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.


We recently have obtained over 10-fold genomic sequence coverage of the Solanum lycopersicum genome on the PacBio RS sequencing platform. This data was merged into our updated assembly using PBJelly***. ***PBJelly is a highly automated pipeline that aligns long sequencing reads from the PacBio RS platform and long reads from the 454 platform to fill and/or reduce captured gaps to produce high-confidence upgraded draft genomes.
English AC, Richards S, Han Y, Wang M, Vee V, et al. (2012) Mind the Gap: Upgrading Genomes with Pacific Biosciences RS Long-Read Sequencing Technology. PLoS ONE 7(11): e47768. doi:10.1371/journal.pone.0047768).
The following are earlier links to a JBrowse genome browser for Tomato Chromosomes 1, 2, 3, 5, and 10 before running PBJelly to incorporate the PacBio sequence data as described above.
  • To go to the JBrowse** link where clicking on the OU BAC goes to the GenBank entry click Here
    The following are links to a JBrowse genome browser for Tomato Chromosomes 1, 2, 3, 5, and 10 before running PBJelly to incorporate the PacBio sequence data.
    • 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".

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Bruce Roe, broe@ou.edu