The repetitive DNA of conifers - lessons from the Norway spruce (Picea abies) genome and resequencing of 5 other conifers

An important part of the Spruce Genome Project is the analysis of genome content and specifically of the repeated regions, since they are believed to make up a very large fraction of the 20 Gbp genome. By taking advantage of the massive amount of sequence data generated in the project, both from the Illumina and 454 platforms, we are able to perform an in-depth analysis of the genome repetitive fraction. This is complemented with a manually curated spruce-specific repeat library based on 454 whole genome shotgun sequences.

The spruce genome is known to be highly repetitive and our initial analyses confirms that repeats represent over 70% of the genome. Most part of these repetitive sequences were characterized as part of transposable elements (TEs). All the major TE classes could be identified in the spruce genome and LTR retrotransposons were the most abundant (59% of all TEs). In addition, a significant portion (9%) of the sequences identified as repetitive is still awaiting further classification. To further characterize the repetitive component of the spruce genome we will apply a comparative approach where we sequence five additional species, i.e. Siberian fir (Abies sibirica), Scot’s pine (Pinus sylvestris), Yew (Taxus Baccata), Juniper (Juniperus communis) and Gnetum (Gnetum gnemon). Although the sequencing depth is not enough (20x coverage for pine and 5x coverage for the others) to make a complete genome assembly for these species, we expect it to be sufficient for the identification of the most abundant repetitive sequences. Based on our experience in spruce, we will also produce manually curated repeat libraries for the five additional species. The evolutionary framework created by this sequencing effort will be exploited not only to study spruce-specific repeats, but also to better understand TE dynamics, including the dating of their expansion, within a broader range of conifers.