Ontology highlight
ABSTRACT:
PROVIDER: PRJNA1264535 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR33613683_1.fastq.gz | Fastqsanger.gz | |||
| SRR33613683_2.fastq.gz | Fastqsanger.gz | |||
| SRR33613684_1.fastq.gz | Fastqsanger.gz | |||
| SRR33613684_2.fastq.gz | Fastqsanger.gz | |||
| SRR33613685_1.fastq.gz | Fastqsanger.gz |
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Project description:Transcriptional plasticity is a major driver of phenotypic differences between species. The lower temperature limit (LTL), namely the lower end of survival temperature, is an important trait delimiting the geographical distribution of a species, however, the genetic mechanisms are poorly understood. We investigated the inter-species transcriptional diversification in cold responses between zebrafish Danio rerio and tilapia Oreochromis niloticus, which were reared at a common temperature (28°C) but have distinct LTLs. We identified significant expressional divergence between the two species in the orthologous genes from gills when the temperature cooled to the LTL of tilapia (8°C). Five KEGG pathways were found sequentially over-represented in the zebrafish/tilapia divergently expressed genes in the duration (12 hour) of 8°C exposure, forming a signaling cascade from metabolic regulation to apoptosis via FoxO signaling. Consistently, we found differential progression of apoptosis in the gills of the two species in which zebrafish manifested a delayed and milder apoptotic phenotype than tilapia, corresponding with a lower LTL of zebrafish. We identified diverged expression in 25 apoptosis-related transcription factors between the two species which forms an interacting network with diverged factors involving the FoxO signaling and metabolic regulation. We propose a genetic network which regulates LTL in fishes. Examination of gene expressional divergence in gill between zebrafish and tilapia
2016-07-03 | E-GEOD-69965 | biostudies-arrayexpress
Project description:The salmon gill poxvirus (SGPV) is a large DNA virus that infects gill epithelial cells in Atlantic salmon and is associated with acute high mortality disease outbreaks in aquaculture. The pathological effects of SGPV infection include gill epithelial apoptosis in the acute phase of the disease and hyperplasia of gill epithelial cells in surviving fish, causing damage to the gill respiratory surface. Transcriptome responses to virus were assessed in gills at different stages of disease
2020-05-30 | GSE151463 | GEO
Project description:Transcriptional plasticity is a major driver of phenotypic differences between species. The lower temperature limit (LTL), namely the lower end of survival temperature, is an important trait delimiting the geographical distribution of a species, however, the genetic mechanisms are poorly understood. We investigated the inter-species transcriptional diversification in cold responses between zebrafish Danio rerio and tilapia Oreochromis niloticus, which were reared at a common temperature (28°C) but have distinct LTLs. We identified significant expressional divergence between the two species in the orthologous genes from gills when the temperature cooled to the LTL of tilapia (8°C). Five KEGG pathways were found sequentially over-represented in the zebrafish/tilapia divergently expressed genes in the duration (12 hour) of 8°C exposure, forming a signaling cascade from metabolic regulation to apoptosis via FoxO signaling. Consistently, we found differential progression of apoptosis in the gills of the two species in which zebrafish manifested a delayed and milder apoptotic phenotype than tilapia, corresponding with a lower LTL of zebrafish. We identified diverged expression in 25 apoptosis-related transcription factors between the two species which forms an interacting network with diverged factors involving the FoxO signaling and metabolic regulation. We propose a genetic network which regulates LTL in fishes.
2016-07-03 | GSE69965 | GEO
Project description:Transport stress is a big threat to most teleost fish during production practice, causing mass loss to the aquaculture industry. Fish gills are mucosa-associated lymphoid tissue that directly contacted with water, which is the good choice to study the mechanism of transport stress. Gills transcriptome results revealed 1551 differentially expressed genes (744 up-regulated and 807 down- regulated) between the control and 16h transportation groups. The top 10 enriched KEGG pathways are all immune-related. After qRT-PCR validation, we found that the toll-like receptors and nod-like receptors signaling pathways mediate the gill’s immune response to transport stress: tlr5, tnfɑ, hsp90ɑ, il-1ß and map2k4 were significantly up-regulated and arrdc2 was significantly down-regulated under transport stress. These results suggested that the transport stress altered innate immunity responses and induced metabolic changes in gills of hybrid yellow catfish. In conclusion, the results provide new perspectives on immune response in yellow catfish against transport stress and provide the possibility of mining resistance genes for future optimize transportation plan.
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Project description:Tilapia Lake Virus (TiLV) poses a significant threat to global tilapia aquaculture, causing high mortality rates and severe economic losses. Despite its impact, the molecular mechanisms of TiLV-host interactions remain poorly understood. This study investigates the proteomic and phosphoproteomic changes in two piscine cell lines, E-11 and RHTiB, following TiLV infection.
2024-09-25 | PXD053604 | JPOST Repository
Project description:aquaculture metagenome under different phosphorus levels
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Project description:Columnaris disease is a prevalent disease in freshwater environments worldwide caused by the ubiquitous aquatic bacterium Flavobacterium species. Adhesion to the external mucosal surfaces of fishes is the initial stage of infection, and the gills specifically have been identified as both a primary target and release site for this pathogen. Previous research has indicated that a predominant US aquaculture product, the hybrid striped bass (Morone chrysops x M. saxatilis), is more susceptible to infection with Flavobacterium columnare (covae) than the maternal white bass (M. chrysops) parental species. Therefore, to further elucidate the differences between these fish we conducted a transcriptomic profiling study examining the differences of gene expression in gill mucosal tissue over time after exposure to F. covae isolate LSU-066-04. Combined with previous work, these data provide a greater understanding of host immune response to a common pathogen in moronids.
2024-05-09 | GSE246056 | GEO
Project description:Streptococcus agalactiae (Lancefield’s group B Streptococcus, GBS) is a major bacterial species of genus Streptococcus and has medical and veterinary importance by affecting mainly humans (Maione et al., 2005; Johri et al., 2006), cattle (Keefe, 1997) and fish (Mian et al., 2009). The GBS is the most important pathogen for the Nile tilapia, a global commodity of the aquaculture sector, causing outbreaks of septicemia and meningoencephalitis (Hernández et al., 2009; Mian et al., 2009).
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Project description:Assessment of in vitro postbiotic capabilities of the probiotic Shewanella putrefaciens Pdp11 growing under different cultivation conditions containing microalgae dietary supplements widely used in aquaculture
2024-07-22 | MSV000095402 | MassIVE
Project description:Ectothermic vertebrates are different from mammals that are sensitive to hypothermia and they have to maintain core temperature for survival. Why and how ectothermic animals can survive, grow and reproduce in low temperature have been for a long time a scientifically challenging and important inquiry to biologists. We used a microarray to profile the gill transcriptome in zebrafish (Danio rerio) after exposure to low temperature. Adult zebrafish were acclimated to a low temperature of 12 °C for 1 (1-d) and 30 d (30-d), and the gill transcriptome was compared to wild types by oligonucleotide microarray hybridization. Results showed 11 and 22 transcripts were found to be upregulated by low-temperature treatment for 1-d and 30-d respectively, while 56 and 70 transcrips were downregulated. The gill transcriptome profiles revealed that ionoregulation-related gene was highly upregulated in cold-acclimated zebrafish. This observation encouraged us to investigate the role of ionoregulatory genes in zebrafish gills during cold acclimation. Cold acclimation caused upregulation of genes that are essential for ionocyte specification, differentiation, ionoregulation, and acid/base balance, and also increased the numbers of cells expressing these genes. mRNA expression of epithelial Ca2+ channel (ECaC), one of these genes, was increased in parallel with the level of Ca2+ influx, revealing a functional compensation after long-term acclimation to cold. Phospho-histone H3 and TUNEL staining showed that the cell turnover rate was retarded in cold-acclimated gills. These results suggest that gills may sustain their functions by yielding mature ionocytes from preexisting undifferentiated progenitors in low-temperature environments.
2008-09-01 | GSE7853 | GEO