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Tomato Genome Build: SL2.5 to SL3.0

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Update on the tomato genome build

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Tomato Genome Build: SL2.5 to SL3.0

  1. 1. Tomato Genome Build SL2.5 SL3.0 Surya Saha, Jeremy Edwards, Prashant Hosmani, Mirella Flores and Lukas Mueller Sol Genomics Network (SGN) Boyce Thompson Institute, Ithaca, NY ss2489@cornell.edu @SahaSurya Slides: http://bit.ly/SOL15bld3
  2. 2. Tomato Genome SGN Workshop, SOL 2015 Whole-genome shotgun and full-length BAC sequences • 454 reads (filtered, 22X) • BAC end Sanger reads (0.18X) • Fosmid end Sanger reads (0.087X) • Selected BACs • Sanger reads (5.2X).
  3. 3. Tomato Build SL2.40 SL2.50 SGN Workshop, SOL 2015 Lindsay Shearer Stephen Stack
  4. 4. SL2.50 Availability JBrowse • Locus pages • Gene pages • FTP site Also at NCBI http://www.ncbi.nlm.nih.gov/assembly/GCF_000188115.3/ SGN Workshop, SOL 2015
  5. 5. CHROMOSOMES SCAFFOLDSCONTIGS Gene to Genome – The BIG picture CONTIG GAPS SCAFFOLD GAPS SGN Workshop, SOL 2015 GENES MAP (chr1) Ovate (chr1) TM2 (chr 9) L2 (chr 10)
  6. 6. State of the SL2.50 Build SGN Workshop, SOL 2015 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% 0 1 2 3 4 5 6 7 8 9 10 11 12 Sequence Scaffold gap length Component gap length
  7. 7. State of the SL2.50 Build SGN Workshop, SOL 2015 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% 0 1 2 3 4 5 6 7 8 9 10 11 12 Sequence Scaffold gap length Component gap length Length 823Mb Sequence 737Mb Contig gaps 43Mb (5.30%) Scaffold gaps 42Mb (5.17%) Total gaps 86Mb (10.47%)
  8. 8. Tomato BAC Resources Bruce Roe HTGS Phase 1: 332 HTGS Phase 2: 520 HTGS Phase 3: 2764 http://www.ncbi.nlm.nih.gov/genbank/htgs/faq SGN Workshop, SOL 2015 ftp://ftp.solgenomics.net/tomato_genome/bacs/
  9. 9. SGN Workshop, SOL 2015 BAC libraries • HindIII (129,024 clones) • EcoRI (72,264 clones) • MboI (52,992 clones) Tomato BAC Resources… 2764 Phase 3 BACs 340,000 high-quality reads 20X of entire genome Mueller et al. 2009
  10. 10. SGN Workshop, SOL 2015 ITAG 2.4 Genes SL2.50 Genome Whole Genome Shotgun assembly Phase 3 BACs 20kb or more
  11. 11. SGN Workshop, SOL 2015 ITAG 2.4 Genes SL2.50 Genome Whole Genome Shotgun assembly Phase 3 BACs 20kb or more No BACs mapped here!!
  12. 12. Workflow SGN Workshop, SOL 2015 Automatic integration of BACs Manual validation NCBI validation
  13. 13. Workflow SGN Workshop, SOL 2015 Automatic integration of BACs Manual validation NCBI validation https://github.com/solgenomics/Bio-GenomeUpdate BAC assemblies Align to SL2.50 • 500bp BAC ends • 100% identity Jeremy Edwards Place BACs
  14. 14. Phrap Assembly (HTGS Phase 3 BACs) SGN Workshop, SOL 2015 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% 1 2 3 4 5 6 7 8 9 10 11 12 Assembled BACs Singleton BACs
  15. 15. Phrap Assembly (HTGS Phase 3 BACs) SGN Workshop, SOL 2015 Chr10 Contig68 10 BACs (242Kb!!) Chr2 Contig185 7 BACs (566Kb!!)
  16. 16. Workflow SGN Workshop, SOL 2015 Automatic integration of BACs Manual validation NCBI validation Prashant Hosmani Mirella Flores
  17. 17. Workflow SGN Workshop, SOL 2015 Automatic integration of BACs Manual validation NCBI validation
  18. 18. SGN Workshop, SOL 2015 0 50 100 150 200 250 300 350 400 450 1 2 3 4 5 6 7 8 9 10 11 12 1041/2764 BACs Integrated • No contained BACs • No single-end mapping BACs
  19. 19. SGN Workshop, SOL 2015 Improved Contiguity 0 500 1000 1500 2000 2500 3000 1 2 3 4 5 6 7 8 9 10 11 12 SL2.50 components SL3.0 components
  20. 20. Gap Reduction 0 500000 1000000 1500000 2000000 2500000 3000000 3500000 4000000 4500000 1 2 3 4 5 6 7 8 9 10 11 12 SL2.50 Ns SL3.0 Ns
  21. 21. Future BioNano optical maps • Integrate sequences from chr 0 into chrs 1-12 • Validation • Improved gap sizing SGN Workshop, SOL 2015 Gabino Sanchez
  22. 22. Future… Annotation of SL3.0 • Lift over ITAG 2.4 annotations from SL2.50 • Maker annotations • ITAG 3.0 annotations SGN Workshop, SOL 2015
  23. 23. Thank you!! Questions?? SGN Workshop, SOL 2015 Slides: http://bit.ly/SOL15bld3

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