Brachypodium distachyon JGI 4X draft genome release policy
Data Release Policy Message to scientists interested in accessing the Brachypodium distachyon 4x genome sequence.
Brachypodium distachyon line Bd21 is currently being sequenced by the US Department of Energy Joint Genome Institute in its ‘Community Sequencing Program’. This small grass, which is closely related to wheat and barley, is being established as a model for research in temperate grasses, including wheat, barley and emerging bioenergy crops. JGI have made rapid progress and aim to complete, by early 2008, an 8x whole genome shotgun sequence assembly supplemented with BAC- based physical maps and targeted finishing. The final quality of this sequence promises to be high. A checkpoint assembly of the 4x shotgun sequence integrated with a physical map of BACs has recently been completed.
As a public service, the raw sequence data and current assemblies of the 4x coverage of the Brachypodium distachyon genome are being made available by the Department of Energy's Joint Genome Institute (JGI) before scientific publication according to the Ft Lauderdale Accord. This balances the imperative of the DOE and the JGI that the data from its sequencing projects be made available as soon and as completely as possible with the desire of the collaborators and the JGI to reserve a reasonable period of time (not to exceed 12 months from completion of the 8x draft sequencing) to publish their results without concerns about potential preemption by other groups. If these data are used for publication, the following acknowledgment should be included: “These sequence data were produced by the US Department of Energy Joint Genome Institute http://www.jgi.doe.gov/.” We request that you notify us upon publication so that this information can be included in the final annotation.
These pre-publication data are preliminary and may contain errors. JGI policy is that early release should aid the progress of science. By accessing these data, you agree not to publish any articles containing analyses of genes or genomic data on a whole genome or chromosome scale prior to publication by JGI and/or its collaborators of a comprehensive genome analysis (“reserved analyses”) using the 8x genome sequence assembly.
Reserved analyses include the identification of complete (whole genome) sets of genomic features such as genes, gene families, regulatory elements, repeat structures, GC content, or any other genome feature, and whole-genome- or chromosome- scale comparisons with other species. The projected time line for completion of the final 8x genome sequence assembly is mid-2008. Thus the embargo on publication of such reserved analyses by researchers outside of the Brachypodium Genome Sequencing Project is expected to extend until mid-2009, though this will be adjusted based on the final assembly completion date. Scientific users are free to publish papers dealing with specific genes or small sets of genes using the draft sequencing data. This letter has been circulated to Journal Editors so that they are aware of the conditions of access and publication detailed above.
The data may be freely downloaded and used by all who respect the restrictions in the previous paragraphs. While still in waiting period status, the assembly and raw sequence reads should not be redistributed or repackaged without permission from the JGI. Any redistribution of the data during this period should carry this notice: “the Joint Genome Institute provides these data in good faith, but makes no warranty, expressed or implied, nor assumes any legal liability or responsibility for any purpose for which the data are used.” Once moved to unreserved status, the data are freely available for any subsequent use.
We prefer that potential users of this sequence assembly contact the Brachypodium Genome Sequencing Project co-directors (John Vogel, Michael Bevan, David Garvin) with their plans so that research activities can be coordinated, as appropriate. The Brachypodium Genome Sequencing Project directors have contacted a range of experts to contribute to the analysis and annotation of the Brachypodium genome. We welcome enquiries from experts about contributing to the genome analysis.
