[Celegans] Open access to waterflea Daphnia genome

Don Gilbert via celegans%40net.bio.net (by gilbertd from net.bio.net)
Thu Jul 12 00:02:38 EST 2007


Dear Biologists,

The arthropod crustacean Daphnia pulex (better known as the water
flea) is a unique emerging model organism, straddling the genome
reach of vertebrate model organisms such as Mouse, insects such
as Drosophila, and nematodes such as Caenorhabditis elegans.

Daphnia shares with C. elegans an interesting and rich gene
structure and wealth of gene duplications.  It has closest gene
homology to the insects, Apis and Drosophila.  However it has
nearly as many unique or strong gene homologies to Mouse as to
insects.

As a model organism for ecology and environmental research for
centuries, Daphnia provides a genome-environment experimental
model unlike any other, where its natural freshwater environments
are readily mimicked in lab, and environmental stresses can be
readily tested in large-scale genomic experiments.

A great example of this genome-environment connection comes from
Daphnia's well known hemoglobin response, called into play as
they rapidly turn blood-red when oxygen is depleted in their
ponds. Among Daphnia's many gene duplications, we find a tandem
cluster of 8 hemoglobin genes
(http://wfleabase.org/genome-summaries/gene-duplicates/).

Whether you work with human or vertebrate genomes, insects, worms
or other eukaryotes, you will find many aspects of interest in
comparing your genomes of interest to this first crustacean draft
genome sequence.

The Daphnia pulex genome will be available on 2007/07/07, in
public early access, with a grand opening scheduled between Fall
2007 and Spring 2008, which will include a Genbank genome
submission and publications.  These sequence data were produced
by the US Department of Energy Joint Genome Institute in
collaboration with the Daphnia Genomics Consortium.

This early access release is made available via 

Daphnia Genome Consortium, http://daphnia.cgb.indiana.edu/
  The DGC website contains Daphnia community documents, analyses,
  and summaries of this emerging model organism's value to
  genomics, ecology, environmental toxicology, evolution,
  and other areas.
  
JGI Genome Portal, http://genome.jgi-psf.org/Dappu1/
  The JGI portal provides gene predictions and homology reports, with
  services for search, BLAST, Genome map Browser
  genes categorized by GO, KEGG, KOG classifications
  and bulk data downloads.

Daphnia genome database at wFleaBase.org provides 
  Summaries of gene homology, structure, phylogeny
    http://wfleabase.org/genome-summaries/
  Genome maps, BLAST, Bulk search services at http://wfleabase.org/
  Daphnia pulex genome data sets in common bulk formats 
    http://wfleabase.org/genome/Daphnia_pulex/current/

Although the time and effort to bring Daphnia's genome to public
access has been large, we believe the quality of this genome data
is high and will be valuable to many areas of genome research. 
Please note the public release status for publication of the JGI
and Daphnia Genome Consortium's data, and respect their
investment of effort on this new model genome.

Scientists wanting to contribute to the open community-wide
annotation project that is currently ongoing should visit
http://dgc.cgb.indiana.edu

-- Don Gilbert 
for Daphnia Genome Consortium



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