The fugu (Takifugu rubripes or Fugu rubripes) genome project was initiated in 1989 by Sydney Brenner and his colleagues Greg Elgar, Sam Aparicio and Byrappa Venkatesh. In 1993, this team showed that the fugu genome is only 390 Mb, about one-eighth the size of the human genome, yet it contains a similar repertoire of genes to humans (Brenner et al., Nature 366:265-268, 1993). Therefore, fugu was proposed as a useful model for annotating the human genome. This, in fact, ushered in the era of comparative genomics. Fugu genome is among the smallest vertebrate genomes and has proved to be a valuable ‘reference’ genome for identifying genes and other functional elements such as regulatory elements in the human and other vertebrate genomes, and for understanding the structure and evolution of vertebrate genomes.

A ‘draft’ sequence of the fugu genome was determined by the International Fugu Genome Consortium in 2002 using the 'whole-genome shotgun' sequencing strategy. The Consortium members included the Institute of Molecular and Cell Biology, Singapore; Joint Genome Institute, Walnut Creek, USA; MRC UK HGMP Resource Center, Cambridge, UK, and Institute for Systems Biology, Seattle, USA. The results of the assembly (v2) are reported in Science 297:1301-1310 (2002). Fugu is the second vertebrate genome to be sequenced, the first being the human genome. This webpage presents the annotation made on the fourth assembly (v4) by the IMCB team using the Ensembl annotation pipeline. We are continuing with the gap filling work and linking of the scaffolds to obtain super-contigs.

Fourth Fugu Genome assembly (October 2004; v4) This assembly is based on ~8.7X coverage of the genome, and includes 7,213 scaffolds, constituting 393 Mb of the genome. 90% of the genome is represented on 1118 scaffolds. The largest scaffold is 7 Mb, and 74 scaffolds are larger than 1 Mb each.

Third Fugu Genome assembly (August 2002; v3) includes 8,597 scaffolds, of length >2kb, constituting 329 Mb of the 400 Mb genome.

Second Fugu Genome assembly (May 2002; v2) includes 12,403 scaffolds, of length >2Kb, constituting 320 Mb of the 400 Mb genome. A preliminary analysis of the annotated genome is reported in Science (2002) 297:1301-1310.