SCIENTISTS ADVOCATE GENOMIC SEQUENCING
OF “LIVING FOSSIL”.
STANFORD, Calif., Mon., Nov. 15, 2004 – A team of Stanford University researchers led by Richard Myers, Ph.D., in collaboration
with Chris Amemiya, Ph.D., of the Benaroya Research Institute in Seattle, campaign in the December issue of Genome Research for deciphering the genetic code of a “living fossil” fish, the coelacanth.
The genomic sequence of this large “hollow-spined” fish, which populates deep-sea volcanic caves, could hold valuable clues
for biologists studying the evolution of vertebrate species. Coelacanths were believed to have been extinct until a live
specimen was discovered in 1938 off the coast of South Africa. Both of the known coelacanth species that survive today, Latimeria
chalumnae and Latimeria menadoensis, are anatomically similar to their fossil relatives. Furthermore, coelacanths have exhibited
little morphological change since their emergence during the Devonian period approximately 360 million years ago.
To date, complete genomic sequences for more than 200 organisms have been obtained, and hundreds more are currently in progress
(www.genomesonline.org). These efforts will enable scientists to perform detailed comparisons of the complete genetic codes
from multiple species, identifying the sequence changes that contributed to evolutionary adaptation and speciation. Although
a wide assortment of species have been chosen for sequencing, ranging from lampreys to armadillos (www.genome.gov/12511858),
Myers observed: “We’re missing an organism that could really shed light on the emergence of land vertebrates. We don’t know
what genomic changes accompanied the transition from water to land, and a coelacanth genome could help identify those events.”
The coelacanth is one of only two living taxa to occupy the critical, highly informative phylogenetic position between ray-finned
fishes and tetrapods. Fleshy, lobed fins, which are one of the defining characteristics of coelacanths, are thought to represent
an intermediate evolutionary stage in the transformation of fins to limbs. Lobe-finned relatives of the coelacanth underwent
morphological alterations that enabled them to emerge from the sea and inhabit terrestrial environments. Both the coelacanth
and the lungfish – the only two living lobe-finned fishes – are related to important evolutionary progenitors of land vertebrates.
However, the lungfish genome is very large (more than 100 billion nucleotides in length), making it technically impractical
to sequence with currently available technology. The coelacanth genome, on the other hand, is estimated to be smaller than
that of human or mouse, making it feasible for whole-genome sequencing.
Jim Noonan, Ph.D., a former graduate student on Myers’ team who carried out much of the work described in the Genome Research article, focused on a small but highly informative genomic segment from the Indonesian coelacanth (Latimeria menadoensis)
called the protocadherin gene cluster. Encoding for proteins involved in the development and maturation of neurons and synapses
in the brain, protocadherin clusters are not present in invertebrates, such as fruit fly (Drosophila melanogaster) or roundworm
(Caenorhabditis elegans), but they are found in more evolutionarily complex species, including all vertebrates. Protocadherin
gene clusters are composed of a tandem array of multiple gene copies, making them particularly prone to aberrant recombination
and thus, to duplication and homogenization. Because this region appears so vulnerable to evolutionary change, Noonan, Amemiya
and Myers predicted that the sequence of the coelacanth protocadherin cluster would be a good indicator of the utility of
the whole coelacanth genome sequence for inferring vertebrate phylogeny.
Jane Grimwood, Jeremy Schmutz and Mark Dickson at the Stanford Human Genome Center generated more than 600,000 nucleotides
of coelacanth genomic sequence spanning the protocadherin gene cluster. Using this sequence, Noonan determined that the structure
of the coelacanth cluster was very similar to the orthologous human cluster. The coelacanth genome has 49 protocadherin cluster
genes organized into the same three subclusters (alpha, beta, and gamma) as the 54 protocadherin cluster genes in human.
In contrast, the zebrafish (Danio rerio) genome contains at least 97 protocadherin genes organized into two distinct clusters,
resulting from a whole-genome duplication event.
A major discovery stemming from this work is that the coelacanth genome appears to be evolving slowly relative to land vertebrates
and the teleost fishes. This makes the coelacanth genome a better reference for comparative sequence analyses involving land
vertebrates than teleost genomes, which are commonly used for such studies but are highly derived due to a whole-genome duplication
event. For these reasons, Myers and colleagues argue that the complete genomic sequence of the coelacanth would be valuable
for identifying important genome modifications that occurred during the evolution of tetrapod species.
The article referenced in this release will be published online as a “Genome Research in Advance” paper on November 15, 2004,
and in the December 1 print issue of Genome Research. The reference for the article is as follows: Noonan, J.P., Grimwood, J., Danke, J., Schmutz, J., Dickson, M., Amemiya,
C.T., Myers, R.M. 2004. Coelacanth genome sequence reveals the evolutionary history of vertebrate genes. Genome Res. 14:
2397-2405. A copy of the paper is available upon request.
Genome Research (www.genome.org) is an international, monthly, peer-reviewed journal published by Cold Spring Harbor Laboratory Press. Launched
in 1995, it is one of the five most highly cited primary research journals in genetics and genomics. The journal publishes
novel genome-based studies and cutting-edge methodologies in comparative and functional genomics, bioinformatics, proteomics,
evolutionary and population genetics, systems biology, epigenetics, and biotechnology.
Cold Spring Harbor Laboratory Press is an internationally renowned publisher of books, journals, and electronic media, located
on Long Island, New York. It is a division of Cold Spring Harbor Laboratory, an innovator in life science research and the
eduction of scientists, students, and the public. For more information, visit www.cshlpress.com.
Summary:
Researchers from Stanford University and the Benaroya Research Institute campaign in the journal Genome Research for the whole-genome
sequencing of a "living fossil" fish, the coelacanth. The scientists determined that the protocadherin gene cluster in the
coelacanth was similar in size and organization to that of humans, but considerably different from that of teleost fishes.
Thus, the researchers propose that the whole-genome sequence of the coelacanth would be a valuable contribution to the field.
Media Contacts:
Scientists:
• Richard M. Myers (650-725-9687; myers{at}shgc.highwire.org; Department of Genetics, Stanford University School of Medicine)
• James Noonan (510-486-7004; jpnoonan{at}lbl.gov;
Genomics Division, Lawrence Berkeley National Laboratory)
• Chris Amemiya (206-583-6573; camemiya{at}benaroyaresearch.org; Benaroya Research Institute)
Author of release:
• Maria A. Smit (516-422-4013; smit{at}cshl.edu; Assistant Editor, Genome Research)
