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US Tomato sequencing project update http://sgn.cornell.edu/ January 14, 2007

US Tomato sequencing project update http://sgn.cornell.edu/ January 14, 2007. US Tomato Genome sequencing. BAC libraries Made two BAC libraries (EcoRI & MboI) in addition to HindIII library BAC end sequence 400,000 BAC end sequence reads 340,000 high quality insert sequences

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US Tomato sequencing project update http://sgn.cornell.edu/ January 14, 2007

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  1. US Tomato sequencing project update http://sgn.cornell.edu/ January 14, 2007

  2. US Tomato Genome sequencing • BAC libraries • Made two BAC libraries (EcoRI & MboI) in addition to HindIII library • BAC end sequence • 400,000 BAC end sequence reads • 340,000 high quality insert sequences • Chromosomes to be sequenced • 1, 10, 11 • Sequenced 17 full BACs to date • > 40 successful FISH hybridizations • $1.8 million in support from NSF (Fall, 06) • Pending proposal for full sequencing of Chromosomes 1, 10, 11

  3. BAC libraries and BAC end sequences 100,000 50,000 50,000 Additional ordered libraries: S. cheesmannii HindIII pBeloBAC11 100,000 clones >100kb avg. S. pennellii HindIII pBeloBAC11 100,000 clones >100kb avg. S. lycopersicum Sau3A cosmid 200,000 clones 20 kb avg. S. lycopersicum Sau3A cosmid >100,000 clones > 20 kb avg. S. lycopersicum sheared fosmid >150,000 clones 40 kb avg. (400,000 target)

  4. TG31 SSR57 T1117 T1706 CT255 T697 T1665 SSR5 CT38 SSR50 T147 CT9 T347 T1566 TG154 cLER17N11 cLEC7P21 SSR349A SSR356 SSR605 SSR586 SSR26 SSR66 T1616 SSR32 SSR40 SSR96 T1494 T1480 T1201 Fw2.2 T562 T634 cLET1I9 SSR331 SSR580 SSR125 SSR103 cLEC7H4 Overgo Project • anchor tomato BACs/contigs on the highly saturated genetic map (F2.2000) • identify the minimum tiling path of BAC clones for BAC-by-BAC sequencing

  5. FISH Image

  6. Bioinformatics • BAC registry database • Central database at SGN that keeps track of the status of every BAC sequenced in the project • SGN Data repository • All sequences, including all primary data (chromatograms and assemblies) are uploaded to the central data repository • Participation in ITAG annotation • Structural Annotation pipeline • Functional Annotation pipeline

  7. Hetero/euchromatin BAC repeat annotation Euchromatin: Gene rich, repeat poor Genes Genes Heterochromatin: Gene poor, repeat rich (red) Repeats

  8. Future plans • Complete and End-sequence Fosmid library (400,000 clones) • Full sequences of chromosome 1, 10 & 11 (estimated 550 BACs) • Support international project partners with BAC libraries and FISH (10 hybes/country) • Continue to run a central bioinformatics hub for data deposition (SGN), project tracking and running shared annotation pipeline

  9. Acknowledgments Steven Tanksley Yimin Xu Nancy Eanetta Jim Giovannoni Ruth White Julia Vrebalov Joyce van Eck Stephen Stack Suzanne Royer SGN: Lukas Mueller Naama Menda Rob Buels Marty Kreuter Chenwei Lin John Binns Beth Skwarecki

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