Tomato Genome SL2.50 and Beyond…
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The tomato reference genome is one of the most widely used genomic resources in the Solanaceae as well as the wider plant research community. We frequently receive questions from the community regarding the assembly versions. This session will explain the changes in the current version of the tomato genome (SL2.50). The current tomato genome build contains numerous inter-contig gaps (median 931bp, mean 1869bp) and inter-scaffold gaps (median 210Kbp, mean 525Kbp). Updates will be provided regarding the forthcoming tomato genome build (SL3.0) that will include finished BACs (HTGS phase 3) for closing the gaps.
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Tomato Genome SL2.50 and Beyond…
- 1. Tomato Genome SL2.50 and Beyond… Surya Saha, Jeremy Edwards and Lukas Mueller Sol Genomics Network (SGN) Boyce Thompson Institute, Ithaca, NY ss2489@cornell.edu @SahaSurya Slides: http://bit.ly/PAGbld230 https://fanart.tv/movie/196/back-to-the-future-part-iii/
- 2. CHROMOSOMES SCAFFOLDSCONTIGS Gene to Genome – The BIG picture SCAFFOLD GAPS CHROMOSOME GAPS SGN Workshop, PAG 2015 GENES TM2 (Chr 9) L2 (Chr 10)
- 3. Tomato Build SL2.40 SL2.50 SGN Workshop, PAG 2015 Lindsay Shearer Stephen Stack
- 4. Genome Assembly @NCBI Contigs • Components Tiling Path file (TPF) • Accession numbers • Can have nested components Accession Golden Path files (AGP) • Scaffold IDs • Orientation • Chromosome from contig AGP • Chromosome from scaffold AGP • Scaffold from contig AGP NCBI
- 5. SGN Workshop, PAG 2015 Jeremy Edwards https://github.com/solgenomics/Bio-GenomeUpdate FISH • Order • Orientation • Gap sizes Tiling Path file (TPF) Accession Golden Path files (AGP) NCBI Gap extension Scaffold flip
- 6. SGN Workshop, PAG 2015 Jeremy Edwards https://github.com/solgenomics/Bio-GenomeUpdate SL2.40 Annotation • SL2.40 AGP • SL2.50 AGP • SL2.40 GFF3 SL2.50 Annotation • SL2.50 GFF3 • Validated via Fasta Errors corrected • Start/end coordinates in different scaffolds • Start > end coordinates for UTRs • Start or end coordinates in gap region • Dropped Solyc03g053140.1 and Solyc12g032910.1
- 7. SL2.50 Availability JBrowse FTP Site SGN Locus/Gene Pages NCBI SGN Workshop, PAG 2015
- 8. SL2.50 Genome Release Genome build 2.5 Fasta + ITAG 2.4 GFFs CHADO FTP site Website JBrowse Blast DBs SGN Workshop, PAG 2015
- 9. State of the SL2.50 Build SGN Workshop, PAG 2015 0 20000000 40000000 60000000 80000000 100000000 120000000 0 1 2 3 4 5 6 7 8 9 10 11 12
- 10. State of the SL2.50 Build SGN Workshop, PAG 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
- 11. State of the SL2.50 Build SGN Workshop, PAG 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 Component gaps 43Mb (5.30%) Scaffold gaps 42Mb (5.17%) Total gaps 86Mb (10.47%)
- 12. SGN Workshop, PAG 2015 https://fanart.tv/movie/196/back-to-the-future-part-iii/
- 13. BAC Resources SGN Workshop, PAG 2015
- 14. BAC Resources Bruce Roe HTGS Phase 1: 332 HTGS Phase 2: 520 HTGS Phase 3: 2751 http://www.ncbi.nlm.nih.gov/genbank/htgs/faq SGN Workshop, PAG 2015
- 15. HTGS Phase 3 BACs SGN Workshop, PAG 2015 Chr 0 53 Chr 1 589 Chr 2 248 Chr 3 137 Chr 4 147 Chr 5 117 Chr 6 104 Chr 7 111 Chr 8 249 Chr 9 119 Chr 10 620 Chr 11 100 Chr 12 86 Unknown 84
- 16. SGN Workshop, PAG 2015 Jeremy Edwards https://github.com/solgenomics/Bio-GenomeUpdate BAC assemblies • Phrap • ACE files BAC sets • Assembled BACs • Singleton BACs Align to SL2.50 • Nucmer • 100bp word size • 500bp minimum alignment • 99% identity Novel sequences • Extensions • Gap coverage
- 17. HTGS Phase 3 BACs SGN Workshop, PAG 2015 0 100 200 300 400 500 600 700 1 2 3 4 5 6 7 8 9 10 11 12
- 18. Phrap Assembly (HTGS Phase 3 BACs) SGN Workshop, PAG 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
- 19. Phrap Assembly (HTGS Phase 3 BACs) SGN Workshop, PAG 2015 Chr10 Contig68 10 BACs (242Kb!!) Chr2 Contig185 7 BACs (566Kb!!)
- 20. Future Work • Manually examine assembled BAC contigs with < 99% identity • Evaluate HTGS phase 2 BACs • Use PCR walking to close gaps • Create TPF files for SL3.0 • Annotate SL3.0 and lift over annotations from SL2.50 SGN Workshop, PAG 2015
- 21. Acknowledgements SGN Workshop, PAG 2015
- 22. SGN Workshop, PAG 2015