Triticeae Genomics and Genetics, 2024, Vol.15, No.1, 31-43 http://cropscipublisher.com/index.php/lgg 34 networks. They can act as sources of genetic innovation by promoting gene duplications, creating new regulatory elements, and influencing gene expression. For instance, the study of TEs in fungal wheat pathogens has shown that TEs can shape genome architecture and affect gene regulation, particularly in relation to pathogenicity (Lorrain et al., 2021). Additionally, the genomic ecosystem of maize highlights how TEs contribute to the diversification of gene regulation and phenotypic traits, emphasizing their evolutionary impact (Stitzer et al., 2021). Figure 2 The role of transposons (TEs) in the genome (Adapted from Colonna Romano and Fanti, 2022) Image caption: Transposable elements (TEs) can exert various deleterious effects on the host genome: (a) Insertion into coding exons causes frameshift mutations, disrupting protein function; (b) They serve as substrates for chromosomal rearrangements, leading to duplication, deletion, inversion, and translocation; (c) Insertion into regulatory regions triggers epigenetic modifications, improperly activating or suppressing gene expression. TEs can be domesticated by the host genome, producing new regulatory signals or coding sequences: (d) Providing new enhancer sequences, altering the spatiotemporal regulation of gene expression; (e) After losing telomerase, non-LTR family retrotransposons participate in telomere maintenance; (f) By offering binding sites for CTCF protein, they help maintain genomic structure (Adapted from Colonna Romano and Fanti, 2022) 2.3 Influence on genome structure TEs profoundly influence genome structure in Triticeae by contributing to genome size variation, chromosomal rearrangements, and the creation of gene-rich regions. The high TE content in Triticeae genomes, as observed in Aegilops speltoides, underlies extensive genome reshuffling and intraspecific diversification (Raskina, 2018). Moreover, recent research has demonstrated that TEs can lead to major chromosomal rearrangements and affect gene expression, contributing to phenotypic variation and adaptation. For example, the reactivation of the Styx element in fungal wheat pathogens triggered significant chromosomal rearrangements, illustrating the dynamic nature of TEs in shaping genome structure (Badet et al., 2023). 3 Methodological Approaches to Study TEs inTriticeae 3.1 Genomic sequencing and annotation Genomic sequencing has been fundamental in advancing our understanding of transposable elements (TEs) in the Triticeae genome. High-throughput sequencing technologies such as Illumina, PacBio, Next Generation Sequencing (NGS): and Oxford Nanopore have enabled researchers to obtain comprehensive genomic data, facilitating the identification and annotation of TEs. For instance, NGS has been instrumental in uncovering the
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