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Coelacanth News - Proposal To Determine Its Genome

Regarding the thread about what got one interested in dinosaurs/science,
reading about the first coelacanth finds was one of those little bits that
got me interested. I'm somewhat surprised that doing its genome was not
thought of before (maybe it was, this is the first I'd read about it).


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

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. ...

... Although a wide assortment of species have been chosen for sequencing,
ranging from lampreys to armadillos (http://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." 
... 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. 
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. 



Article on some findings reported at a recent conference of the African
Coelacanth Ecosystem Programme.

Reports of coelacanth populations off Tanzania.