Fugu: A Compact Reference Vertebrate Genome

The fugu (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 useful ‘reference’ genome for identifying genes and other functional elements such as regulatory elements in 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 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 fifth assembly (v5) by the IMCB team using the Ensembl annotation pipeline.

Assembly statistics

Fifth Fugu Genome Assembly (January 2010; v5)
The v5 assembly (accession number CAAB02000000) was generated by filling some gaps in the v4 assembly and by organizing scaffolds into chromosomes based on a genetic map of fugu. v5 assembly comprises 7,119 scaffolds covering 393 Mb. About 72% of the assembly (282 Mb) is organized into 22 chromosomes. Another 14% of the assembly (56 Mb) is assigned to chromosomes but the orientation and order of these scaffolds are not known (Chr_n_un). The remaining 14% of the assembly (55 Mb) is concatenated into a single sequence (Chr_un). See Kai et al. Genome Biol Evol. 3:424-442 (2011).

Last Update:July 2010
Known protein-coding genes:1,138
Novel protein-coding genes:18,093
RNA genes:593
Genscan gene predictions:27,982
Gene transcripts:19,945
Base Pairs:392,376,244
Golden Path Length:392,800,674
Fourth Fugu Genome Assembly (October 2004; v4)
The v4 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)
The v3 assembly includes 8,597 scaffolds, of length >2kb, constituting 329 Mb of the 400 Mb genome.

Second Fugu Genome Assembly (May 2002; v2)
The v2 assembly 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 297:1301-1310 (2002).


We thank the A*STAR Computational Resource Centre for their computational support.

Queries to fuguhelp at imcb.a-star.edu.sg

LAST UPDATED: 04-Oct-2013

(C) Copyright 2013 Institute of Molecular and Cell Biology, A*STAR, Singapore. All rights reserved.