Info • Daphnia pulex

Status

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

Genome Reference(s)

Funding

The work conducted by the U.S. Department of Energy Joint Genome Institute, a DOE Office of Science User Facility, is supported by the Office of Science of the U.S. Department of Energy under Contract No. DE-AC02-05CH11231.