Transposable element annotation and the development of insertion site-based polymorphism markers in Prunus species

TEs are known to play major roles in genome evolution, and gene regulation, thus linking global genome function to whole genome structure. TEs are ubiquitous in nature, often found in high-copy number, distributed throughout the genome in both hetero- and euchromatin, and show insertional polymorphism both among and within species. It has also been proposed that TE-induced genomic rearrangements and mutations tend to promote local genetic diploidization in polyploid genomes. Because of these characteristics, TE-based molecular markers have great utility for: establishing phylogenies; studying biodiversity; generating dense linkage maps; and they are ideal tools for studying the structure and evolution of the diploid and polyploid Prunus genomes. In order to develop insertion-site based polymorphism (ISBP) markers in Prunus, we first screened the peach genome sequence (http://www.rosaceae.org/peach/genome) for transposable elements, identifying and annotating them with the analysis program REPET TEdenovo and TEannot pipelines (http://urgi.versailles.inra.fr/development/repet/index.php). TEdenovo results were compared with the outputs of several other different programs such as LTRFinder, MUST-MITE  and others. Data were verified manually to generate a full-length TE peach sequence database (named PTED for ‘peach TE database’) that was, in the last step, cross matched with the whole genome sequence of peach through the ISBP Finder software (Paux et al., 2010). The design of TE-based markers is currently under validation using a subset of these ISBP markers in order to confirm that predicted ISBP markers correspond to single genomic loci in a collection of Prunoideae species and Prunus populations segregating for resistance to Plum pox virus (sharka disease).