Sol Genomics Network

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Solanum lycopersicum var. cerasiforme

150 Tomato Genome Resequencing Project

Tomato Immune Response Resequencing

International Tomato Sequencing Project

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International Tomato Genome Sequencing Project

Current Tomato Genome version SL4.0 and Annotation ITAG4.0

We are pleased to announce the release of version SL4.0 of the tomato genome and version ITAG4.0 of the annotation. You can find here more information about the assembly and annotation in thepreprint on bioRxivandslides. The genome data is available from our FTP site (Build SL4.0andITAG4.0),JBrowseApollo gene editorandBlast.

Please use thecontact formto let us know if you notice any issues with SL4.0 or ITAG4.0.

– Only 44Kb of Ns (unknown bases) compared to 81.7Mb in SL3.0

– Only 152 unplaced contigs in Chr 00 compared to 4,374 in SL3.0

– Better annotation of repeat regions in SL4.0

– 80X Pacbio coverage with RSII and Sequel (13kb read N50)

– Canu assembly (N50 5.5 Mb) and Hi-C scaffolding (12 chromosomes and unplaced contigs)

– Validated with Bionano optical maps and 10X linked reads

– 34,075 protein coding genes in ITAG4.0

– Functional descriptions assigned to 29,532 genes

– 29,281 genes preserved from ITAG2.3

– 21,962 of 29,281 preserved genes have been updated

– Most of the updated genes have extensions in the 5 and 3 UTRs

The tomato genome was published inNatureon May 31, 2012, culminating years of work by the Tomato Genome Consortium, a multi-national team of scientists from 14 countries.

The International Tomato Genome Sequencing Project was begun in 2004 by an international consortium including participants from Korea, China, the United Kingdom, India, the Netherlands, France, Japan, Spain, Italy and the United States. The initial approach was to sequence only the euchromatic sequence using a BAC-by-BAC approach, and in total more than 1,200 BACs have been sequenced. In 2009, a complementary whole-genome shotgun approach was initiated, which in conjunction with other data yielded high quality assemblies. The International Tomato Annotation Group (ITAG) annotates the genome builds generated by this combined sequencing approach.

browse genome contigs and official annotations

The official annotation for the tomato genome is provided by theInternational Tomato Annotation Group (ITAG), a multinational consortium, funded in part by theEU-SOL project.

annotation data temporarily unavailable

Initial build, based on the Newbler assembler and containing only 454 sequencing data.

Like 1.00, but with additional 454 runs and improved contamination screen.

All 454 data, bac end and fosmid end data, assembled using the CABOG assembler.

Includes all 454 data, bac ends, fosmid ends, polishing with Solexa and SOLiD data.

Additional scaffold merging using clone end sequences. Scaffolds placed and oriented using multiple physical maps, first release to include chromosome pseudomolecule sequences.

Integration and polishing of tomato BAC sequences

Mask a small number of contaminated regions. Base-compatible with SL2.30.

Small amount of additional contamination removal. Regularize gap sizes to comply with GenBank policies.

Rearrangement of scaffolds and a number of gaps re-sized according to FISH data.

BAC integration, Chr00 integration and BioNano data

assembled PacBio genome scaffolded with Hi-C. Validated using Bionano and 10X linked-reads

If in the course of your work you find errors or other issues with the tomato genome assemblies, please report them using one of the following links:

issue tracker at NCBI (registered curators only)

Heinz 1706 order link at TGRC(the variety used in tomato genome sequencing project)

Tomato FPC pagesat University of Arizona, USA.

Sanger FTP site withMboI BAC library FPC build

TheTomato Genome Annotation pagesat thecomputational biology groupof theUniversity of Naples, Italy.

Tomato mitochondrial genome (Genbank)(the seems defunct as of Dec 2013)

Tomato chloroplast sequence (Genbank)

Optional: Add Missing Accessions to A ListMismatched case

Click the Adjust Case button to align the case in the list with what is in the database.Multiple mismatched case

Items listed here have mulitple case mismatches and must be fixed manually. If accessions need to be merged, contact the database directly.

Replace synonyms with corresponding DB name

Multiple synonym matches have to be resolved manually. Contact database administrators if necessary.

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