September 13, 2005: Update on the Daphnia Genome Project
Source: DGC

News Details:

Dear Colleagues,

We are pleased to bring you up to date on the status of the Daphnia Genome Project. The Joint Genome Institute has now finished nearly all sequencing of our Daphnia pulex isolate (the Chosen One). Although the assembly has not been completed, it appears that the sequence coverage using the whole genome shotgun method is about 9-fold. This coverage is better than anticipated because of the quality of the sequence reads and a smaller than expected genome size; the first draft assembly of the genome at the midway point of the project indicated that the Daphnia genome is less than 200 million bases!

With precise timing, three supporting projects needed for the successful assembly and annotation of the genome sequence are also coming to a close. Researchers at the University of New Hampshire have tiled BAC libraries underway containing large genome fragments, whose mapped restriction sites will help assemble the millions of small genome sequence reads into contiguous strings of nucleotides. UNH will also host the large and medium insert libraries to facilitate the filling of sequence gaps. Researchers at Indiana University have completed a genetic map for Daphnia pulex by placing 183 microsatellite markers into linkage groups representing all 12 chromosomes. These ordered markers help orientate orphan sequences in the genome assembly. Finally, researchers at Indiana University, University of New Hampshire and the Joint Genome Institute finished sequencing the first 50,000 cDNA isolates from 21 separate libraries. So far, 12,600 distinct gene transcripts have been identified. An additional 50,000 cDNAs are cued for sequencing.

At this point of the Daphnia Genome Project, we are working quickly to assess the quality of each data set, to associate the physical and genetic maps into a unified format and to release this information to help promote Daphnia as a research model for ecological and evolutionary genomic studies.

Evaluating the genome assembly

Collaborative efforts are underway to release a high quality draft assembly of the Daphnia genome at our next DGC meeting (January 2006). The genomic contigs and scaffolds will be analyzed to detect misassembled regions using two computational methods, one based on pattern statistics and another based on clone coverage statistics. These algorithms will be refined and combined to produce a probabilistic support index for scaffold junctions, indicating regions of high and low confidence.

Annotation of the genome sequence

The process of annotating the genome is under the direction of JGI and the DGC steering committee. Preliminary annotation will be conducted by a team at JGI based on ab initio methods (e.g., fgenesh), by EST sequence matching, and by Blast results. This will be loaded into tracks that can be viewed using a web browser; examples for other genomes can be found at the JGI Eukaryotic Genomics Website. This tool will be used at a jamboree to be hosted by JGI where about 40 experts from the scientific community will improve this initial annotation by offering corrections and interpretations. Annotators are invited to participate based on their specific area of expertise. An important goal is to also involve as many researchers from the consortium as possible to describe in greater detail the biology of Daphnia 's genome.

The steering committee will facilitate annotation related research of individual laboratories by providing information about who is planning to do what analyses, and by coordinating the publication of manuscripts at an agreed upon date. It will be up to each participating group to reach deadlines for completing their analyses and for submitting their papers. Negotiations are underway to identify an appropriate publisher for a special issue of peer-reviewed research papers entitled “Genome Biology of the Model Crustacean Daphnia”. Our current target for submitting manuscripts is autumn 2006. More details will be available at our next DGC meeting.

Mark your calendars

Our next consortium meeting will be held on January 18-19, 2006. The Center for Genomics and Bioinformatics with the Department of Biology will host this meeting on the campus of Indiana University, in Bloomington. Information about the venue, agenda and registration process will be posted later this month. This meeting promises to be an exciting celebration of our recent accomplishments. We hope to see you there.

Sincerely,

John Colbourne, Indiana U.
Jeff Boore, Joint Genome Institute
Kelley Thomas, U of New Hampshire
Justen Andrews, Indiana U.
Mike Pfrender, Utah State University
Mike Lynch, Indiana University