Oncorhynchus mykiss gairdneri
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA1016365 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR26050900_1.fastq.gz | Fastqsanger.gz | |||
| SRR26050900_2.fastq.gz | Fastqsanger.gz | |||
| SRR26050901_1.fastq.gz | Fastqsanger.gz | |||
| SRR26050901_2.fastq.gz | Fastqsanger.gz | |||
| SRR26050902_1.fastq.gz | Fastqsanger.gz |
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Project description:Mechanisms for thermal adaptation: Transcriptional response to heat stress among desert and montane populations of redband trout
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Project description:Rainbow trout (Oncorhynchus mykiss) is highly sensitive to high-temperature stress as an important economic cold-water fish. While previous research has concentrated on the transcriptomic to acute heat stress in rainbow trout, there remains a gap in knowledge regarding the overarching regulatory mechanisms at the translation level. In our research, we utilized a combination of transcriptomic and translatomic analyses to investigate the intricate molecular response mechanisms in the liver of rainbow trout when subjected to heat stress. Through comprehensive multi-omics analysis, we revealed the dynamic translational pattern of rainbow trout liver under heat stress for the first time. Comparative analysis of ribosome analysis data with RNA-seq data showed that the fold changes of gene expression at the transcriptional level were highly correlated (R2 = 0.83) with those at the translational level globally. In total, 2,203 genes exhibited significant alterations exclusively within the translational level. However, the limited overlap in response genes between transcription and translation under heat stress suggests that these two processes may independently modulate the cellular response to thermal challenges. Significant changes in the translation efficiency of 809 genes were observed under heat stress. Further analysis indicated that the translation efficiency of genes were strongly influenced by sequence characteristics such as GC content, coding sequence length and NMFE. Moreover, 3,468 putative uORFs were identified in 2,676 genes, which potentially modulating translation efficiency of mORFs. These findings provide a novel perspective for understanding the physiological adaptations of rainbow trout in response to changes in ambient temperature.
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Project description:Rainbow trout (Oncorhynchus mykiss) is highly sensitive to high-temperature stress as an important economic cold-water fish. While previous research has concentrated on the transcriptomic to acute heat stress in rainbow trout, there remains a gap in knowledge regarding the overarching regulatory mechanisms at the translation level. In our research, we utilized a combination of transcriptomic and translatomic analyses to investigate the intricate molecular response mechanisms in the liver of rainbow trout when subjected to heat stress. Through comprehensive multi-omics analysis, we revealed the dynamic translational pattern of rainbow trout liver under heat stress for the first time. Comparative analysis of ribosome analysis data with RNA-seq data showed that the fold changes of gene expression at the transcriptional level were highly correlated (R2 = 0.83) with those at the translational level globally. In total, 2,203 genes exhibited significant alterations exclusively within the translational level. However, the limited overlap in response genes between transcription and translation under heat stress suggests that these two processes may independently modulate the cellular response to thermal challenges. Significant changes in the translation efficiency of 809 genes were observed under heat stress. Further analysis indicated that the translation efficiency of genes were strongly influenced by sequence characteristics such as GC content, coding sequence length and NMFE. Moreover, 3,468 putative uORFs were identified in 2,676 genes, which potentially modulating translation efficiency of mORFs. These findings provide a novel perspective for understanding the physiological adaptations of rainbow trout in response to changes in ambient temperature.
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Project description:With the intensification of global warming, rainbow trout is suffering from varying degrees thermal stimulation, heat stress may cause pathological signs or diseases by reducing the immune roles and then lead to mass mortality, so high temperatures severely restrict the development of its aquaculture. Understanding the molecular regulation mechanism of rainbow trout under heat stress is used to take measures to relieve symptoms. We performed multiple transcriptomic analysis of liver tissues from rainbow trout under heat stress (24 °C) and control conditions (18 °C) to identify circRNAs, miRNAs and mRNAs. Changes of non-specific immune parameters revealed that strong stress response of rainbow trout is caused in 24 °C. A total of 324 DEcircRNAs, 105 DEmiRNAs, and 1885 DEmRNAs were identified from six libraries, and ceRNA regulatory network is constructed. 301 circRNA–miRNA and 51 miRNA–mRNA negative correlation pairs were screened from ceRNA regulatory network, and predicted three regulatory correlation pairs that novel_circ_003889 - novel-m0674-3p - hsp90ab1, novel_circ_002325 - miR-18-y - HSPA13 and novel_circ_002446 - novel-m0556-3p - hsp70. Some genes involved in metabolic process, biological regulation or response to stimulus are highly induced at high temperatures. Several important pathways involved in heat stress were characterized, such as Protein processing in endoplasmic reticulum (ER), Estrogen signaling pathway, HIF-1 signaling pathway, etc. These results extend our understanding of the molecular mechanisms of heat stress response and expected to provide a novel insight into develop strategies for relieve heat stress.
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Project description:Redband trout whole genome resequencing
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Project description:RNAseq used to examine gene expression in thermal challenged redband rainbow trout
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Project description:Purpose:Our data significantly advance understanding of heat stress regulatory mechanism of miRNA in the head kidney of rainbow trout Methods:miRNAs of rainbow trout were involved in heat stress were identified by high-throughput sequencing of six small RNA libraries of the kidney tissues under control (18℃) and heat-treated (24℃) conditions Results:high-throughput sequencing was performed to identify miRNAs responsive to heat stress. We obtained 41,991,119 and 43,882,123 raw reads and 39,756,736 and 42,538,331 clean reads from under control (18℃) and heat-treated (24℃) .A total of 392 conserved miRNAs and 989 novel miRNAs were identified, of which 78 miRNAs were expressed in different response to heat stress. In addition to, including 393 negative correlation miRNA-target gene pairs Conclusions:through high-throughput sequencing of the six libraries from head kidney tissue of rainbow trout, the expression level of miRNA has significant changes after heat stress.
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Project description:Transcriptome profiling of rainbow trout liver under moderate heat stress
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Project description:Rainbow trout is a typical cold-water fish, with the intensification of global warming, high temperatures severely restrict the development of aquaculture in summer. Understanding the molecular regulation mechanisms of rainbow trout in response to heat stress will be salutary to alleviate heat stress-related damage. In the present study, we performed transcriptome analysis of liver tissues in rainbow trout under heat stress (24℃) and control (18℃) conditions to identify induced lncRNAs and pathways by heat stress. More than 658 million clean reads and 5,916 lncRNAs were identified from six liver libraries. A total of 927 novel lncRNAs were generated and 428 differentially expressed lncRNAs were screened through stringent thresholds. The RNA-seq results were verified by RT-qPCR. In addition, the regulatory network of important functional lncRNA-mRNA were constructed. GO and KEGG enrichment analysis of target gene of differentially expressed lncRNAs were performed. Many target genes involved in maintaining homeostasis or adapting to stress and stimuli were highly induced under heat stress. Several important regulatory pathways were involved in heat stress, including thyroid hormone signaling pathway, PI3K-Akt signaling pathway, estrogen signaling pathway, etc. This result broadens our understanding of lncRNA associated with heat stress and provides new insights into lncRNA-mediated regulation of rainbow trout heat stress.
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