Plant & Animal Genome Conference

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Presentation transcript:

Plant & Animal Genome Conference Progress with Sequencing Tomato Chromosome 4 Christine Nicholson, Mapping Core Group Karen McLaren, Finishing Group Wellcome Trust Sanger Institute 14th January 2007 Plant & Animal Genome Conference

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 2007 ADDITIONAL FINGERPRINT GENERATION Library No. of clones Average Insert Genome equivalents Coverage in fingerprints End Sequenced ? LE_HBa 129,024 117 kb 15 X 10 X Yes SL_MboI 52,992 135 kb 7 X 6 X SL_EcoI 72,264 95-100 kb - Increased map coverage – fingerprints Fingerprint data – multiple libraries Visible – detect potential deletions Public Assembled database available at: ftp://ftp.sanger.ac.uk/pub/tomato/map/

Chromosome 4 Map – January 2007 47 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 → Continued chromosome 4 verification colony PCR FISH genetic mapping Libraries gridded in-house

Additional Resources FISH Further mapped / anchored markers UK : chromosome 4 markers SGN : screening selected candidate markers (SL_MboI) Sheared fosmid library (end-sequenced) smaller than BACs known insert size Contig extension Gap closure Confirm assembly

Tomato BACs in Sequencing Pipeline Pipeline Stage No. of BACs Picking & BAC Verification* 45 Subcloning 33 Shotgun 6 Assembly Start 10 Auto-prefinishing 15 Finishing QC Checking - Completed 19 *clone identity checks TOTAL : 138

January 2007 - Chromosome 4 Sequence 6,484,856 bp Unique 6,132,674 bp Total Finished Length = 2,181,618 bp

Finishing of Tomato Chromosome 4 2,181,618 bp Finished Sequence from 19 BACs All BACs to HTGS Phase 3 QC team 2000 bp overlap between neighbouring clones minimise redundancy sufficient for final assembly Extensive software suite GAP4

Acknowledgements FUNDING Wellcome Trust Sanger Institute: Jane Rogers Sean Humphray Karen McLaren Helen Beasley Carol Scott Chris Clee Sarah Sims Matt Jones Ratna Shownkeen Stuart McLaren Christine Lloyd Jennifer Harrow Carol Carder Paul Hunt Mark Maddison Richard Clark Kate Fraser Rebecca Hannah 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 Yimin Xu 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 FUNDING

Posters P3 P6

Discussion Points How do we determine gene space as being sequenced? Heterochromatin & euchromatin “definitions” Uploading TPF & AGP files Anchoring additional BACs Finishing strategy