The preliminary 8X draft assembly of the E. grandis genome, which is being sequenced by the US Department of Energy (DOE) Joint Genome Institute (JGI), is available from today in our public Eucalyptus Genome Database (EucalyptusDB). Members of the Eucalyptus research community and the wider plant genomics community are invited to make use of this resource, which is already widely accessed.
Some notes on this release:
- The genome browser in EucalyptusDB has been updated to Generic Genome Browser (GBrowse) version 2.0.
- The browser for the preliminary 4.5X (checkpoint) assembly will remain accessible, but is currently also being updated to GBrowse 2.0.
- The 8X assembly released on EucalyptusDB is the first draft assembly that incorporates all of the Sanger sequences produced for the E. grandis genome. The assembly is still being updated and the current release is therefore likely to be incomplete in some regions and will change in the next release. A more complete draft assembly and draft annotation will be released on Phytozome later in 2010.
- The draft 8X assembly consists of 6043 genome scaffolds covering 693 Mbp. This total is somewhat inflated due to the fact that approximately 20% of the genome is currently assembling into two parallel haplotypes (both included in the 693 Mbp) due to very high heterozygosity in some regions of the E. grandis genome. This will be resolved in the next release of the genome assembly.
The initial analysis of a high quality draft E. grandis genome sequence will be published in 2011. The principal investigators and collaborators of the E. grandis Genome Project intend to publish genome-wide analyses of features such as genes, protein families, metabolic pathways, non-coding RNA and repetitive DNA in the main genome paper, associated papers and in subsequent publications. Interested persons are encouraged to contact the principle investigators (Zander Myburg, Dario Grattapaglia or Jerry Tuskan to coordinate collaborative efforts aimed at producing such publications.
We also invite members of the Eucalyptus research community and all other interested persons to register as members on the EUCAGEN website.