BackgroundTransposable elements (TEs) are ubiquitous components of all genomes. Their variety and abundance, especially in large plant genomes, pose one of the greatest challenges for plant genomics both in a technical and an intellectual sense. TEs are usually seen as “junk” or “selfish” DNA which replicate and move within the environment of their “host” genome. TEs and their host genomes interact in many of ways: TE amplification increases genome size while the host genome has mechanism to remove repetitive DNA. However, emerging data challenges the view of TEs as purely selfish by describing TEs as sources of genetic variation, vehicles of gene movement or providers of novel coding or regulatory sequences. Such research has been patchy and mostly restricted to one specific TE type in a single species or genomic region. With this proposed project, we would like to address the fundamental biological question as to the contribution of TEs to plant genome evolution.Specific aimsThrough systematic bioinformatics analysis of TE in entire plant genomes and comparison of TEs from different species, we would like to study the role of TEs for genome evolution. In particular, we would like to search for patterns that indicate whether they are purely “selfish” or whether they might have an underlying beneficial role for genome evolution. Expected value of the proposed projectOur large-scale approach will provide an improved understanding of the biological role of TEs in plant genome evolution. We expect to be able to identify patterns of diversifying or purifying selection which can then give hints of whether certain TE families have a positive effect on genome evolution or whether they have to be seen as purely selfish. We should also be able to elucidate to what degree purely random genetic drift drives the evolution of TEs and their “host” genome. We anticipate that our results will be the basis for further bioinformatics and wet lab studies on the biological function of TEs and their interaction with their host genomes. Establishment and maintenance of a comprehensive and consistent database for repetitive DNA will strengthen the role of our lab as important hub for exchange of information and expertise on repetitive DNA. This is a position of high strategic value considering the growing speed at which genomic sequences will be produced in the future. Additionally, we hope to contribute to an improvement and growth Bioinformatics research in Zurich.