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

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).

Tomato Build SL2.40 SL2.50

SGN Workshop, SOL 2015

Lindsay Shearer

Stephen Stack

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

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)

State of the SL2.50 Build

SGN Workshop, SOL 2015

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Sequence Scaffold gap length Component gap length

State of the SL2.50 Build

SGN Workshop, SOL 2015

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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%)

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/

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

SGN Workshop, SOL 2015

ITAG 2.4 Genes

SL2.50 Genome

Whole Genome

Shotgun assembly

Phase 3 BACs

20kb or more

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!!

Workflow

SGN Workshop, SOL 2015

Automatic

integration of BACsManual validation NCBI validation

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

Phrap Assembly (HTGS Phase 3 BACs)

SGN Workshop, SOL 2015

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Assembled BACs Singleton BACs

Phrap Assembly (HTGS Phase 3 BACs)

SGN Workshop, SOL 2015

Chr10 Contig68 10 BACs (242Kb!!)

Chr2 Contig185 7 BACs (566Kb!!)

Workflow

SGN Workshop, SOL 2015

Automatic

integration of BACsManual validation NCBI validation

Prashant Hosmani

Mirella Flores

Workflow

SGN Workshop, SOL 2015

Automatic

integration of BACsManual validation NCBI validation

SGN Workshop, SOL 2015

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1041/2764 BACs Integrated

• No contained BACs

• No single-end mapping BACs

SGN Workshop, SOL 2015

Improved Contiguity

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Gap Reduction

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SL2.50 Ns SL3.0 Ns

Future

BioNano optical maps

• Integrate sequences from chr 0 into chrs 1-12

• Validation

• Improved gap sizing

SGN Workshop, SOL 2015

Gabino Sanchez

Future…

Annotation of SL3.0

• Lift over ITAG 2.4 annotations from SL2.50

• Maker annotations

• ITAG 3.0 annotations

SGN Workshop, SOL 2015

Thank you!!

Questions??

SGN Workshop, SOL 2015

Slides: http://bit.ly/SOL15bld3