Genetics Responses to Hypoxia and Reoxygenation Stress in Larimichthys crocea Revealed via Transcriptome Analysis and Weighted Gene Co-Expression Network

Zhang, Hongjie; Ding, Jie; Liu, Cheng; Luo, Shengyu; Gao, Xinming; Wu, Yuanjie; Wang, Jingqian; Wang, Xuelei; Wu, Xiongfei; Shen, Wei; Zhu, Junquan

doi:10.3390/ani11113021

Cited by 9 publications

(2 citation statements)

References 87 publications

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“…In these multiple procedures, oxygen is a vital element to transfer different lipid or carbohydrate into ATP for the survival and functioning of cells. And this pattern was also found in another WGCNA on hypoxia stress in Larimichthys crocea (Zhang et al, 2021).…”

Section: Discussionsupporting

confidence: 73%

Transcriptomic atlas for hypoxia and following re-oxygenation in Ancherythroculter nigrocauda heart and brain tissues: insights into gene expression, alternative splicing, and signaling pathways

Chen,

Hu,

et al. 2024

Front. Genet.

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Hypoxia is a mounting problem that affects the world’s freshwaters, with severe consequence for many species, including death and large economical loss. The hypoxia problem has increased recently due to the combined effects of water eutrophication and global warming. In this study, we investigated the transcriptome atlas for the bony fish Ancherythroculter nigrocauda under hypoxia for 1.5, 3, and 4.5 h and its recovery to normal oxygen levels in heart and brain tissues. We sequenced 21 samples for brain and heart tissues (a total of 42 samples) plus three control samples and obtained an average of 32.40 million raw reads per sample, and 95.24% mapping rate of the filtered clean reads. This robust transcriptome dataset facilitated the discovery of 52,428 new transcripts and 6,609 novel genes. In the heart tissue, the KEGG enrichment analysis showed that genes linked to the Vascular smooth muscle contraction and MAPK and VEGF signaling pathways were notably altered under hypoxia. Re-oxygenation introduced changes in genes associated with abiotic stimulus response and stress regulation. In the heart tissue, weighted gene co-expression network analysis pinpointed a module enriched in insulin receptor pathways that was correlated with hypoxia. Conversely, in the brain tissue, the response to hypoxia was characterized by alterations in the PPAR signaling pathway, and re-oxygenation influenced the mTOR and FoxO signaling pathways. Alternative splicing analysis identified an average of 27,226 and 28,290 events in the heart and brain tissues, respectively, with differential events between control and hypoxia-stressed groups. This study offers a holistic view of transcriptomic adaptations in A. nigrocauda heart and brain tissues under oxygen stress and emphasizes the role of gene expression and alternative splicing in the response mechanisms.

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Section: Discussionsupporting

confidence: 73%

Transcriptomic atlas for hypoxia and following re-oxygenation in Ancherythroculter nigrocauda heart and brain tissues: insights into gene expression, alternative splicing, and signaling pathways

Chen,

Hu,

et al. 2024

Front. Genet.

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“…Halting energyintensive genome duplication processes leverages time for macromolecular repair and allows for energy redirection [118]. Recovery from stressors on the other hand is accompanied by sustained repair processes [119], [120]. The ppp5c is a cross-tissue hub gene in our study involved in cell cycle arrest and DNA damage repair [121] shown dysregulated in sh under severe stress [122].…”

Section: Cellular Stress In Oxygen Minimum Zonementioning

confidence: 83%

Network-based integration of omics, physiological and environmental data in real-world Elbe estuarine Zander

Koll,

Theilen,

Hauten

et al. 2024

Preprint

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Coastal and estuarine environments are under endogenic and exogenic pressures jeopardizing survival and diversity of inhabiting biota. Information of possible synergistic effects of multiple (a)biotic stressors and holobiont interaction are largely missing in the Elbe estuary but are of importance to estimate unforeseen effects on animals’ physiology. Here, we seek to leverage host-transcriptional RNA-seq and gill mucus microbial 16S rRNA metabarcoding data coupled with physiological and abiotic measurements in a network analysis approach to deconvolute the impact of multiple stressors on the health of juvenile Sander lucioperca along one of the largest European estuaries. We find mesohaline areas characterized by gill tissue specific transcriptional responses matching osmosensing and tissue remodeling. Liver transcriptomes instead emphasized that zander from highly turbid areas were undergoing starvation which was supported by compromised body condition. Potential pathogenic bacteria, including Shewanella, Acinetobacter, Aeromonas and Chryseobacterium, dominated the gill microbiome along the freshwater transition and oxygen minimum zone. Their occurrence coincided with a strong adaptive and innate transcriptional immune response in host gill and enhanced energy demand in liver tissue supporting their potential pathogenicity. Overall, we demonstrate the information gain from integration of omics data into biomonitoring of fish and point out bacterial species with disease potential.

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Genome-wide association study identified candidate SNPs and genes associated with hypoxia tolerance in large yellow croaker (Larimichthys crocea)

et al. 2022

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Genetics Responses to Hypoxia and Reoxygenation Stress in Larimichthys crocea Revealed via Transcriptome Analysis and Weighted Gene Co-Expression Network

Cited by 9 publications

References 87 publications

Transcriptomic atlas for hypoxia and following re-oxygenation in Ancherythroculter nigrocauda heart and brain tissues: insights into gene expression, alternative splicing, and signaling pathways

Transcriptomic atlas for hypoxia and following re-oxygenation in Ancherythroculter nigrocauda heart and brain tissues: insights into gene expression, alternative splicing, and signaling pathways

Network-based integration of omics, physiological and environmental data in real-world Elbe estuarine Zander

Genome-wide association study identified candidate SNPs and genes associated with hypoxia tolerance in large yellow croaker (Larimichthys crocea)

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