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

Luisa Orsini; Donald  Gilbert; Ram Podicheti; MIeke Jansen; James B Brown; Omid Shams Solari; Katina I Spanier; John Colbourne; Douglas Rush; Ellen  Decaestecker; Jana Asselman; Karel AC De Schamphelaere; Dieter  Ebert; Christoph R Haag; Jouni Kvist; Christian  Laforsch; Adam Petrusek; Andrew P Beckerman; Tom J Little; Anurag Chaturvedi; Michael E.  Pfrender; Luc De Meester; Mikko J Frilander

doi:10.1038/sdata.2016.30

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

Luisa Orsini, Donald Gilbert, Ram Podicheti, MIeke Jansen, James B Brown, Omid Shams Solari, Katina I Spanier, John Colbourne, Douglas Rush, Ellen Decaestecker, Jana Asselman, Karel AC De Schamphelaere, Dieter Ebert, Christoph R Haag, Jouni Kvist, Christian Laforsch, Adam Petrusek, Andrew P Beckerman, Tom J Little, Anurag ChaturvediMichael E. Pfrender, Luc De Meester, Mikko J Frilander

Biosciences

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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.

Original language	English
Article number	160030
Journal	Scientific Data
Volume	3
DOIs	https://doi.org/10.1038/sdata.2016.30 https://doi.org/10.1038/sdata.2016.30
Publication status	Published - 10 May 2016

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Erratum: daphnia magna transcriptome by RNA-Seq across 12 environmental stressors
Orsini, L., Gilbert, D., Podicheti, R., Jansen, M., Brown, J. B., Solari, O. S., Spanier, K. I., Colbourne, J. K., Rusch, D. B., Decaestecker, E., Asselman, J., De Schamphelaere, K. A. C., Ebert, D., Haag, C. R., Kvist, J., Laforsch, C., Petrusek, A., Beckerman, A. P., Little, T. J., Chaturvedi, A., & 3 othersPfrender, M. E., De Meester, L. & Frilander, M. J., 31 Jan 2017, In: Scientific Data. 4, 1 p., 170006.
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Orsini, L., Gilbert, D., Podicheti, R., Jansen, MI., Brown, J. B., Shams Solari, O., Spanier, K. I., Colbourne, J., Rush, D., Decaestecker, E., Asselman, J., De Schamphelaere, K. AC., Ebert, D., Haag, C. R., Kvist, J., Laforsch, C., Petrusek, A., Beckerman, A. P., Little, T. J., ... Frilander, M. J. (2016). Daphnia magna transcriptome by RNA-Seq across 12 environmental stressors: Daphnia magna transcriptome. Scientific Data, 3, Article 160030 . https://doi.org/10.1038/sdata.2016.30, https://doi.org/10.1038/sdata.2016.30

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title = "Daphnia magna transcriptome by RNA-Seq across 12 environmental stressors: Daphnia magna transcriptome",

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. ",

author = "Luisa Orsini and Donald Gilbert and Ram Podicheti and MIeke Jansen and Brown, {James B} and {Shams Solari}, Omid and Spanier, {Katina I} and John Colbourne and Douglas Rush and Ellen Decaestecker and Jana Asselman and {De Schamphelaere}, {Karel AC} and Dieter Ebert and Haag, {Christoph R} and Jouni Kvist and Christian Laforsch and Adam Petrusek and Beckerman, {Andrew P} and Little, {Tom J} and Anurag Chaturvedi and Pfrender, {Michael E.} and {De Meester}, Luc and Frilander, {Mikko J}",

year = "2016",

month = may,

day = "10",

doi = "10.1038/sdata.2016.30",

language = "English",

volume = "3",

journal = "Scientific Data",

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Orsini, L, Gilbert, D, Podicheti, R, Jansen, MI, Brown, JB, Shams Solari, O, Spanier, KI, Colbourne, J, Rush, D, Decaestecker, E, Asselman, J, De Schamphelaere, KAC, Ebert, D, Haag, CR, Kvist, J, Laforsch, C, Petrusek, A, Beckerman, AP, Little, TJ, Chaturvedi, A, Pfrender, ME, De Meester, L & Frilander, MJ 2016, 'Daphnia magna transcriptome by RNA-Seq across 12 environmental stressors: Daphnia magna transcriptome', Scientific Data, vol. 3, 160030 . https://doi.org/10.1038/sdata.2016.30, https://doi.org/10.1038/sdata.2016.30

TY - JOUR

T1 - Daphnia magna transcriptome by RNA-Seq across 12 environmental stressors

T2 - Daphnia magna transcriptome

AU - Orsini, Luisa

AU - Gilbert, Donald

AU - Podicheti, Ram

AU - Jansen, MIeke

AU - Brown, James B

AU - Shams Solari, Omid

AU - Spanier, Katina I

AU - Colbourne, John

AU - Rush, Douglas

AU - Decaestecker, Ellen

AU - Asselman, Jana

AU - De Schamphelaere, Karel AC

AU - Ebert, Dieter

AU - Haag, Christoph R

AU - Kvist, Jouni

AU - Laforsch, Christian

AU - Petrusek, Adam

AU - Beckerman, Andrew P

AU - Little, Tom J

AU - Chaturvedi, Anurag

AU - Pfrender, Michael E.

AU - De Meester, Luc

AU - Frilander, Mikko J

PY - 2016/5/10

Y1 - 2016/5/10

N2 - 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.

AB - 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.

UR - https://www.ncbi.nlm.nih.gov/pubmed/27164179

U2 - 10.1038/sdata.2016.30

DO - 10.1038/sdata.2016.30

M3 - Article

SN - 2052-4463

VL - 3

JO - Scientific Data

JF - Scientific Data

M1 - 160030

ER -

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

Abstract

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Erratum: daphnia magna transcriptome by RNA-Seq across 12 environmental stressors

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