DNA is the ultimate genetic information carrier. These sequences of nucleotides hold enormous coded data controlling all aspects of functions, including growth, development, and defense of an organism. Genes are the protein coding units that support cellular function. While gene number is similar across species, genome size varies dramatically. One source of this variation is due to transposable elements, which are DNA sequences that are capable of moving from one locus to another in the genome. These sequences are ubiquitous and provide sources of mutations for evolution. Transposable elements are classified into two classes: DNA and RNA elements (retroelements). The elements are further classified into autonomous and non-autonomous elements according to their capability to transpose. Specific elements have been shown to duplicate gene fragments and amplify in the genomes. These elements carrying genes have regulatory, evolutionary, and phenotypic effects. This dissertation illustrates examples of gene duplications by DNA transposons and their interactions with the remainder of the genome. The first entails GingerRoot: A novel DNA transposon encoding integrase-related transposase in plants and animals. This study reveals a unique DNA transposon located in the heterochromatic regions of the genome. The capability of duplicating gene fragments may have allowed them to be retained longer in genomic regions enriched with retrotransposons. The second comprises a study of Nucifera nelumbo landscape of transposable elements. In this basal dicot species, the genic regions have been significantly expanded by the insertion of transposable elements. Interestingly, genes involved in epigenetic pathways are enriched with insertions, suggesting the co-evolution between the transposable elements and the genome surveillance machine. The third study investigates Pack-MULE SlPM37 in Solanum lycopersicum and its relatives. This Pack-MULE element has achieved a higher copy number than any other Pack-MULE elements, and the possible mechanism underlining its amplification has been proposed through detailed characterization of this element and the relevant parental genes. These chapters show how genomes are comprised of varying transposons, how their context influences gene duplication, and the interactions with other genomic components including genes and other transposons. The dynamic interactions between transposable elements and their host genomes suggest the composition and abundance of transposons not only influence the genome size and genome structure, but also the path of evolution.
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