tomato genome build sl3.0
TRANSCRIPT
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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
[email protected] @SahaSurya
Slides: http://bit.ly/SOL15bld3
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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).
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Tomato Build SL2.40 SL2.50
SGN Workshop, SOL 2015
Lindsay Shearer
Stephen Stack
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SL2.50 Availability
JBrowse
• Locus pages
• Gene pages
• FTP site
Also at NCBIhttp://www.ncbi.nlm.nih.gov/assembly/GCF_000188115.3/
SGN Workshop, SOL 2015
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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)
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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
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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%)
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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/
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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
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SGN Workshop, SOL 2015
ITAG 2.4 Genes
SL2.50 Genome
Whole Genome
Shotgun assembly
Phase 3 BACs
20kb or more
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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!!
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Workflow
SGN Workshop, SOL 2015
Automatic
integration of BACsManual validation NCBI validation
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Workflow
SGN Workshop, SOL 2015
Automatic
integration of BACsManual validation NCBI validation
https://github.com/solgenomics/Bio-GenomeUpdate
BAC
assemblies
Align to SL2.50
• 500bp BAC ends
• 100% identity
Jeremy Edwards
Place
BACs
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Phrap Assembly (HTGS Phase 3 BACs)
SGN Workshop, SOL 2015
0%
10%
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40%
50%
60%
70%
80%
90%
100%
1 2 3 4 5 6 7 8 9 10 11 12
Assembled BACs Singleton BACs
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Phrap Assembly (HTGS Phase 3 BACs)
SGN Workshop, SOL 2015
Chr10 Contig68 10 BACs (242Kb!!)
Chr2 Contig185 7 BACs (566Kb!!)
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Workflow
SGN Workshop, SOL 2015
Automatic
integration of BACsManual validation NCBI validation
Prashant Hosmani
Mirella Flores
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Workflow
SGN Workshop, SOL 2015
Automatic
integration of BACsManual validation NCBI validation
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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
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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
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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
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Future
BioNano optical maps
• Integrate sequences from chr 0 into chrs 1-12
• Validation
• Improved gap sizing
SGN Workshop, SOL 2015
Gabino Sanchez
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Future…
Annotation of SL3.0
• Lift over ITAG 2.4 annotations from SL2.50
• Maker annotations
• ITAG 3.0 annotations
SGN Workshop, SOL 2015
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Thank you!!
Questions??
SGN Workshop, SOL 2015
Slides: http://bit.ly/SOL15bld3