1. 13 th January 2008 Plant & Animal Genome Conference Progress with Sequencing Tomato Chromosome 4 Clare Riddle Tomato Project Group Wellcome Trust Sanger Institute

2. A Summary of… Map progress Strategies for additional chromosome coverage Chromosome 4 sequencing and clone selection update BAC Finishing report Copyright Wellcome Trust Medical Photographic Library

3. BAC Library & Map Resources – January 2008 Library No. of clones Average Insert Genome equivalents Fingerprints End Sequenced ? LE_HBa129,024117 kb15 X 10x (88,000 AGI ) Yes (188,130) SL_MboI52,992135 kb7 X 5x (43,000 WTSI) Yes (112,507) SL_EcoI72,26495-100 kb7 X- Yes (101,375) BAC Libraries

4. Additional Resources Fosmid library (end-sequenced Dec 2007) –smaller than BACs –known insert size  Contig extension  Gap closure  Confirm assembly –107,681 tomato reads added to trace archive http://trace.ensembl.org

5. PseudoGoldenPath (PGP) Analysis of Fosmid Library for Contig Extension Fosmid end sequences (from pilot study of 3 plates) deposited by Cornell have been aligned to chromosome 4 sequence Potential Extender Fosmid end sequences from plates 1-150 will be incorporated in to next PGP - January 2008

6. Chromosome 4 Map – January 2008 44 chromosome 4 FPC contigs Tiling paths selected across contigs Additional contig coverage required Strategies to identify further coverage: Screen unanchored markers Walk from contig ends by hybridization Libraries gridded in- house

7. Chromosome Position and Localisation FISH analysis for Chr4 Placement Repeat Assessment of clones to determine heterochromatic/euchromatic boundaries

8. Tomato BACs in Sequencing Pipeline Pipeline StageNo. of BACs Subcloning19 Shotgun3 Assembly Start8 Auto-prefinishing8 Finishing6 QC Checking1 Completed91 TOTAL : 136 15 clones undergoing picking and verification end Dec 2007

9. January 2008 - Chromosome 4 Sequence Chromosome 4 Sequence12,503,233 bp Unique11,949,283 bp Total Finished Length = 9,612,145 bp

10. Finishing of Tomato Chromosome 4 All BACs to HTGS Phase 3 QC team 2000 bp overlap between neighbouring clones  minimise redundancy  sufficient for final assembly Extensive software suite GAP4

11. Acknowledgements Wellcome Trust Sanger Institute: Karen McLaren Clare Riddle Sean Humphray Christine Nicholson Carol Scott Stuart McLaren Matt Jones Christine Lloyd Sarah Sims Karen Oliver Jane Rogers Imperial College London: Gerard Bishop Daniel Buchan James Abbott Sarah Butcher University of Nottingham: Graham Seymour Scottish Crop Research Institute: Glenn Bryan Cornell University: Lukas Mueller Jim Giovannoni Steve Tanksley Colorado State University: Stephen Stack Suzanne Royer Song-Bin Chang Arizona Genomics Institute: Rod Wing Seunghee Lee MIPS/IBI Institute for Bioinformatics: Klaus Mayer Remy Bruggmann Wageningen University : Hans de Jong Dora Szinay FUNDING