November 10, 2008: D. magna genome project update
Source: DGC

News Details:

Dear colleagues,

Only one month after the first assembly at a 3x coverage, the number of participants in the D. magna project has grown to 9 for us to obtain a Dmagna V2.0 assembly based on twice as much coverage of the genome. By contrast to the earlier dataset, the new assembly now includes paired-end sequencing to begin building sequence scaffolds.

Please see the assembly statistics at our wiki page: https://projects.cgb.indiana.edu/display/grp/D.+magna+Genome

Scaffolding Summary
Number of Scaffolds = 8,099
Length of Scaffolds = 76,899,494bp
Avg Length of Scaffolds = 9,494bp
Stdev Length of Scaffolds = 14,649bp
Largest Scaffold = 180,201bp
Number of N50 Scaffolds = 887
Length of N50 Scaffold = 25,437bp
Number of Contigs = 32,100
Length of Contigs = 65,990,419bp
Number of unassembled reads = 3,523,415

As of today, we sequenced 1,77 Gbp, which represents 8.8x coverage of the genome. In the coming weeks, we will obtain (from a generous offer by Roche), another 750+ Mbp of sequence data using beta-test chemistries that provide larger insert paired-end reads. We are shy of three contributors to help finance existing data and to begin analysing the maturing genome assembly. Clearly, we are making great strides together. Please contact me by email if you can contribute to this enterprise.

To answer many questions following the earlier announcement, please find below a list of Q&A.

Q1 - Why should I contribute?

By contributing financially and intellectually to this project, you are participating in this first production of comprehensive genomic resources that is garnered exclusively from the strength of a grass-roots international research community. This project uniquely demonstrates how laboratories of all sizes can help create broadly applicable research tools that are typically reserved to superbly funded institutions. Our approach is particularly important during the current economic downturn, which impacts traditional funding mechanisms for research.

Q2 - What should I expect from my investment?

With sufficient involvement from DGC members, we are set to finish the sequencing part of this project in the coming months. The pace of this project is set by the rate at which individual laboratories contribute $10,000 for single runs of the sequencer. (Indeed, we need your help now, because sequencing has now stopped.) At regular milestones, participants receive improved genome assemblies to begin exploring the data for a group publication, with invited DGC collaborators, that describes results from our comprehensive genome analysis. To protect people's investment, this growing dataset will only be deposited in public databases when the initial analysis and description of the whole genome is complete.

Q3 - How can I help by bootstrapping funds from my existing grant?

There should be no technical restrictions. The CGB will send an invoice, which your department can use to issue a purchase order. In practice, you will be "purchasing" from your grant over 100 Mbp of D. magna sequence data and rights to access the pooled database.

Q4 - I want to participate. But given the rapid pace of this project, there is too little time to obtain a grant and get involved.

Like for earlier DGC projects, the goal is to involve all interested researchers from the community, and to finance the substantial cost of producing and analysing the genomic data. The individual cost of this project is minimized so that alternative sources of funds are possible -- including gifts from your department, college/school dean or from modest institutional funds set aside for pilot projects. Please contact me if a letter of support is needed, which describes our consortium project and how your involvement will create opportunities for future external research and training grants to your group.

Please continue to send your questions and comments. Yet most importantly, get involved early. There is much work ahead of us.

Sincerely, John Colbourne (for the steering committee)

More Details at DGC Web Site