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Sample Daphnia genome maps
Daphnia pulex scaffolds - log50 draft assembly (20050510)

Nine eukaryote proteomes have been aligned to the D. pulex genome, with help from Daphnia Genomics Consortium, TeraGrid and Generic Model Organism Database projects. The D.pulex genome is a 4x preliminary assembly not for public release but provided by Joint Genome Institute to the Daphnia Genomics Consortium. There are some 3804 scaffolds in this prerelease, the first 50 or so are large chunks of chromosomes (1 to 5 megabases of 184 MB genome total). The nine proteomes, with 217,006 total protein sequences, are drawn from organism genome databases, Ensembl and NCBI (see below). Alignment is done using NCBI tBLASTn, with a Grid-aware version of NCBI software developed by Peng Wang at IU, and run on the TeraGrid. The TeraGrid run for this took 12 hours using 64 processors. Blast output is converted to scaffold locations, and displayed for browsing and searching in GMOD GBrowse genome maps. This genome map is available to DGC members at the Daphnia genome database, (password required). These are sample map views:

D. pulex scaffold_1:1000000..2000000

HOX area at D_pulex scaffold_6_2442741..2764842
This appears to a Homeobox area, perhaps the only one with several matching HOX proteins from Drosophila, Worm and Yeast and others.
[Gene links are active on this map]

detailed view blastn:WFms:p3-k202000fw50799 scaffold_6:2725293..2725319 blastn:WFms:p3-l32000fw50561 scaffold_6:2492786..2492810 blastn:WFms:p5-f92000fw50545 scaffold_6:2728163..2737440 blastn:WFms:p5-m242000fw48758 scaffold_6:2692334..2692622 blastn:WFms:pa96-f112000fw52851 scaffold_6:2590065..2590091 blastn:WFms:pa96-g52000fw53789 scaffold_6:2550577..2673662 tblastn:modSC:PHO2|YDL106C scaffold_6:2718107..2718382 tblastn:modDM:Antp-PI scaffold_6:2668675..2688917 tblastn:modDM:Scr-PA scaffold_6:2668663..2759335 tblastn:modDM:abd-A-PB scaffold_6:2585601..2585819 tblastn:modDM:Ubx-PA scaffold_6:2668717..2668875 tblastn:modDM:zen-PA scaffold_6:2585562..2585825 tblastn:modDM:ind-PA scaffold_6:2718092..2759326 tblastn:modDM:Abd-B-PB scaffold_6:2504701..2504895 tblastn:modDM:lab-PA scaffold_6:2688729..2688953 tblastn:modDM:CG15456-PA scaffold_6:2481280..2481438 tblastn:modDM:ftz-PA scaffold_6:2735780..2759413 tblastn:modDM:Dfd-PA scaffold_6:2759075..2759347 tblastn:modDM:CG30291-PA scaffold_6:2490598..2492559 tblastn:modDM:pb-PA scaffold_6:2668648..2759431 tblastn:modDM:CG4848-PA scaffold_6:2487169..2490262 tblastn:modDM:Mlc1-PA scaffold_6:2475323..2475837 tblastn:modDM:CG7056-PA scaffold_6:2688690..2688914 tblastn:modDM:NK7.1-PA scaffold_6:2759111..2759425 tblastn:modCE:ceh-12 scaffold_6:2735729..2735956 tblastn:modCE:ceh-13 scaffold_6:2735780..2735935 tblastn:modCE:egl-5 scaffold_6:2585559..2668878 tblastn:modCE:lin-39 scaffold_6:2668642..2759290 tblastn:modCE:mab-5 scaffold_6:2585568..2759290 tblastn:modCE:mlc-3 scaffold_6:2475484..2475873 tblastn:modCE:nob-1 scaffold_6:2504710..2504883 tblastn:modCE:pal-1 scaffold_6:2585562..2668866 tblastn:modCE:php-3 scaffold_6:2504626..2504919 tblastn:modCE:WBGene00013765 scaffold_6:2490604..2492559

Daphnia microsatellites and ESTs, available at, are also mapped here. Human and Rice tracks are not shown here, but are similar to Mouse and Arabidopsis, respectively. A copy of the proteomes used are available at

  ensAG => "Mosquito", "Anopheles_gambiae.MOZ2a.dec.pep.fa.gz", 
  ncbAT => "Mustard_weed", "Arabidopsis_thaliana_NC_003070-76.fa.gz", 
  modCE => "Worm-e", "Caenorhabditis-elegans_WormBase_WS130_protein-reps.fa.gz", 
  ensDR => "Zebrafish", "Danio_rerio.ZFISH4.dec.pep.fa.gz", 
  modDM => "Fruitfly-m", "Drosophila-melanogaster_FlyBase_r4.0_protein-reps.fa.gz", 
  ensHS => "Human", "Homo_sapiens.NCBI35.dec.pep.fa.gz", 
  modMM => "Mouse", "Mus-musculus_MGI_01282005_protein-reps.fa.gz", 
  modOG => "Rice", "Oryza_Gramene_r16.0_protein-reps.fa.gz", 
  modSC => "Yeast-c", "Saccharomyces-cerevisiae_SGD_08272004_protein-reps.fa.gz", 

This annotation was performed by Don Gilbert,, July 2005, as part of an assessment of the Teragrid as a shared computational resource for genome database projects under the GMOD umbrella. The Daphnia annotation data are available to DGC members now, and to all at first public release of this genome.

Thanks to Dick Repasky, Peng Wang, George Turner, Stephen Simms and others of the IU Teragrid group (,, for effective help overcoming various cyberinfrastructure issues, and for providing a version of BLAST that works well with multiple genomes on Grid systems. Also thanks for support to NSF (TeraGrid and DGC support), NIH (GMOD support to D. Gilbert), and DOE (JGI's Daphnia genome data).