Triticeae Genomics and Genetics, 2024, Vol.15, No.1, 31-43 http://cropscipublisher.com/index.php/lgg 35 sophisticated transcriptional responses governed by TEs in various organisms, highlighting their regulatory roles in health and disease (Marasca et al., 2020). Additionally, the development of specific pipelines, such as PiRATE, has facilitated the accurate annotation of TEs by combining multiple detection and classification tools, as demonstrated in the microalga Tisochrysis lutea (Berthelier et al., 2018). These methodologies are crucial for generating detailed TE libraries and understanding their distribution, activity, and evolutionary impact. In the study of Wicker et al. (2018): the sequencing of the hexaploid bread wheat genome provided a detailed view of TE dynamics, revealing that TEs comprise approximately 85% of the wheat genome and play significant roles in genome organization and evolution (Wicker et al., 2018). The accurate annotation of TEs involves identifying their sequences, classifying them into families and subfamilies, and determining their insertion sites within the genome. This process is supported by databases such as Repbase and tools like Repeat Masker, which provide curated sequences of known TEs for comparison (Wells and Feschotte, 2020). 3.2 Bioinformatics tools and techniques Bioinformatics tools are crucial for analyzing the vast amounts of data generated by genomic sequencing. Programs like RepeatMasker and CENSOR are widely used for detecting and masking repetitive elements, including TEs, in genomic sequences (Zhang et al., 2021). These tools compare genomic sequences against databases of known repetitive elements to identify TEs. Additionally, bioinformatics pipelines such as TEAnnotator integrate multiple tools for a comprehensive analysis of TEs, including their identification, classification, and annotation. Comparative genomics and phylogenetic analysis are also employed to study the evolutionary dynamics of TEs. Comparative genomics allows researchers to identify conserved and lineage-specific TEs by comparing genomes of different Triticeae species, providing insights into TE diversity and evolutionary history (Oggenfuss et al., 2021). 3.3 Experimental approaches Experimental approaches complement genomic and bioinformatics studies by providing functional insights into TEs. Techniques such as PCR-based methods and Southern blotting are used to study the insertion patterns and copy numbers of TEs in the genome (Thiyagarajan et al., 2022). Transposon display, a variation of the PCR technique, allows for the visualization of TE insertions across different genomic backgrounds. In situ hybridization is another powerful technique used to determine the chromosomal locations of TEs. This method involves hybridizing labeled DNA probes specific to TE sequences to chromosomes, allowing for the visualization of TE distribution and abundance within the genome (Raskina, 2018). Additionally, RNA-seq is utilized to study the expression profiles of TEs under various conditions, providing insights into their regulatory roles and responses to environmental stresses (Lorrain et al., 2021). 4 Evolutionary Impact of Transposable Elements onTriticeae TEs are crucial elements in the evolution of the Triticeae genome, influencing genome size, creating new regulatory elements, and contributing to adaptation. Their dynamic nature and ability to generate genetic diversity make them key players in the evolutionary processes shaping the Triticeae and other species. 4.1 Genome expansion and contraction Transposable elements (TEs) are significant contributors to the dynamic nature of the Triticeae genome, influencing both its expansion and contraction. In wheat, for instance, TEs constitute more than 80% of the genome, acting as major drivers of genome evolution (Zhang et al., 2021). The insertion and proliferation of TEs can lead to genome expansion by adding repetitive sequences. Conversely, the removal through recombination and other mechanisms or silencing of TEs can contribute to genome contraction (Oggenfuss et al., 2021). The balance between these processes is crucial for maintaining genome stability and functionality. The rapid expansion of TEs, as observed in other species like sea kraits, can lead to significant genomic changes, including insertions into introns and regulatory regions, which may alter gene expression and contribute to adaptation (Galbraith et al., 2021).
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