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Solanum lycopersicum Chromosome 4 Sequencing Update

Wellcome Trust Medical Photographic Library. Solanum lycopersicum Chromosome 4 Sequencing Update. SOL Germany– October 2008. Introduction. Summary of Project Status at WTSI WTSI will be leaving the project on 31 st Oct 2008

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Solanum lycopersicum Chromosome 4 Sequencing Update

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

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

  3. WTSI Tomato Clone Pipeline HTGS: Phase 1+2 Phase 3

  4. Chromosome 4Sequence Generated • 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. UNORDERED 4 contigs 5 BACs SSR markers Distribution of tomato Chromosome BACs and sequence content Centromere 62 markers 41 markers 124 markers 30 contigs 11 contigs 36 contigs 56 BACs 59 BACs 63 BACs 27 markers 16 markers 61 markers = Heterochromatin = Euchromatin

  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 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) • 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 FUNDING

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