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Questions & Answers

What is the Daphnia Genomics Consortium (DGC)

The DGC is an international network of investigators committed to mounting the freshwater crustacean Daphnia as a model system for ecology, evolution and the environmental sciences. At our first consortium meeting in 2002, a decision was made to initially focus most of the global efforts on the D. pulex complex, based on the broad set of genomic tools that had already been developed, but to also bring the distantly related congener D. magna on board as soon as possible. Eight years later, we have completed a first annotation and deep functional analysis of the draft genome sequence assembly of the D. pulex genome and we are completing the D. magna genome sequencing project.

Along with research activities, the DGC is: (1) coordinating efforts towards building the Daphnia genomics toolbox, which is made available for use by the general community; (2) facilitating collaborative cross-disciplinary investigations; (3) developing bioinformatic strategies for organizing the rapidly growing genome database; and (4) exploring emerging technologies to improve high throughput analyses of molecular and ecological samples. If we are to succeed at creating a new model system for modern life-sciences research, it will need to be a community-wide effort. We hope that you will participate at some level. Membership is open to the research community - contact John Colbourne.

Why assemble a consortium?

Until recently, an enormous effort was needed to apply genetic tools to ecological studies, especially when striving to uncover the mechanisms of phenotypic plasticity and the genetic basis for evolutionary adaptation. An important consequence of the large-scale genome programs of recent years has been the technological advancements that transform such studies from the painstaking hunt for a few accessible genes to the rapid screening of multiple loci for variation linked to specific phenotypic effects. As a consequence, genomic resources targeting an ecologically-focused organism are being developed by the DGC, whose goal is "to develop the Daphnia system to the same depth of molecular, cell and developmental biological understanding as other model systems, but with the added advantage of being able to interpret observations in the context of natural ecological challenges."

What is the history of DGC activities?

November 8, 2001

Planning begins with web-video conference call (9 investigators attend)

September 5, 2002

US National Science Foundation funds DGC research (award 0221837)

October 3-4, 2002

First International DGC meeting in Bloomington, Indiana (26 investigators attend)

March 26, 2003

The Daphnia Genome Sequencing White Paper is distributed

April 28, 2003

US Department of Energy funds D. pulex genome sequence (award DE-AC02-05CH11231) as a collaborative venture between DGC and Joint Genome Institute scientists

August 22, 2003

LISTSERV electronic mailing begins

August 27, 2003

US National Science Foundation funds DGC research (award 0328516)

September 8-9, 2003

2nd International DGC meeting in Manchester, New Hampshire (44 investigators attend)

December, 2003

Pilot project for the production of full-length enriched cDNA libraries is completed

September, 2004

"The Chosen One" (TCO) daphniid isolate is identified and the production of DNA libraries for genome sequencing begins

March 8, 2004

wFleaBase is launched

September 11, 2004

DGC Collaboration Wiki is launched

November, 2004

D. pulex genome sequencing begins at the Joint Genome Institute

December 13, 2004

Trouble in genome project paradise – stock contamination problem detected after 2-fold sequencing of the genome from a strain subsequently called "The Rejected One" (TRO), retrospectively provides valuable polymorphism data

January 10, 2005

UK Natural Environment Research Council funds DGC research

January 11, 2005

Production of new DNA libraries from TCO isolate resumes

May 10, 2005

4-fold genome coverage sequence assembly is produced (half-way mark of the sequencing project)

August, 2005

Draft sequencing of the genome is complete (>8-fold sequence coverage)

January 17-19, 2006

3rd International DGC meeting in Bloomington, Indiana (XX investigators attend) – Announcement is made that sequencing of the genome is completed

April 19, 2006

First D. pulex genetic map is published

September 1, 2006

Genome sequence assembled by three methods for cross-validation

Through February, 2007

Automated annotation of the genome is performed by the JGI and wFleaBase – the genome draft assembly and browsers are released for the community analysis of the data

February 28, 2007

Community Genome Annotation Project and Training is launched

March 8 to April 12, 2007

77 DGC members are trained to manually curate gene annotations via telephone conferences

April, 2007

Over 30 abstracts are submitted by research groups to study specific elements of the genome data for publication

May 14-18, 2007

The Daphnia Genome Annotation Local Jamboree in Bloomington, Indiana, trains 31 participants and produces video tutorial at annotating the genome

July 1, 2007

US National Institutes of Health funds DGC research (award 7R24GM078274)

July 7-9, 2007

4th International Daphnia Genomics Consortium Meeting is held in Bloomington, Indiana (XX investigators attend)

July 7, 2007

Draft D. pulex genome version 1.1 is early released to the public – Announcement is made at the DGC meeting

February 5-7, 2008

Planning begins in Leuven (Belgium) for sequencing D. magna

June 2, 2008

D. magna genome sequencing project begins

May 13, 2009

BioMed Central Thematic Series Daphnia: the companion papers for the genome sequence is launched

September 13-18, 2009

Planning begins in Herzberg (Switzerland) for sequencing the transcriptome of D. galeata

March 26-30, 2010

5th International DGC meeting in Leuven, Belgium (XX investigators attend)

April 16, 2010

D. magna genome sequence assembly and preliminary annotation v2.4 at 22.7x sequence coverage is distributed to participating DGC investigators

August 1, 2010

US National Institutes of Environmental Health Sciences funds DGC research (award 1R01ES019324)

August 21-29, 2010

DGC offers first technical course in Environmental Genomics at Mount Desert Island Biological Laboratory

August 31, 2010

European Science Foundation funds DGC research (EuroEEFG program)

September 22, 2010

First D. magna genetic map is published

February 4, 2011

Publication of the flagship D. pulex genome study supported by over 50 companion papers by participating DGC-member laboratories

February 17, 2011

Publication of reverse genetics (an RNA interference method) for Daphnia magna

March 1-3, 2011

First meeting of the DGC Stressflea project in Leuven, Belgium

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