Ontology highlight
ABSTRACT:
PROVIDER: PRJNA388325 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:Population genomics in lake and stream stickleback populations
| PRJNA237460 | ENA
Project description:Three-spined stickleback (Gasterosteus aculeatus) represents a convenient model to study microevolution - adaptation to freshwater environment. While genetic adaptations to freshwater are well-studied, epigenetic adaptations attracted little attention. In this work, we investigated the role of DNA methylation in the adaptation of marine stickleback population to freshwater conditions. DNA methylation profiling was performed in marine and freshwater populations of sticklebacks, as well as in marine sticklebacks placed into freshwater environment and freshwater sticklebacks placed into seawater. For the first time, we demonstrated that genes encoding ion channels kcnd3, cacna1fb, gja3 are differentially methylated between marine and freshwater populations. We also showed that after placing marine stickleback into fresh water, its DNA methylation profile partially converges to the one of a freshwater stickleback. This suggests that immediate epigenetic response to freshwater conditions can be maintained in freshwater population. Interestingly, we observed enhanced epigenetic plasticity in freshwater sticklebacks that may serve as a compensatory regulatory mechanism for the lack of genetic variation in the freshwater population. Some of the regions that were reported previously to be under selection in freshwater populations also show differential methylation. Thus, epigenetic changes might represent a parallel mechanism of adaptation along with genetic selection in freshwater environment.
2017-05-30 | GSE82310 | GEO
Project description:Three-spined stickleback (Gasterosteus aculeatus) represents a convenient model to study microevolution - adaptation to freshwater environment. While genetic adaptations to freshwater are well-studied, epigenetic adaptations attracted little attention. In this work, we investigated the role of DNA methylation in the adaptation of marine stickleback population to freshwater conditions. DNA methylation profiling was performed in marine and freshwater populations of sticklebacks, as well as in marine sticklebacks placed into freshwater environment and freshwater sticklebacks placed into seawater. For the first time, we demonstrated that genes encoding ion channels kcnd3, cacna1fb, gja3 are differentially methylated between marine and freshwater populations. We also showed that after placing marine stickleback into fresh water, its DNA methylation profile partially converges to the one of a freshwater stickleback. This suggests that immediate epigenetic response to freshwater conditions can be maintained in freshwater population. Interestingly, we observed enhanced epigenetic plasticity in freshwater sticklebacks that may serve as a compensatory regulatory mechanism for the lack of genetic variation in the freshwater population. Some of the regions that were reported previously to be under selection in freshwater populations also show differential methylation. Thus, epigenetic changes might represent a parallel mechanism of adaptation along with genetic selection in freshwater environment. This is the RNA-seq experiment, DNA methylation data (bisulfite-seq) is provided under accession number GSE82310.
2021-11-03 | GSE186925 | GEO
Project description:In order to identify gene expression difference between marine and freshwater stickleback populations, we compared the transcriptomes of seven adult tissues (eye, gill, heart, hypothalumus, liver, pectoral muscle, telencephalon) between a marine population sampled from the mouth of the Little Campbell river in British Columbia (LITC) and a freshwater population (Fishtrap Creek, FTC) from northern Washington. For each population, the sampled individuals were the lab-reared progeny of a single pair of wild-caught parents.
2011-12-30 | GSE34783 | GEO
Project description:Developing stickleback embryos were dissociated and sorted for S-phase and G0/G1-phase cell populations. DNA was extracted from each population and sequenced. In a mixed S-phase population, regions that replicate earlier are at higher copy number (up to 2x) than regions that replicate later. The read depth in S-phase, normalized to the read depth in G-phase, thus represents replication timing.
2018-10-20 | GSE121537 | GEO
Project description:After the end of the last ice age, ancestrally marine threespine stickleback fish (Gasterosteus aculeatus) have undergone an adaptive radiation into freshwater environments throughout the Northern Hemisphere, creating an excellent model system for studying molecular adaptation and speciation. Stickleback populations are reproductively isolated to varying degrees, despite the fact that they can be crossed in the lab to produce viable offspring. Ecological and behavioral factors have been suggested to underlie incipient stickleback speciation. However, reproductive proteins represent a previously unexplored driver of speciation. As mediators of gamete recognition during fertilization, reproductive proteins both create and maintain species boundaries. Gamete recognition proteins are also frequently found to be rapidly evolving, and their divergence may culminate in reproductive isolation and ultimately speciation. As an initial investigation into the contribution of reproductive proteins to stickleback reproductive isolation, we characterized the egg coat proteome of threespine stickleback eggs. In agreement with other teleosts, we find that stickleback egg coats are comprised of homologs to the zona pellucida (ZP) proteins ZP1 and ZP3. We explore aspects of stickleback ZP protein biology, including glycosylation, disulfide bonding, and sites of synthesis, and find many substantial differences compared to their mammalian homologs. Furthermore, molecular evolutionary analyses indicate that ZP3, but not ZP1, has experienced positive Darwinian selection across teleost fish. Taken together, these changes to stickleback ZP protein architecture suggest that the egg coats of stickleback fish, and perhaps fish more generally, have evolved to fulfill a more protective functional role than their mammalian counterparts.
2021-05-26 | PXD017489 | Pride