Скачать презентацию Progress with Sequencing Tomato Chromosome 4 Clare Riddle Скачать презентацию Progress with Sequencing Tomato Chromosome 4 Clare Riddle

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

A Summary of… Map progress Strategies for additional chromosome coverage Chromosome 4 sequencing and 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

BAC Library & Map Resources – January 2008 BAC Libraries Library No. of clones BAC Library & Map Resources – January 2008 BAC Libraries Library No. of clones Average Insert Genome equivalents Fingerprints End Sequenced ? LE_HBa 129, 024 117 kb 15 X 10 x (88, 000 AGI) Yes (188, 130) SL_Mbo. I 52, 992 135 kb 7 X 5 x (43, 000 WTSI) Yes (112, 507) SL_Eco. I 72, 264 95 -100 kb 7 X - Yes (101, 375)

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

Pseudo. Golden. Path (PGP) Analysis of Fosmid Library for Contig Extension Fosmid end sequences Pseudo. Golden. Path (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

Chromosome 4 Map – January 2008 • 44 chromosome 4 FPC contigs • Tiling 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 inhouse

Chromosome Position and Localisation • FISH analysis for Chr 4 Placement • Repeat Assessment Chromosome Position and Localisation • FISH analysis for Chr 4 Placement • Repeat Assessment of clones to determine heterochromatic/euchromatic boundaries

Tomato BACs in Sequencing Pipeline Stage No. of BACs Subcloning 19 Shotgun 3 Assembly Tomato BACs in Sequencing Pipeline Stage No. of BACs Subcloning 19 Shotgun 3 Assembly Start 8 Auto-prefinishing 8 Finishing 6 QC Checking 1 Completed 91 TOTAL : 136 15 clones undergoing picking and verification end Dec 2007

January 2008 - Chromosome 4 Sequence 12, 503, 233 bp Unique 11, 949, 283 January 2008 - Chromosome 4 Sequence 12, 503, 233 bp Unique 11, 949, 283 bp Total Finished Length = 9, 612, 145 bp

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

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