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| Status |
Public on Mar 04, 2019 |
| Title |
Genome-wide stress responses to copper and arsenic in a field population of Daphnia. |
| Organism |
Daphnia magna |
| Experiment type |
Expression profiling by high throughput sequencing
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| Summary |
Over the past decade, significant advances have been made to unravel molecular mechanisms of stress response in different ecotoxicological model species. Within this study, we focus on population level transcriptomic responses of a natural population of Daphnia magna Straus, (1820), to heavy metals. We aim to characterize the population level transcriptomic responses, which include standing genetic variation, and improve our understanding on how populations respond to environmental stress at a molecular level. We studied population level responses to two heavy metals, copper and arsenic, and their binary mixture across time. Transcriptomic patterns identified significantly regulated gene families and genes at the population level including cuticle proteins and resilins. Furthermore, some of these differentially regulated gene families, such as cuticle proteins, were also significantly enriched for genetic variations including SNPs and MNPs. In general, genetic variation was observed in specific gene families, many of which are known to be involved in stress response. Overall, our results indicate that molecular stress responses can be identified within natural populations and that linking molecular mechanisms with genetic variation at the population level could contribute significantly to adverse outcome frameworks.
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| Overall design |
We exposed a field population of daphnia to copper, arsenic and a mixture of copper and arsenic and extracted RNA at different time points
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| Contributor(s) |
Asselman J, Semmouri I, Jackson C, Keith N, Van Nieuwerburgh F, Deforce D, Shaw J, De Schamphelaere KA |
| Citation(s) |
30817885 |
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| Submission date |
Nov 07, 2018 |
| Last update date |
Mar 20, 2019 |
| Contact name |
Jana Asselman |
| E-mail(s) |
jana.asselman@ugent.be
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| Phone |
+32 9 264 37 64
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| Organization name |
Ghent University
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| Lab |
Laboratory of Environmental Toxicology and Aquatic Ecology
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| Street address |
Coupure Links 653 (Building F, 2nd floor)
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| City |
Gent |
| ZIP/Postal code |
9000 |
| Country |
Belgium |
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| Platforms (1) |
| GPL25778 |
Illumina HiSeq 3000 (Daphnia magna) |
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| Samples (48)
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| Relations |
| BioProject |
PRJNA504445 |
| SRA |
SRP168044 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE122265_NormalizedCounts_Transcriptome.txt.gz |
1.2 Mb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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