Plant genome sizes can vary several orders of magnitude between species. Such differences are due in many cases to polyploidy but, more generally, to differences in the amount of repetitive DNA present in the genome.

I am interested in the mechanisms that allow plants to tolerate such large amounts of DNA, which is mostly composed by retrotransposable elements. These elements must be silenced, probably epigenetically, in order to avoid substantial genomic damage. One possible epigenetic mechanism to silence transposons involves DNA methylation and, consistently, plant transposable elements are generally heavily methylated. This differential methylation of repetitive DNA can be used to selectively clone genes, which is the basis of the methylation filtration (MF) technique. The application of this technique to several large plant genomes resulted in significant gene enrichment of genomic shotgun libraries. Furthermore, the combination of traditional genomic sequencing strategies with MF in large plant genomes, such as those of maize and wheat, can not only provide high quality sequence information of genes but also a methylation profile of the gene-space. Interestingly, mammalian genes are methylated as well as transposable elements. Thus, though MF cannot be used for gene selection in mammals, it can be used for genome profiling. I intend to use the new ultra-high throughput sequencing technologies (i.e. 454 and Solexa) to generate genome-wide profiles of DNA methylation as well as transcription, chromatin modification, DNA binding proteins, DNA replication origins, etc. Comparison of these genome-wide features in smaller and evolutionary distant plant genomes, such as Selaginella or algae, can shed light on fundamental genome control mechanisms.