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.

Daphnia magna microRNAs respond to nutritional stress and ageing but are not transgenerational

“…Of the 116 miRNAs (5p and 3p) we quantified, 4256 potential mRNA targets were identified, an average of 37 per miRNA, a figure possibly further inflated by overaggressive annotation of the D. magna genome (Ye et al., ). Currently, there are 29,128 gene predictions, but this may drop significantly with future resources, as was the case for Daphnia pulex (Colbourne et al., ; Orsini et al., ; Ye et al., ). Functional characterization of the processes regulated by miRNAs of interest is therefore inaccurate at best.…”

First‐generation annotations for the fathead minnow (Pimephales promelas) genome

“…Although it has been common practice for several years to observe specific transcript levels in response to chemical exposure via qPCR or microarrays, recently there has been an increased interest in whole‐transcriptome sequencing. Van Delft et al demonstrated that RNA sequencing can be used to detect differentially expressed genes in human cells exposed to benzo[ a ]pyrene , and others are beginning to lay the foundations for the use of RNA‐seq in Daphnia and in fish species for the purpose of ecotoxicology research. The ability to map RNA‐seq reads to a reference genome gives a more complete and unbiased view into the transcriptome, and allows researchers to identify novel transcripts, even while using short read lengths such as those offered by Illumina technologies .…”

Contrasting patterns of divergence at the regulatory and sequence level in European Daphnia galeata natural populations

“…Although various aspects like phylogeography, functional morphology, physiology, and life history evolution have been in the limelight of Daphnia research for several decades (Eads et al, ), Daphnia genomics investigations have begun only in the last decade with the availability of the Daphnia pulex genome (Colbourne et al, ). A considerable number of studies (e.g., Bento et al, ; Miner, De Meester, Pfrender, Lampert, & Hairston, ; Orsini et al, ; Yampolsky et al, ) on biotic and abiotic factors have been carried out showing how Daphnia respond to environmental perturbations by changes in gene expression. However, little is known about the intraspecific variability at the gene expression level in Daphnia , since the above‐mentioned studies focused on stressor‐driven responses using a limited number of genotypes.…”

“…Although various aspects like phylogeography, functional morphology, physiology, and life history evolution have been in the limelight of Daphnia research for several decades (Eads et al, 2008), Daphnia genomics investigations have begun only in the last decade with the availability of the Daphnia pulex genome (Colbourne et al, 2011). A considerable number of studies (e.g., Bento et al, 2017;Miner, De Meester, Pfrender, Lampert, & Hairston, 2012;Orsini et al, 2016;Yampolsky et al, 2014) To sum up, elucidating the mechanisms by which natural selection acts on gene expression evolution remains a challenge (e.g., Fraser, 2011;Romero, Ruvinsky, & Gilad, 2012). Unraveling the relative consequences of drift versus natural selection on gene expression profiles plays an important role in understanding species divergence and local adaptation.…”