International Tomato Genome Sequencing Project

Current Tomato Genome version SL4.0 and Annotation ITAG4.0 [ New ]
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 the preprint on bioRxiv and slides. The genome data is available from our FTP site (Build SL4.0 and ITAG4.0), JBrowse, Apollo gene editor and Blast.

Please use the contact form to let us know if you notice any issues with SL4.0 or ITAG4.0.

Build highlights SL4.0
Annotation highlights ITAG4.0

   - Only 44Kb of N's (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
   - ITAG4.0 has 4,794 novel 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

Tomato Genome Published

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

Press Releases


China | Germany | Max Planck | Helmholtz | Israel | Japan | Korea | Spain | United Kingdom | The Netherlands | USA: University of Oklahoma | Colorado State University | Boyce Thompson Institute

The Tomato Genome in the News

Nature | Reuters India | New York Times | BBC | Natural History Museum, London | VTM Het Nieuws (Belgium) | more Belgian links | Die Zeit (Germany) | | Reuters UK | El Mundo (Spain) | Publico (Spain) | ABC (Spain) | Agenciasinc (Spain) | Le Figaro (France) | Sciences Et Avenir (France) | (Russia) | TheMarker (Israel)

Data release policy 
All data is openly and freely available on SGN, MIPS, and Genbank.

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.

Official annotation browse genome contigs and official annotations 
The official annotation for the tomato genome is provided by the International Tomato Annotation Group (ITAG), a multinational consortium, funded in part by the EU-SOL project.
annotation data temporarily unavailable
Tomato genome sequence builds  
Clone sequences  
Other tomato genome pages on SGN