July 7, 2007: Daphnia genome sequence in public early access
Source: DGC

News Details:

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 is available starting 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 JGI Genome Portal http://www.jgi.doe.gov/Daphnia/

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 http://wFleaBase.org/ provides

- Summaries of gene homology, structure, phylogeny

http://wfleabase.org/genome-summaries/

- Daphnia pulex genome data sets in common bulk formats

http://wfleabase.org/genome/ (the common URL for model organism genome data)
http://wfleabase.org/genome/Daphnia_pulex/current/ (genome sequence, gene predictions, ESTs, as Fasta and GFF v3)

- Genome maps, BLAST, Bulk search services

http://wfleabase.org/gbrowse/ (GBrowse Genome Maps)
http://wfleabase.org/blast/ (NCBI BLAST Sequence searches)
http://wfleabase.org/biomart/ (BioMart Genome bulk search/retrieval)
http://wfleabase.org/pasa/ (PASA EST analysis web portal)

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.

The terms of use for pre-publication of genome data are found at: https://dgc.cgb.indiana.edu/display/daphnia/Terms+of+use+for+pre-publication+data

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

More Details at DGC Web Site