Maize Genomics and Genetics 2024, Vol.15, No.3, 147-159 http://cropscipublisher.com/index.php/mgg 151 4.2 Comparative analysis between maize and teosinte Comparative genomic studies between maize (Zea mays L.) and its wild progenitor, teosinte (Zea mays ssp. parviglumis), reveal significant differences in TE content and distribution. Teosinte, which serves as an important genetic resource for maize improvement, has a distinct TE landscape compared to domesticated maize. For instance, genes in teosinte exhibit more transcript isoforms and are enriched in RNA modification pathways, suggesting a more complex regulatory network influenced by TEs (Li et al., 2021a). Moreover, the intergenic regions in teosinte are extensively altered by TEs, indicating that these elements have played a crucial role in the genomic divergence between maize and teosinte (Li et al., 2021a). This divergence is not only a result of TE insertions but also due to the differential retention and amplification of specific TE families. Such comparative analyses underscore the evolutionary impact of TEs on the genetic architecture of Zea species. 4.3 Methods used for identifying and mapping transposons Several advanced methodologies have been developed to identify and map TEs in the maize genome. One such method involves the use of single-molecule long-read sequencing, which allows for the accurate annotation of TEs without the need for a reference genome (Li et al., 2021a). This approach has been particularly useful in characterizing the TE landscape in teosinte, providing insights into the genomic changes that accompanied maize domestication. Another effective technique is the use of a capture-based assay, which targets specific transposon polymorphisms across various maize genotypes. This method has demonstrated high reliability, with a consistency rate of 98.6% when compared to PCR-based assays (Li et al., 2021b). By integrating transposon polymorphism data with gene expression profiles, researchers can identify TEs that influence gene expression, thereby elucidating their functional roles in the genome. Additionally, bioinformatics tools such as TIR-Learner have been developed to enhance the detection and annotation of TIR elements. This ensemble method combines homology-based and de novo machine-learning approaches, significantly improving the accuracy and efficiency of TIR element annotation (Su et al., 2019). Such tools are essential for understanding the full extent of TE diversity and their impact on genome structure and function. The distribution and abundance of TEs in Zea genomes are shaped by a combination of evolutionary processes and methodological advancements. Comparative analyses between maize and teosinte highlight the role of TEs in genome evolution, while innovative techniques for TE identification and mapping continue to refine our understanding of their contributions to genetic diversity. 5 Impact of Transposons on Genetic Architecture 5.1 Gene expression regulation Transposons, also known as transposable elements (TEs), play a significant role in the regulation of gene expression. These mobile genetic elements can act as sources of transcriptional modulatory elements, such as gene promoters and enhancers, splicing and termination sites, and regulatory non-coding RNAs. This ability allows transposons to influence the expression of nearby genes, either enhancing or repressing their activity (Elbarbary et al., 2016; Branco and Chuong, 2020). For instance, the insertion of a transposon near a gene can introduce new regulatory sequences that alter the gene's expression pattern, potentially leading to novel phenotypic traits. Moreover, transposons have driven the evolution of host defense mechanisms that have been repurposed for gene regulation. These mechanisms include the silencing of transposons through DNA methylation and histone modification, which can also affect the expression of nearby genes. The interplay between transposons and gene regulation is complex and context-dependent, often requiring specialized analytical tools to dissect their functional roles (Figure 2) (Branco and Chuong, 2020; Bhat et al., 2022). 5.2 Genome size and structure Transposons contribute significantly to the size and structure of genomes. In maize (Zea mays), for example,
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