Sorghum Genome Sequence announcement

[Claire Hebbard]

To: Gramene List-serve

Here is a letter from Dr. Andrew Paterson concerning the Sorghum 
Genome Sequence.

[begin letter]

20 Nov 2006
TO: Anyone interested in the sorghum genome sequence (please 
circulate this as widely as possible).

As you may know, the US Department of Energy Joint Genome Institute, 
under its 'Community Sequencing Program' has made rapid progress 
toward its commitment to provide 8X sequence coverage of the genome 
of Sorghum bicolor L. genotype, BTx623.  These data will be combined 
with publicly
available sequences, assembled into 'contigs' (contiguous sequences 
without gaps) and 'scaffolds' (reconstructed stretches with any gaps 
spanned by at least two end-sequenced clones), and integrated with 
extensive physical and genetic maps to yield genetically-oriented 
pseudomolecules that are anticipated to substantially cover most 
sorghum chromosomes.

Sorghum sequence assemblies will be made available in advance of 
publication, under the principles of the 'Ft Lauderdale' agreement 
(http://72.14.209.104/search?q=cache:ag5ZX7CDIdkJ:www.wellcome.ac.uk/assets/wtd003207.pdf+Ft+Lauderdale+sequence&hl=en&gl=us&ct=clnk&cd=1) 
to protect the interests of scientists who wish to share 
pre-publication data with the community, i.e. with a request that 
users defer publication of any whole-genome scale analyses until the 
sequencing group has published its primary analysis.  Leading 
scientific journals are also being notified.  A 4x assembly is now 
available at https://www.jgi.doe.gov/downloads/Sorghum_bicolor.  Use 
Sorghum_bicolor and ^ico at hgr as login and password, respectively.  We 
anticipate that the genetically- oriented 8x assembly will be 
available in early 2007, barring unexpected delays.

A team has been assembled to conduct initial annotation and analysis 
of the sequence for publication in a leading refereed journal. 
Although many dimensions of the planned analysis are covered, 
inquiries about possible participation in this effort should be 
directed to Dr Paterson (paterson at uga.edu).  Team members are 
responsible for providing their own funding to support their 
participation.

Since the primary publication of the sequence will only be able to 
succinctly describe a few key features, two leading journals have 
offered to consider companion papers that address specific features 
in detail, for coordinated publication shortly following the primary 
sequence, in a 'special section' or perhaps 'special issue'.

1. Genome Research (www.genome.org/) has agreed to consider 
large-scale genomic studies that present novel data of biological 
significance.

2. The Plant Genome (www.crops.org/genome/) has agreed to consider 
research that shows clear potential for translating genomic 
technology into agronomic advancement.

Both journals will review sorghum genome-related submissions 
according to their established mechanisms and standards. At an 
appropriate time, the respective journals will provide further 
details. We hope that this information is useful in planning for 
engagement of these new genomic resources for
sorghum in your work.  We also hope that you share our excitement 
about these new resources, which promise to add new dimensions to our 
understanding of botanical and genomic diversity, as well as new 
opportunities for improvement of leading food, feed, forage & turf, 
and biofuels crops.  We encourage you to consider how the sorghum 
sequence might fit into your research plans, to submit manuscripts to 
the coordinated reviews as appropriate, and to contact us with any 
questions.

Andrew H. Paterson
Lead Proposer, CSP Sorghum Sequencing Project
Chair, Sorghum Genomics Executive Committee

Daniel S. Rokhsar                                                
Program Head for Computational Genomics
Joint Genome Institute


[end letter]



-- 
*******************************************
Claire Hebbard
Gramene Outreach Coordinator
G15 Bradfield Hall
Ithaca, NY 14853

www.gramene.org

ph: 607-255-4199
*******************************************
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://brie4.cshl.edu/pipermail/gramene/attachments/20061129/efbad458/attachment.html>