title: Daphnia magna transcriptome by RNA-Seq across 12 environmental stressors.
abstract: 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.
authors.affiliation: Environmental Genomics Group, School of Biosciences, University of Birmingham, Birmingham B15 2TT, UK.
authors.forename: Luisa
authors.initials: L
authors.lastname: Orsini
authors.affiliation: Biology Department, Indiana University, 1001 E. Third Street, Bloomington, Indiana 47405, USA.
authors.forename: Donald
authors.initials: D
authors.lastname: Gilbert
authors.affiliation: School of Informatics and Computing, Indiana University, 919 E. Tenth Street, Bloomington, Indiana 47408, USA.|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.
authors.forename: Ram
authors.initials: R
authors.lastname: Podicheti
authors.affiliation: Laboratory of Aquatic Ecology, Evolution and Conservation, University of Leuven, Ch. Deberiotstraat 32, Leuven 3000, Belgium.
authors.forename: Mieke
authors.initials: M
authors.lastname: Jansen
authors.affiliation: Department of Genome Dynamics Lawrence Berkeley National Laboratory, University of California Berkeley, Berkeley, California 94720, USA.
authors.forename: James B
authors.initials: JB
authors.lastname: Brown
authors.affiliation: Department of Genome Dynamics Lawrence Berkeley National Laboratory, University of California Berkeley, Berkeley, California 94720, USA.
authors.forename: Omid Shams
authors.initials: OS
authors.lastname: Solari
authors.affiliation: Laboratory of Aquatic Ecology, Evolution and Conservation, University of Leuven, Ch. Deberiotstraat 32, Leuven 3000, Belgium.
authors.forename: Katina I
authors.initials: KI
authors.lastname: Spanier
authors.affiliation: Environmental Genomics Group, School of Biosciences, University of Birmingham, Birmingham B15 2TT, UK.
authors.forename: John K
authors.initials: JK
authors.lastname: Colbourne
authors.affiliation: 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.
authors.forename: Douglas B
authors.initials: DB
authors.lastname: Rusch
authors.affiliation: Aquatic Biology, Interdisciplinary research Facility Life Sciences KU Leuven Campus Kortrijk, E. Sabbelaan 53, Kortrijk B-8500, Belgium.
authors.forename: Ellen
authors.initials: E
authors.lastname: Decaestecker
authors.affiliation: Laboratory of Environmental Toxicology and Aquatic Ecology, GhEnToxLab,Ghent University, Ghent, Belgium.
authors.forename: Jana
authors.initials: J
authors.lastname: Asselman
authors.affiliation: Laboratory of Environmental Toxicology and Aquatic Ecology, GhEnToxLab,Ghent University, Ghent, Belgium.
authors.forename: Karel A C
authors.initials: KA
authors.lastname: De Schamphelaere
authors.affiliation: Universität Basel, Zoologisches Institut, Vesalgasse 1, Basel 4051, Switzerland.
authors.forename: Dieter
authors.initials: D
authors.lastname: Ebert
authors.affiliation: 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.
authors.forename: Christoph R
authors.initials: CR
authors.lastname: Haag
authors.affiliation: Institute of Biotechnology, University of Helsinki, PO Box 56, Viikinkaari 9, 00014, Helsinki Finland.
authors.forename: Jouni
authors.initials: J
authors.lastname: Kvist
authors.affiliation: Animal Ecology I and Bayreuth Center of Ecology and Environmental Research (BayCEER), University of Bayreuth, Bayreuth 95440, Germany.
authors.forename: Christian
authors.initials: C
authors.lastname: Laforsch
authors.affiliation: Department of Ecology, Faculty of Science, Charles University in Prague, Viničná 7, Prague CZ-12844, Czech Republic.
authors.forename: Adam
authors.initials: A
authors.lastname: Petrusek
authors.affiliation: Department of Animal and Plant Science, University of Sheffield Alfred Denny Building, Western Bank, Sheffield S10 2TN, UK.
authors.forename: Andrew P
authors.initials: AP
authors.lastname: Beckerman
authors.affiliation: Ashworth Laboratories, Institute of Evolutionary Biology, University of Edinburgh, Kings Buildings, Edinburgh EH9 3JT, UK.
authors.forename: Tom J
authors.initials: TJ
authors.lastname: Little
authors.affiliation: Laboratory of Aquatic Ecology, Evolution and Conservation, University of Leuven, Ch. Deberiotstraat 32, Leuven 3000, Belgium.
authors.forename: Anurag
authors.initials: A
authors.lastname: Chaturvedi
authors.affiliation: Department of Biological Sciences and Environmental Change Initiative, Galvin Life Science Center, Notre Dame, Indiana 46556, USA.
authors.forename: Michael E
authors.initials: ME
authors.lastname: Pfrender
authors.affiliation: Laboratory of Aquatic Ecology, Evolution and Conservation, University of Leuven, Ch. Deberiotstraat 32, Leuven 3000, Belgium.
authors.forename: Luc
authors.initials: L
authors.lastname: De Meester
authors.affiliation: Institute of Biotechnology, University of Helsinki, PO Box 56, Viikinkaari 9, 00014, Helsinki Finland.
authors.forename: Mikko J
authors.initials: MJ
authors.lastname: Frilander
mesh_terms: D000818:Animals; D001483:Base Sequence; D003621:Daphnia / Q000235:genetics*; D030541:Databases, Genetic; D059647:Gene-Environment Interaction; D016678:Genome; D012313:RNA / Q000235:genetics; D059467:Transcriptome
chemical_list: D012313:RNA