Shotgun metagenome Profiling of Freshwater Snails
Ontology highlight
ABSTRACT:
PROVIDER: PRJEB97425 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:Invasive freshwater snails form novel microbial relationships
| PRJEB40881 | ENA
Project description:Transcriptional profile of snails exposed to irradiated E. paraensei miricidia and four days later challenged with S. mansoni miricidia. Compared to snails exposed to only irradiated E. paraensei miricidia.
2011-07-30 | GSE28293 | GEO
Project description:Transcriptional profile of BS-90 snails injected with a cocktail of four FREP3 specific 27-mer DSiRNA oligos and two hours later exposed to S. mansoni miricidia. Compared to BS-90 snails injected with a cocktail of three GFP specific DSiRNA oligos and two hours later exposed to S. mansoni miricidia. Experiments were done over the course of 49 days. Snails were collected (10each) at 2 and 4 dpe to S. mansoni for comparison.
2012-04-01 | GSE33525 | 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.
2017-05-30 | GSE82310 | GEO
Project description:shotgun metagenome sequencing Metagenome
| PRJNA1020264 | ENA
Project description:Alviniconcha snails Genome sequencing and assembly
| PRJNA1245653 | 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. This is the RNA-seq experiment, DNA methylation data (bisulfite-seq) is provided under accession number GSE82310.
2021-11-03 | GSE186925 | GEO
Project description:Transcriptional profile of snails exposed to irradiated E. paraensei miricidia and four days later challenged with S. mansoni miricidia. Compared to snails exposed to only irradiated E. paraensei miricidia. Each replicate is comprised of 1 individual snail from the specified treatment group. Six replicates of each treatment were analyzed on the Snail oligo array.
2011-07-29 | E-GEOD-28293 | biostudies-arrayexpress
Project description:Metagenome data from soil samples were collected at 0 to 10cm deep from 2 avocado orchards in Channybearup, Western Australia, in 2024. Amplicon sequence variant (ASV) tables were constructed based on the DADA2 pipeline with default parameters.
2025-06-15 | GSE298403 | GEO
Project description:MotivationWhole metagenome shotgun sequencing is a powerful approach for assaying the functional potential of microbial communities. We currently lack tools that efficiently and accurately align DNA reads against protein references, the technique necessary for constructing a functional profile. Here, we present PALADIN-a novel modification of the Burrows-Wheeler Aligner that provides accurate alignment, robust reporting capabilities and orders-of-magnitude improved efficiency by directly mapping in protein space.ResultsWe compared the accuracy and efficiency of PALADIN against existing tools that employ nucleotide or protein alignment algorithms. Using simulated reads, PALADIN consistently outperformed the popular DNA read mappers BWA and NovoAlign in detected proteins, percentage of reads mapped and ontological similarity. We also compared PALADIN against four existing protein alignment tools: BLASTX, RAPSearch2, DIAMOND and Lambda, using empirically obtained reads. PALADIN yielded results seven times faster than the best performing alternative, DIAMOND and nearly 8000 times faster than BLASTX. PALADIN's accuracy was comparable to all tested solutions.Availability and implementationPALADIN was implemented in C, and its source code and documentation are available at https://github.com/twestbrookunh/paladin.Contactanthonyw@wildcats.unh.edu.Supplementary informationSupplementary data are available at Bioinformatics online.
| S-EPMC5423455 | biostudies-literature