Background About the Pufferfish

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Background About the Pufferfish

• Fugu is a teleost fish belonging to the order
  Tetraodontiformes.
• Fugu rubripes, an eukaryota and vertebrate, more
  commonly known as the Japanese pufferfish.
• There are nearly 100 kinds of pufferfish
  worldwide.
• They can grow up to 70.0 cm. 
• The Fugu genome is the first vertebrate genome to
  be draft sequenced after human.

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Human vs. Torafugu

• Fugu are our very distant cousins.
• Fish have nearly all of the same organ systems
  and physiology as humans, in contrast to flies
  and worms.
• Three quarters of the pufferfish's 31,000 genes
  have direct human counterparts.
• Among the 25 of human genes without counterparts
  in Fugu are key genes involved in the human
  immune system and metabolic regulation. 
• Conserved linkages found between Fugu and human
  genes indicate the preservation of chromosomal
  segments from the common vertebrate ancestor, but
  with some shuffling of gene order, segmental
  duplications, chromosomal rearrangements and
  'loss' and 'gain' of introns.
• Nearly 1,000 genes in the pufferfish Fugu
  rubripes are apparently identical to previously
  unidentified ones in humans.

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How Big is the Fugu Genome?

• Pufferfish have the smallest known vertebrate
  genomes, only 390 million bases long, which is
  about eight times small than the 3000 Mb human
  genome, yet contains many genes similar to
  humans.
• Fugu has 22 pairs of chromosomes.  The pufferfish
  genome is so condensed that the genes are
  contained in about 15 percent, compared to the
  human genome with only 3 percent, repetitive DNA
  accounts for less than one-sixth of the sequence.
• Intergenic regions and introns in the Fugu are
  highly compressed and the average gene density is
  about one gene per 10 kb. 
• It has been found that the number of genes in the
  pufferfish is approximately the same as in man.

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When was the genome of the fugu rubripes
completely sequenced?

• On October 26, 2001, the completion of the Fugu
  sequencing project was announced at the 13th
  International Genome Sequencing and Analysis
  Conference (GSAC) in San Diego, California.

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Why the Pufferfish was Chosen to be Sequenced

• Fugu was proposed as a model vertebrate genome to
  understand the more complex human genome and
  other vertebrate genomes. It is expected that
  comparisons of the human genome with that of Fugu
  will help us understand the information encoded
  in the human genome. This, in turn, paves the way
  for finding new drugs to cure diseases.

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Advantages of Studying the Genome of the
Pufferfish

• One advantage is that puffer fishs genome is
  condensed and contains less repetitive sequences
  is that it helps save time and is cost effective,
  making it easier to get from one end of a
  pufferfish gene to the other end and from one
  gene to the next when determining DNA sequence on
  continuous stretches of chromosomes.

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Another advantage

• to studying the pufferfish is that, compared to
  other important model organisms, including
  fruitflies, the pufferfish is closer to humans on
  the evolutionary scale, and will have more of the
  same genes.

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What Have We Gained?

• As many as a quarter of all human proteins could
  not be recognized in the pufferfish sequence when
  the two genomes were compared directly. It has
  been speculated that the human complexity must
  have arisen from differences in gene splicing or
  gene expression.
• It has been discovered that their exist presence
  of a relative handful of "giant" genes - genes,
  which appear bigger than their human
  counterparts, it has also been found that there
  are other areas of conserved synteny between
  pufferfish and human genomes.

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• Comparisons between the pufferfish and human
  genome show the evolution of the protein
  sequences, and to predict the existence of human
  genes, and elements that control or regulate the
  activity of genes. Comparing with the pufferfish
  genes, about 1000 human genes have been found
  which had not been found in other databases.

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How Was the Fugu Genome Mapped?

• Researchers first chopped the DNA into fragments
  four million pieces, small enough to be
  sequenced. DNA fragments were sequenced at random
  and the order then assembled in a computer, the
  so called "whole genome shotgun"(WGS) method.

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Who Started the Fugu Genome Project?

• The Fugu genome project was initiated in
  Cambridge, Britain, in 1989 by Sydney Brenner and
  his colleagues Greg Elgar, Sam Aparicio and
  Byrappa Venkatesh. The Institute of Molecular and
  Cell Biology (IMCB) took up the research soon
  afterwards. The genome was sequenced by the
  International Fugu Genome Consortium.

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Pufferfish Pictures