October 20, 2008: The D. magna genome sequencing project
Source: DGC
News Details:
The community-wide annotation project for the Daphnia pulex genome is drawing to a close. Within the next two months, we will have altogether submitted over 40 manuscripts for publication within special series by BMC and by SCIENCE that will feature the first description of a crustacean genome sequence. More importantly, with the publication of this work, we will celebrate official recognitions of a new model system for environmental genomics. These achievements are phenomenal. The project’s success is a direct consequence of our community’s commitment to building shared resources that enable interdisciplinary investigations. The students within our laboratories are first to benefit from these new opportunities.
The Daphnia Genomics Consortium grows to involve researchers from around the globe; there are over 350 investigators from 17 countries who are receiving this message. Recall that a decision was made at our meeting in 2002 to initially focus most of the global efforts on the D. pulex complex, because of the broad set of genomic tools that were already being developed. Yet, this early plan included an understanding that a similar concerted effort would be devoted to the distantly related congener D. magna as soon as possible. Now is the time.
Arguably, research interest in D. magna is greater than for all other species, mainly because of its important role in toxicological studies and in formulating regulations by environmental protection agencies. Over 100 years of testing how synthetic chemicals impact survivorship, life-history and distribution of Daphnia produced more than 7,000 research articles. Of the nearly 500,000 records in the ECOTOX database, D. magna represent 8% of all experimental data for aquatic organisms; it is the only aquatic organism among the top 25 test species that can be used inexpensively.
We are launching the D. magna genome sequencing project. Our goal is to produce a draft genome assembly and annotation, with associated databases and functional genomic tools within the next 1-2 years. The experience of DGC members, combined with technological advancements allows for a new approach to this challenge; we sequence the genome as an in-consortium, self-funded project. We want you to participate.
We ask: Can you contribute single runs of the genome sequencer that produces 100-750 Mbp of data per run? A strong response to this call will ensure a rapid completion of the sequencing part of this project. One run of the sequencer costs $10,000. By contributing to this collective dataset, your lab will benefit from immediate access to intermediate and final draft assemblies ahead of the full public release of the data. For good reason, we should all expect an enthusiastic response.
Fueled by funding from six DGC labs, sequencing of the D. magna genome began on June 2, 2008, as a proof of principle. Please see URL below.
By September 26, we produced a pre-assembly from 622.6 Mbp of sequence data.
- Number of Contigs = 542,302
- Total Bases Assembled = 85,132,859 bp
- Average Length of Contigs = 157 bp
- Standard Deviation of Contigs = 190 bp
- Maximum Contig size = 4,094 bp
This pre-assembly release wets our appetites and is ours to explore, including data files, basic blast search, and genome browser map of D. pulex with the "Daphnia magna" aligned contigs. So far, the D. magna reads align to 17,000 D. pulex annotated genes.
http://wfleabase.org/genome/Daphnia_magna_prerelease/
With additional funding from DGC labs we will make rapid progress in sequencing and assembling this new genome. If we are fortunate enough to collect more funds than needed for sequencing the D. magna Finish Clone XInb3, and to cover auxiliary bioinformatics costs, we will openly discuss charging ahead by sequencing another isolate or (better yet) a species from a third subgenus to help inform the evolutionary history of the genus. For now, let the D. magna genome project begin!
More Details at DGC Web Site
