Ontology highlight
ABSTRACT:
PROVIDER: PRJNA558948 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR9915310_1.fastq.gz | Fastqsanger.gz | |||
| SRR9915310_2.fastq.gz | Fastqsanger.gz | |||
| SRR9915311_1.fastq.gz | Fastqsanger.gz | |||
| SRR9915311_2.fastq.gz | Fastqsanger.gz | |||
| SRR9915302_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 cold stress is considered the bottleneck problem limiting the development of red tilapia industry. Fish (initial weight: 72.71±1.32 g) was divided into the cold stressed group (C) and the control normal water temperature group (N). The water temperature was reduced by 2℃ per day from 20℃ to 8℃ in cold group, and the control group kept the water temperature at 20℃ during the experiment. At the end of the experiment, the gill(G)、liver(L) and skin(S) tissues from the fish of cold(C) group and control normal water temperature (N) group were taken. The DIA proteome analysis of 18 samples was completed, and 6341 trusted proteins containing quantitative information were obtained. Our aim is to understand the protein expression profiles of cold stress in red tilapia.
2024-08-15 | PXD052625 | Pride
Project description:Dissolved oxygen (DO) is the basis of fish survival, and proper DO level is an important condition to ensure the normal growth of fish. Hypoxic environment is prone to disturb the normal breathing and metabolism of fish, which in turn affects their growth and survival. Gill tissue is the respiratory organs of fish and is in direct contact with the external environment. However, there are few reports on the molecular regulatory mechanism of genetically improved farmed tilapia (GIFT, Oreochromis niloticus) gill tissues in response to hypoxia. Here, we first examine the hypoxia-induced damage of gill tissue by hematoxylin-eosin staining, and then constructed miRNA and mRNA libraries of GIFT gill tissue at 96h of hypoxia stress by a high-throughput sequencing technology, each library has three biological replicates. Gill lamellae of GIFT showed capillary rupture and red blood cell enlargement and overflow under hypoxia stress. Transcription sequencing results showed that the clean reads of miRNA libraries were 9,627,953-13,544,660; the clean reads of mRNA libraries were 43,817,776-53,130,102. Based on the miRNA-mRNA pairs screening principles and mRNA sequencing results, we selected and verified seven differentially expressed miRNAs and their potential target genes. The sequencing results were consistent with the qRT-PCR validation results. These selected miRNA-mRNA pairs are mainly concentrated in the signaling pathways of immune response and metabolic regulation. This study provides new insights into the mechanisms of fish adaptation under hypoxic stress.
2023-02-22 | GSE145788 | GEO
Project description:Dissolved oxygen (DO) is the basis of fish survival, and proper DO level is an important condition to ensure the normal growth of fish. Hypoxic environment is prone to disturb the normal breathing and metabolism of fish, which in turn affects their growth and survival. Gill tissue is the respiratory organs of fish and is in direct contact with the external environment. However, there are few reports on the molecular regulatory mechanism of genetically improved farmed tilapia (GIFT, Oreochromis niloticus) gill tissues in response to hypoxia. Here, we first examine the hypoxia-induced damage of gill tissue by hematoxylin-eosin staining, and then constructed miRNA and mRNA libraries of GIFT gill tissue at 96h of hypoxia stress by a high-throughput sequencing technology, each library has three biological replicates. Gill lamellae of GIFT showed capillary rupture and red blood cell enlargement and overflow under hypoxia stress. Transcription sequencing results showed that the clean reads of miRNA libraries were 9,627,953-13,544,660; the clean reads of mRNA libraries were 43,817,776-53,130,102. Based on the miRNA-mRNA pairs screening principles and mRNA sequencing results, we selected and verified seven differentially expressed miRNAs and their potential target genes. The sequencing results were consistent with the qRT-PCR validation results. These selected miRNA-mRNA pairs are mainly concentrated in the signaling pathways of immune response and metabolic regulation. This study provides new insights into the mechanisms of fish adaptation under hypoxic stress.
2023-02-26 | GSE146050 | GEO
Project description:Purpose: The aim of this study was to RNA-sequencing (RNA-seq) to investigate further the gill transcriptome during the early stage of infection, prior to the appearance of mucoid lesions on the gills of amoebic gill disease (ADG)-affected fish. Methods: This study investigated the gill transcriptomic profile of pre-clinical AGD using RNA-sequencing (RNA-seq) technology. RNA-seq libraries generated at 0, 4, 7, 14 and 16 days post inoculation (dpi) RNA-seq data was validated using real-time, quantitative PCR (qPCR) analysis. Results: This study identified 29,357 Differentially Expressed Genes (DEGs) over the course of 16 days follwing exposure to N.perurans , the caustative agent of Amoebic gill disease. With many genes differentially regualted at more tehn one time point, the number of individual gene identified as down-regulated was 8,524 and up-regulated was 10,826. DEGs mapped to 224 Gene Ontology (GO) terms, 27 reference pathways in the Kyoto Encyclopedia of Genes and Genomes (KEGG) and 15 Reactome Gene Sets. Conclusions:Molecular diagnostics and histopathology, but not gill scores, provided an accurate record of disease progression during early stage onset of AGD, prior to evidence of clinical signs on the gill. At 7 days post infection (dpi), there was evidence of innate immune response activation and a concomitant immune suppression involving signalling pathways for cytokines, specifically interleukins.
2021-07-13 | GSE179972 | GEO
Project description:Myxozoa, a unique group of obligate endoparasites within the phylum Cnidaria, can cause emerging diseases in both wild and cultured fish populations. Recently, the myxozoan Myxobolus bejeranoi has been identified as a prevalent pathogen infecting the gills of cultured hybrid tilapia, resulting in considerable mortality rates. M. bejeranoi can infect fish at an early-life stage and demonstrates rapid and efficient proliferation along with modulation of its host immune system. Proliferation is confined within a gramulomata, or termed cyst, that generates a cellular barrier with the attempt to prevent parasite spreading to surrounding tissues. In this study, we employed a proteomic approach to examine the impact of M. bejeranoi infection on fish gills, with a particular emphasis the cyst walls. Enrichment analysis showed increased immune response and oxidative stress within the infected gill tissue, with the most pronounced effects observed at the cyst walls. The intense immune reaction included a consortium of endopeptidase inhibitors, potentially combating the proteases arsenal secreted by the Myxozoa. Analysis of the cysts proteome indicated that cell-cell adhesion molecules via keratin intermediate filaments contribute to the structural integrity of the rigid cysts. However, this barrier confining M. bejeranoi is not impenetrable and the infection will impact the overall gill tissue and eventually in severe cases the effect will be systematic. This research deepens our understanding of the proteomic elements constructing the cysts walls which enable its distinctive nature from rest of the gill tissue at the interface between the host and the myxozoan parasite.
2024-06-23 | PXD051329 | Pride