Sequencing the tomato genome at the University of Oklahoma

Sequencing Solanaceae lycopersicum Cultivar Heinz 1706-BG at the University of Oklahoma

The approximately 950 Mb tomato, Solanaceae lycopersicum, genome (see the SOL Genomics Network web site) is being sequenced by the International Tomato Sequencing Consortium as part of the International Solanaceae Genomics Project (SOL).

Here is the link to the Tomato Genome BAC-by-BAC Sequencing Statistics at the solgenomics.net site at the Boyce Thompson Institute USDA/ARS and to our Solanum lycopersicum Sequencing Progress at OU web page.

The following are links to a JBrowse genome browser for Tomato Chromosomes 1, 2, 3, 5, and 10.

To go to the JBrowse** link where clicking on the OU BAC goes to the GenBank entry click Here
To go to the JBrowse link where clicking on the OU BAC goes to the BAC crossmatched to the tomato genome, click Here
** Mitchell E. Skinner, Andrew V. Uzilov, Lincoln D. Stein, Christopher J. Mungall and Ian H. Holmes. JBrowse: A next-generation genome browser. Genome Res. 19:1630-1638 (2009).

The US group consist of:

Jim Giovannoni, PI, at the Boyce Thompson Institute USDA/ARS, and Co-PIs
Bruce Roe at the University of Oklahoma,
Joyce Van Eck at Cornell University,
Lukas Miller at Cornell University, and
Steve Stack at Colorado State University
We are funded by NSF grant #0820612 to contribute to the whole genome shotgun initiative as well as sequence chromosomes 1 and 10 using a combined mapped BAC-based and WGS approach.

In the summer of 2009, we begun receiving well characterized Solanaceae lycopersicum BACs from Jim Giovannoni's group at the Boyce Thompson Institute at Cornell University, Ithica, NY.

Our present plan is to sequence each of these BACs to completion All of the data will be released into GenBank following the Bermuda Rules and links to this data are provided at http://www.genome.ou.edu/tomato_table.html

Our trace data for the whole genome shotgun reads on the 454 is available in the NCBI Sequence Read Archive at http://www.ncbi.nlm.nih.gov/sra/SRX029427?report=full

Acknowledgments

Should you find this data useful and wish to reference it prior to its publication should credit "The International Tomato Genome Sequencing Consortium".

Bruce Roe, broe@ou.edu