Integrating computational and experimental analyses to study plant transposable elements
Holligan, Dawn H.
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Transposable elements (TEs) are the single largest component of most eukaryotic genomes and account for more than half the DNA content in some of these organisms. This dissertation contains several studies designed to investigate the abundance and amplification of different TE types in plant genomes. The research presented in the first half of this dissertation focuses on the identification and analysis of TEs in the model legume Lotus japonicus (Lotus) using a combined computational and experimental approach. Lotus belongs to the Leguminosae family, one of the largest plant families, containing several agronomically important species, such as soybean and garden pea. The availability of a significant amount (32.4Mb at the time of this study) of Lotus genome sequence has permitted, for the first time, comprehensive TE analysis in a legume species. While computer-assisted analysis facilitated a determination of TE abundance and diversity, the availability of complete BAC sequences permitted identification of full-length TEs, which facilitated the design of tools for genome wide experimental analysis. The second half of this dissertation presents research aimed at understanding how MITEs are able to amplify to very high copy numbers in the host genome. MITEs are highly abundant in plants and animals, comprising > 100,000 copies in Oryza sativa (rice) and ~16% in A. Aegypti (mosquito). The analysis described in Chapter 4 involves the use of a large-scale yeast assay to examine the functional relationship between the rice Stowaway-like MITEs and their putative transposase sources, Osmars (Tc1/Mariner-like). Results from these analyses provide insight into different TE superfamilies and how they interact within host genomes.