Triticeae Genomics and Genetics, 2024, Vol.15, No.1, 31-43 http://cropscipublisher.com/index.php/lgg 38 that TEs contribute to the unique genomic features of barley and other Triticeae species (Thiyagarajan et al., 2022). Comparative genomic analyses between barley and other Triticeae genomes have provided valuable insights into the evolutionary mechanisms driving genome diversification within this group. 5.3Rye (Secale cereale) Rye, known for its resilience and ability to grow in poor soil conditions, also exhibits a genome significantly shaped by TEs. Comparative studies have highlighted that TEs in rye contribute to its large genome size and genetic diversity. The genome of rye contains a substantial proportion of Class I retrotransposons, which play a key role in shaping its genomic structure and evolutionary trajectory (Markova and Mason-Gamer, 2015). Comparative studies of TE abundance in rye and its relatives have revealed significant differences in the distribution and composition of these elements. For example, the TE family Sabrina is highly abundant in rye, similar to other Triticeae species, suggesting a conserved role in genome evolution(Divashuk et al., 2019). The study of TEs in rye has also provided insights into the mechanisms of polyploidization and speciation within the Triticeae tribe (Figure 4). The relationships between the genomes of rye and other Triticeae species, based on TE abundance, highlight the role of these elements in the evolutionary history of the tribe. Figure 4 Overall structure of PIF-like transposons and their conserved transposase domains (Adapted from Markova and Mason-Gamer, 2015) Image caption: (A) PIF-like transposons contain two open reading frames (ORFs): where ORF2 includes a "DDE" motif composed of three conserved amino acids, essential for the function of the transposase, Black triangles represent terminal inverted repeat sequences (TIRs): and pink rectangles indicate the open reading frames; (B) Comparison of the conserved transposase domains and their corresponding "DD" parts from Brachypodium, Oryza, Zea, and five representative Triticeae species. Shaded rectangles represent intron regions, bold arrows indicate the location of ORF2 amplification primers; numbers denote specific clone sequences within each cereal species (Adapted from Markova and Mason-Gamer, 2015) Markova and Mason-Gamer (2015) found that the ORF2 of PIF-like transposons contains a critical "DDE" motif (Figure 4A). After comparing conserved transposase domain sequences across multiple species, the "DD" part showed high conservation, but there were variations in intron length (Figure 4B). This indicates the conservation of core functional areas and the variability of non-coding regions in PIF-like transposons, suggesting that these transposons have similar functions across different species while also adapting to various genomic environments. Rye has been particularly useful in studying horizontal transfer of TEs among Triticeae species. Evidence indicates that certain TE families have been transferred horizontally between rye and other Triticeae members,
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