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The gar (Lepisosteus oculatus): an ancient fish species with hard, diamond-shaped scales © David Solomon

The gar: a genetic bridge between humans and fish

The genome of the gar, an ancient fish species, has just been sequenced thanks to an international collaboration in which INRA took part. Genetically speaking, the gar is as similar to humans as it is to zebrafish; the latter is a model species used in biomedical research. This work, published in Nature Genetics, will help researchers explore a host of undiscovered facets of human biology.

Updated on 05/25/2018
Published on 03/15/2016
Keywords: fish - biology

The gar (Lepisosteus oculatus) is an ancient fish species with hard, diamond-shaped scales and an elongated mouth filled with needle-like teeth. Its genome is highly conserved, which means that it shares a large number of similarities with both the human and zebrafish genomes. As a result, it can serve as a genetic “bridge” between humans and teleost fishes1 and thus may contribute to major advances in biomedical research. The gar’s genome was sequenced thanks to international research efforts headed by the University of Oregon in collaboration with the Massachusetts Institute of Technology and Harvard University.  INRA’s Fish Physiology and Genomics Institute (Rennes) also made a significant contribution.

A slowly evolving fish

The researchers found that the gar had conserved several ancestral genetic elements that had been lost in other fish species and in humans. It has been labeled a bridge species because the gar has numerous genes found in humans but not in zebrafish but also shares several genes with zebrafish that are not present in humans.

The gar’s evolutionary story began some 450 million years ago, when vertebrates split into two large groups. The first group would eventually form the tetrapods, such as birds and mammals (including humans). The second gave rise to the bony fishes. In this second group, a duplication event occurred in which the entire genome was copied. After this event, the bony fish lineage followed an evolutionary trajectory that would lead to the teleost fishes, such as the zebrafish, the stickleback, the salmon, the trout, the tuna, and the halibut, as well as most aquarium fish. The taxon that included the gar diverged from the other bony fishes before the appearance of the teleosts and did not experience the duplication event. Consequently, the gar’s genome conserved certain ancestral elements that were lost from the zebrafish genome, for example. It contains numerous whole chromosomes that are presumably similar to those found in the ancestor to all vertebrates.

A key to understanding gene evolution following duplication

It is easier to compare the genomes of gars and humans because the gar does not have all the additional gene copies found in the zebrafish that resulted from the genome-duplication event.  Researchers at INRA’s Fish Physiology and Genomics Institute examined differences in gene evolution in the gar and the zebrafish. When a gene is duplicated, there are two possible outcomes. First, the two copies can split up responsibility for the ancestral functions. Alternatively, one of the copies can acquire a new function while the other retains the ancestral functions.

Understanding how the functions of duplicated genes change is crucial to our understanding of evolutionary biology. It will also help biomedical researchers more effectively use model fish species.

    

The gar is a genetic “bridge” between teleost fishes and humans because its genetic sequences can be aligned with those of both groups; in contrast, human and teleost sequences cannot be aligned directly. © INRA, Nature Genetics
The gar is a genetic “bridge” between teleost fishes and humans because its genetic sequences can be aligned with those of both groups; in contrast, human and teleost sequences cannot be aligned directly © INRA, Nature Genetics

  

1The teleost fishes (infraclass Teleostei) appeared around 350 million years ago and account for most modern fishes. The group comprises more than 30,000 species, which is almost the total number of vertebrate species

  

Reference:
Ingo Braasch et al. The spotted gar genome illuminates vertebrate evolution and facilitates human-teleost comparisons. Nature Genetics, 7 March 2016, DOI: 10.1038/ng.3526

Contact(s)
Scientific contact(s):

  • Julien Bobe (33 (0)2 23 48 70 07) INRA Fish Physiology and Genomics Institute
  • Yann Guiguen (33 (0)2 23 48 50 09) INRA Fish Physiology and Genomics Institute
Press Relations:
INRA News Office (33 (0)1 42 75 91 86)
Associated Division(s):
Animal Physiology and Livestock Systems
Associated Centre(s):
Brittany-Normandy

The PhyloFish Project

The discoveries described above resulted from the PhyloFish Project, which is using phylogenomics, namely a RNA-Seq approach, to study duplicated genes in teleost fishes. This project is funded by the French National Research Agency (ANR) and is headed by Julien Bobe and Yann Guiguen of the INRA Fish Physiology and Genomics Institute (Rennes). John Postlethwait (University of Oregon, USA), who led the international effort to sequence the gar genome, is a research collaborator.

For more information: Project description on the French National Research Agency website (in French)