Journal article

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

  • Orsini L Environmental Genomics Group, School of Biosciences, University of Birmingham, Birmingham B15 2TT, UK.
  • Gilbert D Biology Department, Indiana University, 1001 E. Third Street, Bloomington, Indiana 47405, USA.
  • Podicheti R School of Informatics and Computing, Indiana University, 919 E. Tenth Street, Bloomington, Indiana 47408, USA.
  • Jansen M Laboratory of Aquatic Ecology, Evolution and Conservation, University of Leuven, Ch. Deberiotstraat 32, Leuven 3000, Belgium.
  • Brown JB Department of Genome Dynamics Lawrence Berkeley National Laboratory, University of California Berkeley, Berkeley, California 94720, USA.
  • Solari OS Department of Genome Dynamics Lawrence Berkeley National Laboratory, University of California Berkeley, Berkeley, California 94720, USA.
  • Spanier KI Laboratory of Aquatic Ecology, Evolution and Conservation, University of Leuven, Ch. Deberiotstraat 32, Leuven 3000, Belgium.
  • Colbourne JK Environmental Genomics Group, School of Biosciences, University of Birmingham, Birmingham B15 2TT, UK.
  • Rusch DB Center for Genomics and Bioinformatics, Indiana University, School of Informatics and Computing, Indiana University, 1001 E. Third Street, 919 E. Tenth Street, Bloomington, Indiana 47408, USA.
  • Decaestecker E Aquatic Biology, Interdisciplinary research Facility Life Sciences KU Leuven Campus Kortrijk, E. Sabbelaan 53, Kortrijk B-8500, Belgium.
  • Asselman J Laboratory of Environmental Toxicology and Aquatic Ecology, GhEnToxLab,Ghent University, Ghent, Belgium.
  • De Schamphelaere KA Laboratory of Environmental Toxicology and Aquatic Ecology, GhEnToxLab,Ghent University, Ghent, Belgium.
  • Ebert D Universität Basel, Zoologisches Institut, Vesalgasse 1, Basel 4051, Switzerland.
  • Haag CR Centre d'Ecologie Fonctionnelle et Evolutive-CEFE UMR 5175, CNRS-Université de Montpellier-Université Paul-Valéry Montpellier-EPHE, campus CNRS, 1919, route de Mende, Montpellier, Cedex 5 34293, France.
  • Kvist J Institute of Biotechnology, University of Helsinki, PO Box 56, Viikinkaari 9, 00014, Helsinki Finland.
  • Laforsch C Animal Ecology I and Bayreuth Center of Ecology and Environmental Research (BayCEER), University of Bayreuth, Bayreuth 95440, Germany.
  • Petrusek A Department of Ecology, Faculty of Science, Charles University in Prague, Viničná 7, Prague CZ-12844, Czech Republic.
  • Beckerman AP Department of Animal and Plant Science, University of Sheffield Alfred Denny Building, Western Bank, Sheffield S10 2TN, UK.
  • Little TJ Ashworth Laboratories, Institute of Evolutionary Biology, University of Edinburgh, Kings Buildings, Edinburgh EH9 3JT, UK.
  • Chaturvedi A Laboratory of Aquatic Ecology, Evolution and Conservation, University of Leuven, Ch. Deberiotstraat 32, Leuven 3000, Belgium.
  • Pfrender ME Department of Biological Sciences and Environmental Change Initiative, Galvin Life Science Center, Notre Dame, Indiana 46556, USA.
  • De Meester L Laboratory of Aquatic Ecology, Evolution and Conservation, University of Leuven, Ch. Deberiotstraat 32, Leuven 3000, Belgium.
  • Frilander MJ Institute of Biotechnology, University of Helsinki, PO Box 56, Viikinkaari 9, 00014, Helsinki Finland.
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  • 2016-05-11
Published in:
  • Scientific data. - 2016
English 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.
Language
  • English
Open access status
gold
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https://sonar.ch/global/documents/299107
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