Triticeae Genomics and Genetics, 2024, Vol.15, No.1, 31-43 http://cropscipublisher.com/index.php/lgg 32 The study of TEs in plant genomes has a rich history, dating back to the pioneering work of Barbara McClintock in the 1940s, who discovered "jumping genes" in maize. Since then, TEs have been recognized as major players in genome evolution, contributing to genetic variation, genome size expansion, and regulatory network modifications. In Triticeae, advances in genomic technologies have allowed for the detailed identification and characterization of numerous TE families, enhancing our understanding of their roles in genome evolution, gene regulation, and adaptability (Wicker et al., 2018). Recent studies have highlighted the significant role of TEs in shaping the genome structure and function, influencing gene expression, and facilitating adaptation to environmental changes (Zhang et al., 2021; Papon et al., 2023). This study aims to elucidate the role of transposable elements in the evolution of the Triticeae genome. By synthesizing current research findings, we seek to provide a comprehensive understanding of how TEs contribute to genetic diversity, genome evolution, and the adaptive potential of Triticeae species. This study will explore the mechanisms by which TEs influence genome dynamics, the evolutionary implications of TE activity, and the potential applications of this knowledge in crop improvement and breeding programs. 1 Types and Mechanisms of Transposable Elements inTriticeae 1.1 Classification of transposable elements Transposable elements (TEs) in the Triticeae genomes are broadly classified into two main classes based on their mechanisms of transposition: Class I elements, or retrotransposons, and Class II elements, or DNA transposons. Class I elements, also known as retrotransposons, move via an RNA intermediate. These are further subdivided into Long Terminal Repeat (LTR) retrotransposons and non-LTR retrotransposons. LTR retrotransposons, such as Ty1-copia and Ty3-gypsy, are particularly prevalent in the Triticeae genomes and are characterized by their long terminal repeats which flank the coding regions of the transposon (Sabot and Schulman, 2009). Non-LTR retrotransposons include LINEs (Long Interspersed Nuclear Elements) and SINEs (Short Interspersed Nuclear Elements) (Klein and O’Neill, 2018; Colonna Romano and Fanti, 2022): where LINEs are autonomous and SINEs depend on the enzymatic machinery of LINEs for their movement (Wicker et al., 2013). Class II elements, or DNA transposons, move through a "cut-and-paste" mechanism. Examples include the Tn3 family transposons, which utilize a replicative transposition mechanism (Lima-Mendez et al., 2020). These are categorized into several superfamilies such as CACTA transposons and MITEs (Miniature Inverted-repeat Transposable Elements). CACTA transposons, like the Caspar family, are significantly present in the Triticeae genomes and play a critical role in genome organization (Wicker et al., 2003). MITEs, being non-autonomous elements, rely on the transposase enzymes of other transposons for their movement and are often associated with gene regions, impacting their regulation and evolution (Wicker et al., 2001). 1.2 Mechanisms of transposition The transposition mechanisms of TEs differ between Class I and Class II elements (Figure 1). Retrotransposons (Class I elements) utilize a copy-and-paste mechanism (Figure 1a and Figure 1b). This process begins with the transcription of the retrotransposon into RNA, which is then reverse transcribed into DNA by the enzyme reverse transcriptase. The newly synthesized DNA is subsequently integrated into a new location in the genome by the integrase enzyme (Sabot and Schulman, 2009). This process can lead to an increase in the number of copies of the element within the genome (Klein and O’Neill, 2018; Ali et al., 2021). In contrast, DNA transposons (Class II elements) follow a cut-and-paste mechanism (Figure 1c). Here, the transposon is first excised from its original location in the genome by the transposase enzyme. The excised DNA element is then inserted into a new genomic location, completing the transposition process (Wicker et al., 2003). Some DNA transposons can also mediate duplications via transposition-independent mechanisms, such as gap filling, or transposition-dependent mechanisms, such as replication fork switching (Lima-Mendez, 2020; Tan et al., 2021). 1.3 Distribution and abundance inTriticeae genomes The distribution and abundance of TEs in Triticeae genomes are highly variable and significant. TEs constitute a substantial portion of the Triticeae genomes, with LTR retrotransposons alone accounting for 55%~70% of the
RkJQdWJsaXNoZXIy MjQ4ODYzNQ==