1. Solanum lycopersicum Chromosome 4 Sequencing Update SOL Germany– October 2008 Wellcome Trust Medical Photographic Library

2. Summary of Project Status at WTSI WTSI will be leaving the project on 31 st Oct 2008 Transfer of BAC selection/contig building QC- checking is on the move to Imperial College London Introduction

3. WTSI Tomato Clone Pipeline Pipeline Stage Number of BACs 2007 Number of BACs 2008 Subcloning340 Shotgun211 Assembly Start70 Auto-prefinishing30 Finishing1133 QC Checking42 Finished63147 Total143183 Phase 3 Phase 1+2 HTGS:

4. Chromosome 4 Sequence Generated Total Sequence Available19,815,026 bp Total Unique Sequence19,527,597 bp Total amount of Finished Sequence = 15,244,914 bp

5. Some facts and figures We have 81 contigs on chr4 (80 contigs with sequence available). Average contig length is just under 250 kb. The average number of BACs per contig is 2.3. The largest sequence contigs are in the range of 450kb-500kb with 5 or 6 BACs.

6. Distribution of tomato Chromosome BACs and sequence content Centromere = Euchromatin = Heterochromatin 62 markers 41 markers 124 markers 30 contigs11 contigs 36 contigs 56 BACs 59 BACs63 BACs SSR markers 4 contigs 5 BACs UNORDERED 27 markers16 markers61 markers

7. Summary of Progress on Chromosome 4 81 map contigs have been built on chromosome 4 (AGP files) 119 BACs/44 contigs definitely on chr4 in FISH/ IL mapped 58 BACs under confirmation but have chr4 marker sequence ~60 Markers for which BACs have not been identified. ~13 BACs have been sequenced to HTGS3 and placed on chr0, definitely not on chr4 (others initiated, in same contig etc but stopped in pipeline). 22 Missing markers missing sequence?

8. Summary of what we will do next 1) Confirm chr4 location of BACs that lack chr4 marker sequence and or have conflicting map location. IL mapping. 2) Use missing marker sequences to identify further BACs (3D pools) and confirm chr4 location using IL mapping. 3) Use 3D BAC pools to identify BACs to extend current contigs. 4) Analyse output from X2 GS-FLX and X2 Illumina sequencing runs on cDNA from chr4 IL and parental lines to identify SNPs and further chr4 markers. 5) Use any markers from (4) to isolate further BACs for sequencing.

9. Acknowledgements Wellcome Trust Sanger Institute: Carol Churcher Jane Rogers Sean Humphray Clare Riddle and Mapping Core Group Karen McLaren and Finishing Team 46 Stuart McLaren and Pre-finishing Team 58 Christine Lloyd and QC Team 57 Karen Oliver Matt Jones Carol Scott Imperial College London: Gerard Bishop Daniel Buchan James Abbott Sarah Butcher Rosa Lopez-Cobollo University of Nottingham: Graham Seymour Scottish Crop Research Institute: Glenn Bryan Cornell University: Lukas Mueller Jim Giovannoni MIPS/IBI Institute for Bioinformatics: Klaus Mayer Remy Bruggmann FISH Resources Stephen Stack Group (Colorado) Hans de Jong (Wageningen) Dora Szinay (Wageningen) FUNDING