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Open Access Publications from the University of California

Daphnia magna transcriptome by RNA-Seq across 12 environmental stressors.

  • Author(s): Orsini, Luisa
  • Gilbert, Donald
  • Podicheti, Ram
  • Jansen, Mieke
  • Brown, James B
  • Solari, Omid Shams
  • Spanier, Katina I
  • Colbourne, John K
  • Rusch, Douglas B
  • Decaestecker, Ellen
  • Asselman, Jana
  • De Schamphelaere, Karel AC
  • Ebert, Dieter
  • Haag, Christoph R
  • Kvist, Jouni
  • Laforsch, Christian
  • Petrusek, Adam
  • Beckerman, Andrew P
  • Little, Tom J
  • Chaturvedi, Anurag
  • Pfrender, Michael E
  • De Meester, Luc
  • Frilander, Mikko J
  • et al.

The full exploration of gene-environment interactions requires model organisms with well-characterized ecological interactions in their natural environment, manipulability in the laboratory and genomic tools. The waterflea Daphnia magna is an established ecological and toxicological model species, central to the food webs of freshwater lentic habitats and sentinel for water quality. Its tractability and cyclic parthenogenetic life-cycle are ideal to investigate links between genes and the environment. Capitalizing on this unique model system, the STRESSFLEA consortium generated a comprehensive RNA-Seq data set by exposing two inbred genotypes of D. magna and a recombinant cross of these genotypes to a range of environmental perturbations. Gene models were constructed from the transcriptome data and mapped onto the draft genome of D. magna using EvidentialGene. The transcriptome data generated here, together with the available draft genome sequence of D. magna and a high-density genetic map will be a key asset for future investigations in environmental genomics.

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