International Tomato Genome Sequencing Project
Current Tomato Genome version SL4.0 and Annotation ITAG4.0 [ New ]
- 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.
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
|Data release policy|
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.|
|Tomato genome sequence builds|
|Other tomato genome pages on SGN|
- Heinz 1706 order link at TGRC (the variety used in tomato genome sequencing project)
- Tomato FPC pages at University of Arizona, USA.
- Sanger FTP site with MboI BAC library FPC build
- Software links at Sanger
- The Tomato Genome Annotation pages at the computational biology group of the University of Naples, Italy.
- Tomato mitochondrial genome (Genbank) (the site mitochondrialgenome.org seems defunct as of Dec 2013)
- Tomato chloroplast sequence (Genbank)