It may seem an unlikely beast for comparison, but the poisonous puffer fish Fugu rubripes will tell us a lot about ourselves. So says an international consortium of researchers who announced the sequencing of the creature's genome on Friday at the 13th International Genome Sequencing and Analysis Conference in San Diego, Calif.
The puffer fish genome contains basically the same genes and regulatory sequences as the human one¿but without all the so-called junk DNA. Indeed, whereas the human genome contains nearly three billion base pairs, that of the Fugu has only 365 million such units of information. With the compact Fugu genome to guide them, the scientists say, locating genes in the comparatively cluttered human genome will be much easier.
To sequence the Fugu genome, the researchers employed what is known as a whole genome shotgun strategy. "We first chopped the genome up into pieces that are small enough to sequence," team member Dan Rokhsar of the Joint Genome Institute in Walnut Creek, Calif., explains. "The challenge was then to reassemble the genome by putting together nearly four million of these overlapping fragments¿in the same way that you'd put together a giant jigsaw puzzle." The scientists met this challenge using a sophisticated computational algorithm.
Chris Tan of the Institute for Molecular and Cell Biology in Singapore notes that the sequencing of the Fugu genome will enable much more accurate estimates of the gene repertoire in humans. He adds that "we will also now be able to refine many of the features of the noncoding regions that may prove to have regulatory control over genes expressed in the human genome."