Salmo marmoratus (Marble trout), Salmo trutta (Brown trout)
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA485234 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR7687453_1.fastq.gz | Fastqsanger.gz | |||
| SRR7687453_2.fastq.gz | Fastqsanger.gz | |||
| SRR7687454_1.fastq.gz | Fastqsanger.gz | |||
| SRR7687454_2.fastq.gz | Fastqsanger.gz | |||
| SRR7687455_1.fastq.gz | Fastqsanger.gz |
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Similar Datasets
Project description:Brown trout (Salmo trutta) WGS anadromous & resident Irish populations
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Project description:Major histocompatibility complex (MHC) class I-linked microsatellite data and parental assignment data for a group of wild brown trout (Salmo trutta L.) provide evidence of closer spatial aggregation among fry sharing greater numbers of MHC class I alleles under natural conditions. This result confirms predictions from laboratory experiments demonstrating a hierarchical preference for association of fry sharing MHC alleles. Full-siblings emerge from the same nest (redd), and a passive kin association pattern arising from limited dispersal from the nest (redd effect) would predict that all such pairs would have a similar distribution. However, this study demonstrates a strong, significant trend for reduced distance between pairs of full-sibling fry sharing more MHC class I alleles reflecting their closer aggregation (no alleles shared, 311.5 ± (s.e.)21.03 m; one allele shared, 222.2 ± 14.49 m; two alleles shared, 124.9 ± 23.88 m; P<0.0001). A significant trend for closer aggregation among fry sharing more MHC class I alleles was also observed in fry pairs, which were known to have different mothers and were otherwise unrelated (ML-r = 0) (no alleles: 457.6 ± 3.58 m; one allele (422.4 ± 3.86 m); two alleles (381.7 ± 10.72 m); P<0.0001). These pairs are expected to have emerged from different redds and a passive association would then be unlikely. These data suggest that sharing MHC class I alleles has a role in maintaining kin association among full-siblings after emergence. This study demonstrates a pattern consistent with MHC-mediated kin association in the wild for the first time.
| S-EPMC3313050 | biostudies-other
Project description:A total of 55 individuals were analysed: 15 migratory brown trout (Salmo trutta) individuals from the Redon river, 15 sedentary brown trout (S. trutta) individuals from the Redon river, 15 sedentary brown trout (S. trutta) individuals from the Chevenne river, and 10 Atlantic salmon (S. salar) individuals of a hatchery strain. For each individual, RNA was isolated twice from different parts of the same tissue, independently reverse transcribed into Cy3-labeled cDNA and then probed on two different slides, which leads to total of 110 single slide experiments.
2006-03-27 | E-MEXP-123 | biostudies-arrayexpress
Project description:Density-dependence is a major ecological mechanism that is known to limit individual growth. To examine if compensatory growth (unusually rapid growth following a period of imposed slow growth) in nature is density-dependent, one-year-old brown trout (Salmo trutta L.) were first starved in the laboratory, and then released back into their natural stream, either at natural or at experimentally increased population density. The experimental trout were captured three times over a one-year period. We found no differences in growth, within the first month after release (May-June), between the starved fish and the control group (i.e. no evidence of compensation). During the summer however (July-September), the starved fish grew more than the control group (i.e. compensation), and the starved fish released into the stream at a higher density, grew less than those released at a natural density, both in terms of weight and length (i.e. density-dependent compensation). Over the winter (October-April), there were no effects of either starvation or density on weight and length growth. After the winter, starved fish released at either density had caught up with control fish in body size, but recapture rates (proxy for survival) did not indicate any costs of compensation. Our results suggest that compensatory growth in nature can be density-dependent. Thus, this is the first study to demonstrate the presence of ecological restrictions on the compensatory growth response in free-ranging animals.
| S-EPMC3643939 | biostudies-literature
Project description:Metapopulation dynamics over the course of an invasion are usually difficult to grasp because they require large and reliable data collection, often unavailable. The invasion of the fish-free freshwater ecosystems of the remote sub-Antarctic Kerguelen Islands following man-made introductions of brown trout (Salmo trutta) in the 1950's is an exception to this rule. Benefiting from a full long term environmental research monitoring of the invasion, we built a Bayesian dynamic metapopulation model to analyze the invasion dynamics of 85 river systems over 51 years. The model accounted for patch size (river length and connections to lakes), alternative dispersal pathways between rivers, temporal trends in dynamics, and uncertainty in colonization date. The results show that the model correctly represents the observed pattern of invasion, especially if we assume a coastal dispersal pathway between patches. Landscape attributes such as patch size influenced the colonization function, but had no effect on propagule pressure. Independently from patch size and distance between patches, propagule pressure and colonization function were not constant through time. Propagule pressure increased over the course of colonization, whereas the colonization function decreased, conditional on propagule pressure. The resulting pattern of this antagonistic interplay is an initial rapid invasion phase followed by a strong decrease in the invasion rate. These temporal trends may be due to either adaptive processes or environmental gradients encountered along the colonization front. It was not possible to distinguish these two hypotheses. Because invasibility of Kerguelen Is. freshwater ecosystems is very high due to the lack of a pre-existing fish fauna and minimal human interference, our estimates of invasion dynamics represent a blueprint for the potential of brown trout invasiveness in pristine environments. Our conclusions shed light on the future of polar regions where, because of climate change, fish-free ecosystems become increasingly accessible to invasion by fish species.
| S-EPMC3749212 | biostudies-literature
Project description:Many Norwegian rivers and lakes are regulated for hydropower, which affects freshwater ecosystems and anadromous fish species, such as sea trout (Salmo trutta). Lakes are an important feature of many anadromous river systems. However, there is limited knowledge on the importance of lakes as habitat for sea trout and how hydropower affects the behaviour of sea trout in lakes. To investigate this, we conducted an acoustic telemetry study. A total of 31 adult sea trout (532 ± 93 mm total length) were captured by angling in river Aurlandselva, Norway, and tagged between July 20 and August 12, 2021. The tags were instrumented with accelerometer, temperature, and depth sensors, which provided information on the sea trout's presence and behaviour in lake Vassbygdevatnet. Our results indicate that there was a large prevalence of sea trout in the lake during the spawning migration, and that the sea trout were less active in the lake compared to the riverine habitats. An increase in activity of sea trout in the lake during autumn might indicate that sea trout spawn in the lake. However, the discharge from the high-head storage plant into the lake did not affect the depth use or activity of sea trout in the lake. Furthermore, the large prevalence of spawners in the lake during autumn will likely cause an underestimation of the size of the sea trout population in rivers with lakes during annual stock assessment. In conclusion, our results could not find evidence of a large impact of the discharge on the behaviour of sea trout in the lake.
| S-EPMC10576395 | biostudies-literature
Project description:We present a genome assembly from an individual female Salmo trutta (the brown trout; Chordata; Actinopteri; Salmoniformes; Salmonidae). The genome sequence is 2.37 gigabases in span. The majority of the assembly is scaffolded into 40 chromosomal pseudomolecules. Gene annotation of this assembly on Ensembl has identified 43,935 protein coding genes.
| S-EPMC8488904 | biostudies-literature
Project description:Yadong trout (Salmo trutta) Raw sequence reads
| PRJNA1171601 | ENA
Project description:The proliferative darkening syndrome (PDS) is an annually recurring disease that causes species-specific die-off of brown trout (Salmo trutta fario) with a mortality rate of near 100 % in pre-alpine rivers of central Europe. So far the etiology and causation of this disease is still unclear. The objective of this study was to identify the cause of PDS using a next-generation technology detection pipeline. Following the hypothesis that PDS is caused by an infectious agent, brown trout specimens were exposed to water from a heavily affected pre-alpine river with annual occurrence of the disease. Specimens were sampled over the entire time period from potential infection through death. Transcriptomic analysis (microarray) and RT-qPCR of brown trout liver tissue evidenced strong gene expression response of immune-associated genes. Messenger RNA of specimens with synchronous immune expression profiles were ultra-deep sequenced using next-generation sequencing technology (NGS). Bioinformatic processing of generated reads and gap-filling Sanger re-sequencing of the identified pathogen genome revealed strong evidence that a piscine-related reovirus is the causative organism of PDS. The identified pathogen is phylogenetically closely related to the family of piscine reoviruses (PRV) which are considered as the causation of different fish diseases in Atlantic and Pacific salmonid species such as Salmo salar and Onchorhynchus kisutch. This study also highlights that the approach of first screening immune responses along a timeline in order to identify synchronously affected stages in different specimens which subsequently were ultra-deep sequenced is an effective approach in pathogen detection. In particular, the identification of specimens with synchronous molecular immune response patterns combined with NGS sequencing and gap-filling re-sequencing resulted in the successful pathogen detection of PDS.
2015-06-26 | GSE70257 | GEO
Project description:BACKGROUND:Tetracapsuloides bryosalmonae is a myxozoan parasite which causes economically important and emerging proliferative kidney disease (PKD) in salmonids. Brown trout, Salmo trutta is a native fish species of Europe, which acts as asymptomatic carriers for T. bryosalmonae. There is only limited information on the molecular mechanism involved in the kidney of brown trout during T. bryosalmonae development. We employed RNA sequencing (RNA-seq) to investigate the global transcriptome changes in the posterior kidney of brown trout during T. bryosalmonae development. METHODS:Brown trout were exposed to the spores of T. bryosalmonae and posterior kidneys were collected from both exposed and unexposed control fish. cDNA libraries were prepared from the posterior kidney and sequenced. Bioinformatics analysis was performed using standard pipeline of quality control, reference mapping, differential expression analysis, gene ontology, and pathway analysis. Quantitative real time PCR was performed to validate the transcriptional regulation of differentially expressed genes, and their correlation with RNA-seq data was statistically analyzed. RESULTS:Transcriptome analysis identified 1169 differentially expressed genes in the posterior kidney of brown trout, out of which 864 genes (74%) were upregulated and 305 genes (26%) were downregulated. The upregulated genes were associated with the regulation of immune system process, vesicle-mediated transport, leucocyte activation, and transport, whereas the downregulated genes were associated with endopeptidase regulatory activity, phosphatidylcholine biosynthetic process, connective tissue development, and collagen catabolic process. CONCLUSION:To our knowledge, this is the first RNA-seq based transcriptome study performed in the posterior kidney of brown trout during active T. bryosalmonae development. Most of the upregulated genes were associated with the immune system process, whereas the downregulated genes were associated with other metabolic functions. The findings of this study provide insights on the immune responses mounted by the brown trout on the developing parasite, and the host molecular machineries modulated by the parasite for its successful multiplication and release.
| S-EPMC6884850 | biostudies-literature