Fugu: A Compact Model Vertebrate Genome

Abstract

The genome of the Japanese pufferfish, Takifugu rubripes (fugu), 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 regulatory elements in the human genome. Generation of a comprehensive genetic map of fugu and its integration with the genome assembly has increased the utility of fugu in genetic and evolutionary studies. The fugu genome resources should help to unravel the genetic basis of speciation in the Takifugu lineage, which has experienced an explosive speciation in the marine environment within a relatively short period. Given the plans to sequence genomes of up to 10 000 vertebrates in order to understand their evolutionary origin and diversity, fugu will continue to serve as a valuable ‘reference’ vertebrate genome.

Key Concepts:

  • Fugu, a marine pufferfish, was proposed as a model genome to understand better the human genome, mainly because of its compact genome size (1/8th the size of human genome).

  • Comparison of fugu and human genomes enabled the identification of many new human genes and a few thousand gene regulatory elements in the human genome.

  • The availability of a high‐resolution genetic map and its integration with the genome assembly has made fugu a more attractive genome model to study the evolution of vertebrates.

  • A combination of two alleles of the Amhr2 gene determines sex in fugu.

  • Because of its phylogenetic position and compact genome size, fugu will continue to serve as a useful ‘reference’ vertebrate genome.

Keywords: Takifugu rubripes; compact vertebrate genome; comparative genomics; conserved noncoding elements; teleost; genetic map; explosive speciation; sex determination; enhancers

Figure 1.

Evolutionary relationships of selected vertebrates. Divergence times are based on fossil records (Benton and Donoghue, ; Donoghue et al., ).

Figure 2.

The sex‐determining locus in fugu. Horizontal arrows denote the transcriptional orientation of genes. The red arrow indicates the position of the SNP within exon 9 of Amhr2 gene which correlates with phenotypic sex.

Figure 3.

VISTA plot of the extended HoxD locus of fugu and human. Fugu sequence was used as the base. A threshold of ≥70% identity across >100 bp windows was used for detecting conserved sequences (peaks). x‐Axis represents the base sequence and y‐axis represents percent identity. Blue peaks represent conserved exons and pink peaks represent conserved noncoding elements (CNEs).

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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.

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Elgar G (2004) Identification and analysis of cis‐regulatory elements in development using comparative genomics with the pufferfish, Fugu rubripes. Seminars in Cell and 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.

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 and Yap WH (2005) Comparative genomics using fugu: a tool for the identification of conserved vertebrate cis‐regulatory elements. BioEssays 27: 100–107.

Woolfe A, Goode DK, Cooke J et al. (2007) CONDOR: a database resource of developmentally associated conserved non‐coding elements. BMC Developmental Biology 7: 100.

Web Links

Fugu Genome Project.http://www.fugu‐sg.org

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Ravi, V, and Venkatesh, B(Apr 2013) Fugu: A Compact Model Vertebrate Genome. In: eLS. John Wiley & Sons Ltd, Chichester. http://www.els.net [doi: 10.1002/9780470015902.a0006147.pub3]