Daphnia pulicaria
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA762352 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| Other | ||||
| SRR17837100_1.fastq.gz | Fastqsanger.gz | |||
| SRR17837100_2.fastq.gz | Fastqsanger.gz | |||
| SRR17837101_1.fastq.gz | Fastqsanger.gz | |||
| SRR17837101_2.fastq.gz | Fastqsanger.gz |
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Project description:To profile the Daphnia species methylome and to achieve a better understanding of the level of variations in the methylome of Daphnia species, we performed whole genome bisulfite sequencing (WGBSeq) of adult Daphnia magna Bham2 strain and Daphnia pulex Eloise Butler strain (EB45 and EB31 strains). We also analysed the correlation between gene expression and methylation in the two species, using data generated in this study and RNA-seq data from Orsini, et al. 2016. We found that methylation percentage across the genome of Daphnia spp. follows a bimodal distribution. Furthermore, CpG methylation in Daphnia predominantly occurs at coding regions. Although methylation levels significantly decrease towards the 3’ end of a gene with a significant drop in methylation levels from one exon to the neighbouring intron, there is a clear spike in relative methylation levels between exon and intron boundaries, which may be linked to regulation of splicing. We further demonstrate that DNA methylation in Daphnia is responsive to intrinsic and extrinsic factors. We also compared the methylation and gene expression correlations found in Daphnia to publicly available dataset from two other invertebrate species (Apis mellifera and Nasonia vitripennis) and two vertebrate species (Homo sapiens and Mus musculus). We observed that similar to other invertebrates, Daphnia’s genome is sparsely methylated at a lower level and the methylation is predominantly focused at gene body while in vertebrate species the genome is heavily methylated (global methylation). Although the level and distribution of methylation across CpG sites is different between vertebrates and invertebrates it is possible that methylation density at coding regions has the same function between vertebrates and invertebrates. We demonstrate evolutionary conservation of a positive correlation between high methylation density at coding regions and gene expression across vertebrates and invertebrates, leading to potentially ensuring continuous high expression of genes required throughout the life in both vertebrates and invertebrates.
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Project description:The cuticles of arthropods, including aquatic crustaceans like Daphnia, provide an interface between the organism and its environment. Thus, the cuticle’s structure influences how the organism responds to and interacts with its surroundings. Here, we used label-free quantification proteomics to provide a proteome of the molted cuticle of Daphnia magna, which has long been a prominent subject of studies on ecology, evolution, and developmental biology, anddetected 278 high confidence proteins. Using protein sequence domain and functional enrichment analyses, we identified chitin-binding structural proteins and chitin modifying enzymes as most abundant protein groups in the cuticle proteome.Structural cuticular protein families showed a similar distribution to those found in other arthropods and indicated proteins responsible for the soft and flexible structure of the Daphnia cuticle . Finally, cuticle protein genes were clustered as tandem gene arrays in the Daphnia genome, indicating their importance for adaptation to environmental change. The cuticle proteome presented here will be a valuable resource to the Daphnia research community, informing investigations on diverse topics such as the genetic basis of interactions with predators and parasites.
2024-09-02 | PXD040228 | Pride
Project description:The cuticles of arthropods, including aquatic crustaceans like Daphnia, provide an interface between the organism and its environment. Thus, the cuticle’s structure influences how the organism responds to and interacts with its surroundings. Here, we used label-free quantification proteomics to provide a proteome of the molted cuticle of Daphnia magna, which has long been a prominent subject of studies on ecology, evolution, and developmental biology, anddetected 278 high confidence proteins. Using protein sequence domain and functional enrichment analyses, we identified chitin-binding structural proteins and chitin modifying enzymes as most abundant protein groups in the cuticle proteome.Structural cuticular protein families showed a similar distribution to those found in other arthropods and indicated proteins responsible for the soft and flexible structure of the Daphnia cuticle . Finally, cuticle protein genes were clustered as tandem gene arrays in the Daphnia genome, indicating their importance for adaptation to environmental change. The cuticle proteome presented here will be a valuable resource to the Daphnia research community, informing investigations on diverse topics such as the genetic basis of interactions with predators and parasites.
2024-09-02 | PXD040304 | Pride