Daphnia pulex v1.0

Status

v.1.0 (July 5, 2007): Daphnia pulex genome assembly v1.0. The assembly release version 1.0 of whole genome shotgun reads was constructed with the JGI assembler, Jazz, using paired end sequencing reads at a coverage of 8.7x. After trimming for vector and quality, 1,591,853 reads assembled into 9080 scaffolds totaling 227.1 Mbp. Further exclusion of contaminant and mis-assembled scaffolds reduced this to 5191 scaffolds, with a total length of 197.3 Mbp. Roughly half of the genome is contained in 103 scaffolds all at least 469.5 Kb in length.The current draft release, version 1.0, includes a total of 30,907 gene models predicted and functionally annotated using the JGI annotation pipeline.

Collaborators

  • John Kenneth Colbourne, Center for Genomics and Bioinformatics, Indiana University
  • Daphnia Genomics Consortium
    Michael Pfrender, Utah State University
    Jeffrey Boore, University of California
    Michael Lynch, Indiana University
    W. Kelley Thomas, University of New Hampshire
    Donald Gilbert, Indiana University
    Joshua Hamilton, Dartmouth College
    Justen Andrews, Indiana University

References

Colbourne JK, Pfrender ME, Gilbert D, Thomas WK, Tucker A, Oakley TH, Tokishita S, Aerts A, Arnold GJ, Basu MK, Bauer DJ, Cáceres CE, Carmel L, Casola C, Choi JH, Detter JC, Dong Q, Dusheyko S, Eads BD, Fröhlich T, Geiler-Samerotte KA, Gerlach D, Hatcher P, Jogdeo S, Krijgsveld J, Kriventseva EV, Kültz D, Laforsch C, Lindquist E, Lopez J, Manak JR, Muller J, Pangilinan J, Patwardhan RP, Pitluck S, Pritham EJ, Rechtsteiner A, Rho M, Rogozin IB, Sakarya O, Salamov A, Schaack S, Shapiro H, Shiga Y, Skalitzky C, Smith Z, Souvorov A, Sung W, Tang Z, Tsuchiya D, Tu H, Vos H, Wang M, Wolf YI, Yamagata H, Yamada T, Ye Y, Shaw JR, Andrews J, Crease TJ, Tang H, Lucas SM, Robertson HM, Bork P, Koonin EV, Zdobnov EM, Grigoriev IV, Lynch M, Boore JL. The ecoresponsive genome of Daphnia pulex.. Science. 2011 Feb 4;331(6017):555-61.

Links

Funding

This work was performed under the auspices of the US Department of Energy's Office of Science, Biological and Environmental Research Program and the by the University of California, Lawrence Livermore National Laboratory under Contract No. W-7405-Eng-48, Lawrence Berkeley National Laboratory under contract No. DE-AC03-76SF00098 and Los Alamos National Laboratory under contract No. W-7405-ENG-36.