Data · dataset · 2018
De novo assemblies, annotations, and gene expression profiling of gill epithelium from 16 species of Fundulus killifish in response to salinity change.
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P51 Ion and Acid-Base Regulation in Fish Symposium# ICBF2018 13th International Congress on the Biology of FishCalgary, Alberta, July 15-19, 2018 Estuaries are characterized by periodic fluxes in salinity.
Description
Many species of North American killifish (Fundulus) are estuarine specialists and harbor euryhaline phenotypes. Three clades within Fundulus independently radiated into freshwater environments and have lost their abilities to tolerate high salinity.
We use Fundulus as a comparative model system for studying the physiological and genetic mechanisms that diverge between euryhaline and freshwater species. We examined 16 estuarine and freshwater species with representation from each of three clades. Fish from all species were acclimated to either brackish or fresh water then exposed to an acute brackish water challenge.
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Gill transcriptome data were collected. To enable multi-species comparisons, reference transcriptome assemblies were generated de novo for each species then used to analyze transcriptional responses to salinity change by clade and physiology. We find differences in the gene expression between euryhaline and freshwater species, some of which are shared across clades, implicating molecular mechanisms that contribute to divergent osmoregulatory physiologies.
Fundulus Multispecies Osmotic Transcriptome Sequencing Project (FMOTSP) doi.org/10.17605/OSF.IO/M4XEG Analysis scripts:github.com/ljcohen/RNAseq_15killifish Raw data:ncbi.nlm.nih.gov/bioproject/473009
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Where it is published
- Repository landing page figshare.com/articles/De_novo_assemblies_annotations_and_gene_expression_pr… ↗
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- DOI doi.org/10.6084/m9.figshare.6827201.v2 ↗
DOI / persistent id · from DataCite
Documentation and papers
Catalogue records · 2
- DataCite API api.datacite.org/dois/10.6084/m9.figshare.6827201.v2 ↗
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- DataCite Commons commons.datacite.org/doi.org/10.6084/m9.figshare.6827201.v2 ↗
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Topics
- Stated by source
- Agriculture, forestry, and fisheries
- Inferred from text
- Fisheries sciences 75% · RNA sequencing 65% · Sequencing 75%
Provenance · 1 source records, 12 field assertions
| Source | Key | Last seen | Raw |
|---|---|---|---|
| DataCite | 10.6084/m9.figshare.6827201.v2 | 15 d ago | JSON v1 |
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|---|---|---|---|
| access_level | source · DataCite | connector:datacite@1.0.0 | /data/attributes/rightsList |
| byte_size | source · DataCite | connector:datacite@1.0.0 | |
| concepts[field].anzsrc:group:3005 | enrichment · DataCite | taxonomy-embedding@1.1.0 | title+keywords+description (75%) |
| concepts[field].fos:agriculture-forestry-and-fisheries | source · DataCite | connector:datacite@1.0.0 | |
| concepts[modality].local:modality:rna-seq | enrichment · DataCite | keyword-concept-rules@1.0.0 | title+description (65%) |
| concepts[modality].local:modality:sequencing | enrichment · DataCite | keyword-concept-rules@1.0.0 | title+description (75%) |
| created_date | source · DataCite | connector:datacite@1.0.0 | |
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| updated_date | source · DataCite | connector:datacite@1.0.0 |