proportion located near coding genes, suggesting a potential impact on gene expression (Keidar-Friedman et al., 2018).These elements contribute to genetic diversity and evolutionary adaptations, with studies indicating that MITE insertions are associated with functional variations in wheat genes (Ubi et al., 2022). Moreover, TEs play a crucial role in the
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