Whole genome sequencing reads of 15 threespine sticklebacks from Greenland and Denmark
Ontology highlight
ABSTRACT:
PROVIDER: PRJEB15181 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| ERR1599900_1.fastq.gz | Fastqsanger.gz | |||
| ERR1599900_2.fastq.gz | Fastqsanger.gz | |||
| ERR1599910_1.fastq.gz | Fastqsanger.gz | |||
| ERR1599910_2.fastq.gz | Fastqsanger.gz | |||
| ERR1599901_1.fastq.gz | Fastqsanger.gz |
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Project description:RNA sequencing was used to measure global gene expression in wild caught threespine sticklebacks. Native freshwater and marine fish were acclimated in water of different salinities before the gene expression in kidney was measured. The comparative transcriptomic analysis allowed the identification of salt-responsive genes.
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Project description:Genome-wide DNA methylation patterns in wild samples of two morphotypes of threespine stickleback (Gasterosteus aculeatus)
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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
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.
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Project description:In this study, we used whole genome comparative oligonucleotide microarrays to investigate the brain transcriptomic response to predator cues using the threespine stickleback, Gasteroteus aculeatus. We showed that exposure to olfactory, visual and tactile cues of a predator (rainbow trout, Oncorhynchus mykiss) for six days resulted in subtle but significant transcriptomic changes in the brain of sticklebacks. Gene functional analysis and gene ontology (GO) enrichment revealed that the majority of the transcripts differentially expressed between the fish exposed to predator cues and the control group are primarily related to antigen processing and presentation (involving primarily the major histocompatibility complex (MHC)), transmission of synaptic signals, brain metabolic processes, gene regulation, or visual perception. Pathway analysis identified synaptic long-term depression, RAN signaling, relaxin signaling and phototransduction as the top four pathways that were over-represented.
2011-04-24 | GSE21599 | GEO
Project description:Genome characterization, prevalence and transmission mode of a novel picornavirus associated with the Threespine Stickleback (Gasterosteus aculeatus)
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Project description:Restriction site Associated DNA (RAD) tags are a genome-wide representation of every site of a particular restriction enzyme by short DNA tags. Most organisms segregate large numbers of DNA sequence polymorphisms that disrupt restriction sites, which allow RAD tags to serve as genetic markers spread at a high-density throughout the genome. Here, we demonstrate the applicability of RAD markers for both individual and bulk-segregant genotyping. First, we show that these markers can be identified and typed on pre-existing microarray formats. Second, we present a method that uses RAD marker DNA to rapidly produce a low-cost microarray genotyping resource that can be used to efficiently identify and type thousands of RAD markers. We demonstrate the utility of the former approach by using a tiling path array for the fruit fly to map a recombination breakpoint, and the latter approach by creating and utilizing an enriched RAD marker array for the threespine stickleback. The high number of RAD markers enabled localization of a previously identified region, as well as a second novel region also associated with the lateral plate phenotype. Taken together, our results demonstrate that RAD markers, and the method to develop a RAD marker microarray resource, allow high-throughput, high-resolution genotyping in both model and non-model systems. Keywords: microarray genotyping
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Project description:Schistocephalus solidus is a cestode parasite that is thought to manipulate the behaviour of its threespine stickleback host Gasterosteus aculeatus. It has been hypothesized that the worm could liberate in its external environment “manipulation factors” that would ultimately interfere with the host’s physiology and behaviour. The objective of this project is to describe the whole proteomic content of the proteome and of the secretome of a putative manipulative parasite, Schistocephalus solidus, with the aim to identify proteins that could be involved in the behavioural perturbations of the threespine stickleback.
2021-09-09 | PXD016844 | Pride
Project description:Gene expression in threespine stickleback gonads from three parapatric lake-river population pairs
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Project description:In this study, we used whole genome comparative oligonucleotide microarrays to investigate the brain transcriptomic response to predator cues using the threespine stickleback, Gasteroteus aculeatus. We showed that exposure to olfactory, visual and tactile cues of a predator (rainbow trout, Oncorhynchus mykiss) for six days resulted in subtle but significant transcriptomic changes in the brain of sticklebacks. Gene functional analysis and gene ontology (GO) enrichment revealed that the majority of the transcripts differentially expressed between the fish exposed to predator cues and the control group are primarily related to antigen processing and presentation (involving primarily the major histocompatibility complex (MHC)), transmission of synaptic signals, brain metabolic processes, gene regulation, or visual perception. Pathway analysis identified synaptic long-term depression, RAN signaling, relaxin signaling and phototransduction as the top four pathways that were over-represented. Adult fish were placed in six different 26L tanks with three fish per tank in a partially recirculating flow-through system. Half of the tanks were assigned to the control group and the other half to the experimental group.10 samples were selected for microarray analysis. The ten samples comprised five biological replicates in the experimental group (fish exposed to predator cues) and five biological replicates in the control group (fish not exposed to predator cues), and were evenly distributed across tanks. The cDNA labeling (single color), hybridization, washing and scanning steps were performed in the NimbleGen microarray gene expression service department.
2011-04-24 | E-GEOD-21599 | biostudies-arrayexpress