Ontology highlight
ABSTRACT:
PROVIDER: PRJNA865387 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:ddRAD sequencing of Common Whelk, Buccinum undatum
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Project description:Population genomics of Buccinum undatum
| PRJEB53993 | ENA
Project description:The anadromous Atlantic salmon undergo preparatory physiological transformations before seawater entry, referred to as smoltification. Little is known about the photoperiod-influence and genome regulatory processes driving smoltification such as the large scale changes in lipid metabolism and energy homeostasis in the developing smolt liver. To shed light on this, we performed a smoltification trial using contrasting photoperiod regimes and generate a transcriptome data from livers throughout smoltification and after seawater transfer. In this experiment two groups of Atlantic salmon were reared for a total of 46 weeks from the parr stage, through smoltification, and seawater transfer. After 21 week from first feeding, the experiment group was given artificial winter photoperiod (8 hours light, 16 hours dark) for 8 weeks to induce smoltification before returning to constant light. The second control group received constant light throughout the experiment. Liver tissue was sampled from individuals first at week 1, 21 weeks after first feeding, then again at week 10, after the winter period, at week 19, after the expected smoltification time, and lastly at week 25, after transfer to seawater.
2022-05-16 | E-MTAB-11746 | biostudies-arrayexpress
Project description:Due to difficulties inherent in designating conservation units for effective species management and conservation, the use of multiple complementary sources of information is required to identify and assess the designation of conservation units based on the degree of variation among populations within a species. In this study, we combined estimates of microsatellite and transcriptomic variation to assess the population structure and potential for adaptive variation of threatened Atlantic salmon, Salmo salar, among rivers in the Bay of Fundy. In general, population structure identified by genetic differentiation was consistent with the patterns of variation in gene expression. Both data sets provided clear indication of strong regional differentiation between rivers located within the inner Bay of Fundy relative to rivers located within the outer Bay of Fundy or the Southern Uplands region. There was also support for more refined population structure; there was some differentiation in both microsatellite and gene expression patterns between salmon from rivers in the two regions of the inner Bay of Fundy: Chignecto Bay and Minas Basin. Consistent patterns apparent in the genetic and transcriptomic dataset indicate that Atlantic salmon populations from the inner and outer Bay of Fundy reflect unique genetic lineages, with some evidence of unique genetic legacies between regions of the inner Bay of Fundy, and even between individual rivers within a region. Consistency of the microarray data across two years helps to validate the use of this technique as a useful tool in assessment of variation among wild populations for species conservation. Atlantic salmon samples used in this analysis were collected from Mactaquac and Coldbrook Biodiversity Centres on the east coast of Canada. In year one, eight individuals were hybridized per strain (five strains; 40 individuals in total). This design incorporated dye-swap replicates in which two slides were hybridized with the same pair of individuals, but the dyes were swapped for one of the slides. Therefore, in year one a total of 40 slides were used. Because of the large number of strains assessed in year two (12), dyes were balanced across slides to maximize biological replication. Six individuals were hybridized per strain; three of these were labelled with Cy3, and three were labelled with Cy5 (for a total of 36 arrays in year two).
2010-05-19 | E-GEOD-19111 | biostudies-arrayexpress
Project description:Due to difficulties inherent in designating conservation units for effective species management and conservation, the use of multiple complementary sources of information is required to identify and assess the designation of conservation units based on the degree of variation among populations within a species. In this study, we combined estimates of microsatellite and transcriptomic variation to assess the population structure and potential for adaptive variation of threatened Atlantic salmon, Salmo salar, among rivers in the Bay of Fundy. In general, population structure identified by genetic differentiation was consistent with the patterns of variation in gene expression. Both data sets provided clear indication of strong regional differentiation between rivers located within the inner Bay of Fundy relative to rivers located within the outer Bay of Fundy or the Southern Uplands region. There was also support for more refined population structure; there was some differentiation in both microsatellite and gene expression patterns between salmon from rivers in the two regions of the inner Bay of Fundy: Chignecto Bay and Minas Basin. Consistent patterns apparent in the genetic and transcriptomic dataset indicate that Atlantic salmon populations from the inner and outer Bay of Fundy reflect unique genetic lineages, with some evidence of unique genetic legacies between regions of the inner Bay of Fundy, and even between individual rivers within a region. Consistency of the microarray data across two years helps to validate the use of this technique as a useful tool in assessment of variation among wild populations for species conservation. Atlantic salmon samples used in this analysis were collected from Mactaquac and Coldbrook Biodiversity Centres on the east coast of Canada. In year one, eight individuals were hybridized per strain (five strains; 40 individuals in total). This design incorporated dye-swap replicates in which two slides were hybridized with the same pair of individuals, but the dyes were swapped for one of the slides. Therefore, in year one a total of 40 slides were used. Because of the large number of populations assessed in year two (12), dyes were balanced across slides to maximize biological replication. Six individuals were hybridized per strain; three of these were labelled with Cy3, and three were labelled with Cy5 (for a total of 36 arrays in year two).
2010-05-19 | E-GEOD-19119 | biostudies-arrayexpress
Project description:The anadromous Atlantic salmon undergo preparatory physiological transformations before seawater entry, referred to as smoltification. Little is known about the photoperiod-influence and genome regulatory processes driving smoltification such as the large scale changes in lipid metabolism and energy homeostasis in the developing smolt liver. To shed light on this, we performed a smoltification trial using contrasting photoperiod regimes and generate ATAC-seq data from livers throughout smoltification and after seawater transfer to assess the differences in chromatin accessibility. In this experiment Atlantic salmon were reared for a total of 46 weeks from the parr stage, through smoltification, and seawater transfer. After 21 week from first feeding, the group was given artificial winter photoperiod (8 hours light, 16 hours dark) for 8 weeks to induce smoltification before returning to constant light. Liver tissue was sampled from individuals first at week 1, 21 weeks after first feeding, then again at week 10, after the winter period, at week 19, after the expected smoltification time, and lastly at week 25, after transfer to seawater.
2024-02-02 | E-MTAB-13743 | biostudies-arrayexpress