Fugu: The Pufferfish Model Genome

B Venkatesh, Institute of Molecular and Cell Biology, Singapore

Published online: March 2008

DOI: 10.1002/9780470015902.a0006147.pub2

The genome of the Japanese pufferfish, Fugu rubripes, which is among the smallest vertebrate genomes, is an attractive model vertebrate genome, and was the first vertebrate genome to be sequenced after the human genome. It has proved to be valuable for discovering novel genes and evolutionarily conserved gene regulatory elements in the human genome, and continues to serve as a ‘reference’ genome for understanding the evolution of vertebrate genomes.

Keywords: Fugu rubripes; compact vertebrate genome; comparative genomics; conserved noncoding elements; teleost

Figure 1. Evolutionary relationships of some ‘model’ vertebrates. The divergence times indicated at the nodes are from Benton and Donoghue (2007).
Figure 2. The largest block of conserved syntenic genes in human and fugu genomes. The human locus (Chr7p15.1 to p15.3) is about 5.4 Mb long and the fugu locus is 333 kb long (adapted from Figure 1 in Lee et al. (2006)).
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 References
    Aparicio S, Chapman J, Stupka E et al. (2002) Whole-genome shotgun assembly and analysis of the genome of Fugu rubripes. Science 297: 1301–1310.
    Benton MJ and Donoghue PC (2007) Paleontological evidence to date the tree of life. Molecular Biology and Evolution 24: 26–53.
    Christoffels A, Koh EGL, Chia J et al. (2004) Fugu genome analysis provides evidence for a whole-genome duplication early during the evolution of ray-finned fishes. Molecular Biology and Evolution 21: 1146–1151.
    Kai W, Kikuchi K, Fujita M et al. (2005) A genetic linkage map for the tiger pufferfish, Takifugu rubripes. Genetics 171: 227–238.
    Lee AP, Koh EGL, Tay A, Brenner S and Venkatesh B (2006) Highly conserved syntenic blocks at the vertebrate Hox loci and conserved regulatory elements within and outside Hox gene clusters. Proceedings of the National Academy of Sciences of the USA 103: 6994–6999.
    Venkatesh B, Lu SQ, Dandona N et al. (2005) Genetic basis of tetrodotoxin resistance in pufferfishes. Current Biology 15: 2069–2072.
    Volff JN, Bouneau L, Ozouf-Costaz C and Fischer C (2003) Diversity of retrotransposable elements in compact pufferfish genomes. Trends in Genetics 19: 674–678.
    Woolfe A and Elgar G (2007) Comparative genomics using Fugu reveals insights into regulatory subfunctionalization. Genome Biology 8: R53.
    Woolfe A, Goodson M, Goode DK et al. (2005) Highly conserved non-coding sequences are associated with vertebrate development. PLoS Biology 3: e7.
    Yu WP, Brenner S and Venkatesh B (2003) Duplication, degeneration and subfunctionalization of the nested synapsin-Timp genes in Fugu. Trends in Genetics 19: 180–183.
 Further Reading
    Bernardi G (2000) Isochores and the evolutionary genomics of vertebrates. Gene 241: 3–17.
    Brenner S, Elgar G, Sandford R et al. (1993) Characterization of the pufferfish (Fugu) genome as a compact model vertebrate genome. Nature 366: 265–268.
    Elgar G (2004) Identification and analysis of cis-regulatory elements in development using comparative genomics with the pufferfish, Fugu rubripes. Seminars in Cell & Developmental Biology 15: 715–719.
    Jaillon O, Aury JM, Brunet F et al. (2004) Genome duplication in the teleost fish Tetraodon nigroviridis reveals the early vertebrate proto-karyotype. Nature 431: 946–957.
    Kikuchi K, Kai W, Hosokawa A et al. (2007) The sex-determining locus in the tiger pufferfish, Takifugu rubripes. Genetics 175: 2039–2042.
    Ovcharenko I, Stubbs L and Loots GG (2004) Interpreting mammalian evolution using Fugu genome comparisons. Genomics 84: 890–895.
    Pennacchio LA, Ahituv N, Moses AM et al. (2006) In vivo enhancer analysis of human conserved non-coding sequences. Nature 444: 499–502.
    Tanaka M, Hale LA, Amores A et al. (2005) Developmental genetic basis for the evolution of pelvic fin loss in the pufferfish Takifugu rubripes. Developmental Biology 281: 227–239.
    Venkatesh B, Gilligan P and Brenner S (2000) Fugu: a compact vertebrate reference genome. FEBS Letters 476: 3–7.
    Venkatesh B and Yap WH (2005) Comparative genomics using fugu: a tool for the identification of conserved vertebrate cis-regulatory elements. BioEssays 27: 100–107.
 Web Links
    ePath Joint Genome Institute. Fugu pages. http://fugu.jgi-psf.org
    ePath IMCB Fugu Genome Project. http://www.fugu-sg.org

Related Sub-Topics:

Evolutionary Genomics
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Article Title: Fugu: The Pufferfish Model Genome
 
How to Cite close
Venkatesh, B(Mar 2008) Fugu: The Pufferfish Model Genome. In: eLS. John Wiley & Sons Ltd, Chichester. http://www.els.net [doi: 10.1002/9780470015902.a0006147.pub2]