Takifugu (Fugu) rubripes v4.0
 
Status

The current release, version 4.0 includes a total of 26,721 gene models. Genes have been predicted and functionally annotated using the JGI annotation pipeline.

Compared with the earlier release of JGI and ENSEMBL models, the models have been improved with better support by homologs or ESTs, more complete models, removal of small fragments and transposons.

An initial analysis of the Fugu genome appears in Science. The manuscript describes Fugu v.2.0, a 5.4X whole genome shotgun assembly of 4.1 million fragments. The supporting data for this publication is available to download (Fugu v.2.0). The original 4.1X sequence was released in October 2001 as Fugu v.1.0.

When referencing a Fugu scaffold, be sure to also note the assembly version number. Scaffold IDs from different assemblies are unrelated to each other.

 
Releases

Scaffold IDs between different versions are NOT related to each other. To describe the analysis results of Fugu sequences obtained from this site, please be sure to reference the version number in addition to Aparicio et al., Science 2002.

v.4.0 (October 29. 2004): This whole genome shotgun assembly was constructed with the JGI assembler, JAZZ, paired end sequencing reads at a coverage of 8.5X produced at JGI, Myriad Genetics, and Celera Genomics. All reads are plasmid, cosmid, or BAC end-sequences, with the predominant coverage coming from 2 kb insert plasmids. The assembly contains 7,213 scaffolds totaling more than 393 million base pairs; half of the sequence is contained in the 125 largest scaffolds. Gene modeling and analysis were performed at JGI.

v.3.0 (August 26, 2002):This whole genome shotgun assembly was constructed with the JGI assembler, JAZZ, paired end sequencing reads at a coverage of 5.7X produced at JGI, Myriad Genetics, and Celera Genomics. All reads are plasmid, cosmid, or BAC end-sequences, with the predominant coverage coming from 2 kb insert plasmids. The assembly contains 20,379 scaffolds totaling 319 million base pairs; the largest 679 scaffolds total 160 million base pairs. Gene modeling and analysis were performed at JGI, Singapore, Cambridge, and the Institute for Systems Biology.

v.2.0 (July 25, 2002): This whole genome shotgun assembly was constructed with the JGI assembler, JAZZ, from 4.1 million sequencing reads (5.4X sequence coverage) produced at JGI, Myriad Genetics, and Celera Genomics. All reads are plasmid, cosmid, or BAC end-sequences, with the predominant coverage coming from 2 kb insert plasmids. The assembly contains 12,403 scaffolds totaling 332 million base pairs. Gene modeling and analysis were performed at JGI, Singapore, Cambridge, and the Institute for Systems Biology.

v.1.0 (October 26, 2001): This whole genome shotgun assembly was constructed with the JGI assembler, JAZZ, from 3.1 million sequencing reads (4.1X sequence coverage) produced at JGI, Myriad Genetics, and Celera Genomics. All reads are plasmid, cosmid, or BAC end-sequences with the predominant coverage from 2 kb insert plasmids. Gene modeling and analysis were performed at JGI, Singapore, and Cambridge.

Collaborators
(Walnut Creek, CA, USA)
IMCB Fugu Genome Project (Singapore)

UK Human Genome Mapping Project (Hinxton, UK)

IInstitute of Molecular and Cell Biology (Singapore)

   « Marine Molecular Genetics Lab, IMCB

   « Genome Sequencing and Analysis

Molecular Sciences Institute (Berkeley, CA, USA)

Institute for Systems Biology (Seattle, WA, USA)
Closure Plans
A vigorous effort to close the Fugu genome is underway at the IMCB Singapore, HGMP Cambridge, ISB Seattle, and JGI. A combination of PCR and clone based methods are being used to identify linked scaffolds and sequence connecting regions as well as sequencing captured gaps within the whole genome shotgun scaffolds. Selected regions of interest will also be finished.
Resources
Fugu tissue sources can be obtained from Greg Elgar. The Fugu cosmid and BAC libraries used in the sequencing project are available from the Human Genome Mapping Project in Cambridge.
Funding

This work was performed under the auspices of the US Department of Energy's Office of Science, Biological and Environmental Research Program and the by the University of California, Lawrence Livermore National Laboratory under Contract No. W-7405-Eng-48, Lawrence Berkeley National Laboratory under contract No. DE-AC03-76SF00098 and Los Alamos National Laboratory under contract No. W-7405-ENG-36.

Sequencing at Myriad Genetics and Celera Genomics was provided by contract to the National University of Singapore.