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Yu D, Zhou M, Chen W, Ding Z, Wang C, Qian Y, Liu Y, He S, Yang L. Characterization of transcriptome changes in saline stress adaptation on Leuciscus merzbacheri using PacBio Iso-Seq and RNA-Seq. DNA Res 2024; 31:dsae019. [PMID: 38807352 PMCID: PMC11161863 DOI: 10.1093/dnares/dsae019] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2024] [Revised: 05/22/2024] [Accepted: 05/28/2024] [Indexed: 05/30/2024] Open
Abstract
Leuciscus merzbacheri is a native fish species found exclusively in the Junggar Basin in Xinjiang. It exhibits remarkable adaptability, thriving in varying water conditions such as the saline waters, the semi-saline water, and the freshwater. Despite its significant economic and ecological value, the underlying mechanisms of its remarkable salinity tolerance remain elusive. Our study marks the first time the full-length transcriptome of L. merzbacheri has been reported, utilizing RNA-Seq and PacBio Iso-Seq technologies. We found that the average length of the full-length transcriptome is 1,780 bp, with an N50 length of 2,358 bp. We collected RNA-Seq data from gill, liver, and kidney tissues of L. merzbacheri from both saline water and freshwater environments and conducted comparative analyses across these tissues. Further analysis revealed significant enrichment in several key functional gene categories and signalling pathways related to stress response and environmental adaptation. The findings provide a valuable genetic resource for further investigation into saline-responsive candidate genes, which will deepen our understanding of teleost adaptation to extreme environmental stress. This knowledge is crucial for the future breeding and conservation of native fish species.
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Affiliation(s)
- Dan Yu
- School of Ecology and Environment, Tibet University, Lhasa, 850000, China
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, China
| | - Min Zhou
- School of Life Sciences, Jianghan Universily, Wuhan 430056, China
| | - Wenjun Chen
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, China
- College of Advanced Agricultural Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Zufa Ding
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, China
- College of Fisheries, Huazhong Agricultural University, Wuhan, 430070, China
| | - Cheng Wang
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, China
- College of Advanced Agricultural Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yuting Qian
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, China
- College of Advanced Agricultural Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yang Liu
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, China
- College of Advanced Agricultural Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Shunping He
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, China
| | - Liandong Yang
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, China
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Dettleff P, Toloza C, Fuentes M, Aedo J, Zuloaga R, Estrada JM, Molina A, Valdés JA. Gills de novo assembly reveals oxidative stress, unfolded protein, and immune response on red cusk-eel (Genypterus chilensis) under thermal stress. MARINE ENVIRONMENTAL RESEARCH 2024; 196:106440. [PMID: 38479297 DOI: 10.1016/j.marenvres.2024.106440] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/17/2023] [Revised: 02/18/2024] [Accepted: 03/07/2024] [Indexed: 03/23/2024]
Abstract
The heat waves on the South Pacific coast could lead to thermal stress in native fish. The red cusk-eel (Genypterus chilensis) is relevant for Chilean artisanal fisheries and aquaculture diversification. This study examined the effect of high-temperature stress in the gills of G. chilensis in control (14 °C) and high-temperature stress (19 °C) conditions. High-temperature stress induces a significant increase in gills cortisol levels. Additionally, oxidative damage was observed in gills (protein carbonylation and lipoperoxidation). RNA-seq data was used to build the first transcriptome assembly of gills in this species (23,656 annotated transcripts). A total of 1138 down-regulated and 1531 up-regulated transcripts were observed in response to high-temperature stress in gills. The enrichment analysis showed immune response and replication enriched processes (on down-regulated transcripts), and processes related to the folding of proteins, endoplasmic reticulum, and transporter activity (on up-regulated transcripts). The present study showed how gills could be affected by high-temperature stress.
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Affiliation(s)
- Phillip Dettleff
- Escuela de Medicina Veterinaria, Facultad de Agronomía y Sistemas Naturales, Facultad de Ciencias Biológicas y Facultad de Medicina, Pontificia Universidad Católica de Chile, Santiago, 7820436, Chile.
| | - Carla Toloza
- Facultad de Ciencias de la Vida, Universidad Andrés Bello, Santiago, 8370186, Chile
| | - Marcia Fuentes
- Facultad de Ciencias de la Vida, Universidad Andrés Bello, Santiago, 8370186, Chile; Interdisciplinary Center for Aquaculture Research (INCAR), Concepción, 4030000, Chile
| | - Jorge Aedo
- Departamento de Biología y Química, Facultad de Ciencias Básicas, Universidad Católica del Maule, Talca, 3466706, Chile
| | - Rodrigo Zuloaga
- Facultad de Ciencias de la Vida, Universidad Andrés Bello, Santiago, 8370186, Chile; Interdisciplinary Center for Aquaculture Research (INCAR), Concepción, 4030000, Chile
| | - Juan Manuel Estrada
- Centro de Investigación Marina Quintay (CIMARQ), Universidad Andrés Bello, Quintay, 2340000, Chile
| | - Alfredo Molina
- Facultad de Ciencias de la Vida, Universidad Andrés Bello, Santiago, 8370186, Chile; Interdisciplinary Center for Aquaculture Research (INCAR), Concepción, 4030000, Chile
| | - Juan Antonio Valdés
- Facultad de Ciencias de la Vida, Universidad Andrés Bello, Santiago, 8370186, Chile; Interdisciplinary Center for Aquaculture Research (INCAR), Concepción, 4030000, Chile.
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Supplementation with Queen Bee Larva Powder Extended the Longevity of Caenorhabditis elegans. Nutrients 2022; 14:nu14193976. [PMID: 36235629 PMCID: PMC9573043 DOI: 10.3390/nu14193976] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2022] [Revised: 09/13/2022] [Accepted: 09/19/2022] [Indexed: 11/17/2022] Open
Abstract
Queen bee larva (QBL) is one kind of important edible insect that is harvested during royal jelly production process. QBL has many physiological functions; however, limited information is available regarding its antiaging effects. In this study, the antiaging function of freeze-dried QBL powder (QBLP) was investigated by combining the Caenorhabditis elegans (C. elegans) model and transcriptomics. The administration of QBLP to C. elegans was shown to improve lifespan parameters. Additionally, QBLP improved the mobility of nematodes. Transcriptome analysis showed the differentially expressed genes (DEGs) were significantly enriched in Gene Ontology (GO) terms that were almost all related to the biological functions of cell metabolism and stress, which are associated with lifespan. The Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis suggested that the lifespan of C. elegans was related to the longevity regulating pathway-worm. The expression levels of the key genes sod-3, gst-6, hsp-12.6, lips-7, ins-8, and lips-17 were upregulated. sod-3, hsp-12.6, lips-7, and lips-17 are downstream targets of DAF-16, which is an important transcription factor related to lifespan extension. CF1038 (daf-16(mu86)) supplemented with QBLP did not show a life-prolonging. This indicates that the antiaging function of QBLP is closely related to daf-16. Thus, QBLP is a component that could potentially be used as a functional material to ameliorate aging and aging-related symptoms.
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Zhao H, Wang Q, Zhao H, Chen C. Transcriptome profiles revealed high- and low-salinity water altered gill homeostasis in half-smooth tongue sole (Cynoglossus semilaevis). COMPARATIVE BIOCHEMISTRY AND PHYSIOLOGY. PART D, GENOMICS & PROTEOMICS 2022; 42:100989. [PMID: 35421665 DOI: 10.1016/j.cbd.2022.100989] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/24/2022] [Revised: 03/27/2022] [Accepted: 04/06/2022] [Indexed: 06/14/2023]
Abstract
Salinity is an important environmental factor that affects fish growth, development, and reproduction. As euryhaline fish, half-smooth tongue sole (Cynoglossus semilaevis) are a suitable species for deciphering the salinity adaptation mechanism of fish; however, the molecular mechanisms underlying low- and high-salinity responses remain unclear. In this study, RNA-seq was applied to characterize the genes and regulatory pathways involved in C. semilaevis gill responses to high- (32 ppt), low- (8 ppt), and control-salinity (24 ppt) water. Gills were rich in mitochondria-rich cells (MRCs) in high salinity. Compared with control, 2137 and 218 differentially expressed genes (DEGs) were identified in low and high salinity, respectively. The enriched functions of most DEGs were metabolism, ion transport, regulation of cell cycle, and immune response. The DEGs involved in oxidative phosphorylation, citrate cycle, and fatty acid metabolism were down-regulated in low salinity. For ion transport, high and low salinity significantly altered the expressions of prlr, ca12, and cftr. In cell cycle arrest and cellular repair, gadd45b, igfbp5, and igfbp2 were significantly upregulated in high and low salinity. For immune response, il10, il34, il12b, and crp increased in high and low salinity. Our findings suggested that alterations in material and energy metabolism, ions transport, cell cycle arrest, cellular repair, and immune response, are required to maintain C. semilaevis gill homeostasis under high and low salinity. This study provides insight into the divergence of C. semilaevis osmoregulation mechanisms acclimating to high and low salinity, which will serve as reference for the healthy culture of C. semilaevis.
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Affiliation(s)
- Huiyan Zhao
- Tianjin Key Laboratory of Aqua-Ecology and Aquaculture, Tianjin 300392, China; College of Fisheries, Tianjin Agricultural University, Tianjin 300392, China
| | - Qingkui Wang
- Tianjin Key Laboratory of Aqua-Ecology and Aquaculture, Tianjin 300392, China; College of Fisheries, Tianjin Agricultural University, Tianjin 300392, China.
| | - Honghao Zhao
- Tianjin Key Laboratory of Aqua-Ecology and Aquaculture, Tianjin 300392, China; College of Fisheries, Tianjin Agricultural University, Tianjin 300392, China
| | - Chengxun Chen
- Tianjin Key Laboratory of Aqua-Ecology and Aquaculture, Tianjin 300392, China; College of Fisheries, Tianjin Agricultural University, Tianjin 300392, China
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The time course of molecular acclimation to seawater in a euryhaline fish. Sci Rep 2021; 11:18127. [PMID: 34518569 PMCID: PMC8438076 DOI: 10.1038/s41598-021-97295-3] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2021] [Accepted: 08/17/2021] [Indexed: 11/25/2022] Open
Abstract
The Arabian pupfish, Aphanius dispar, is a euryhaline fish inhabiting both inland nearly-freshwater desert ponds and highly saline Red Sea coastal lagoons of the Arabian Peninsula. Desert ponds and coastal lagoons, located respectively upstream and at the mouths of dry riverbeds (“wadies”), have been found to potentially become connected during periods of intense rainfall, which could allow the fish to migrate between these different habitats. Flash floods would therefore flush Arabian pupfish out to sea, requiring a rapid acclimation to a greater than 40 ppt change in salinity. To investigate the molecular pathways of salinity acclimation during such events, a Red Sea coastal lagoon and a desert pond population were sampled, with the latter exposed to a rapid increase in water salinity. Changes in branchial gene expression were investigated via genome-wide transcriptome measurements over time from 6 h to 21 days. The two natural populations displayed basal differences in genes related to ion transport, osmoregulation and immune system functions. These mechanisms were also differentially regulated in seawater transferred fish, revealing their crucial role in long-term adaptation. Other processes were only transiently activated shortly after the salinity exposure, including cellular stress response mechanisms, such as molecular chaperone synthesis and apoptosis. Tissue remodelling processes were also identified as transient, but took place later in the timeline, suggesting their importance to long-term acclimation as they likely equip the fish with lasting adaptations to their new environment. The alterations in branchial functional pathways displayed by Arabian pupfish in response to salinity increases are diverse. These reveal a large toolkit of molecular processes important for adaptation to hyperosmolarity that allow for successful colonization to a wide variety of different habitats.
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Li J, Xue L, Cao M, Zhang Y, Wang Y, Xu S, Zheng B, Lou Z. Gill transcriptomes reveal expression changes of genes related with immune and ion transport under salinity stress in silvery pomfret (Pampus argenteus). FISH PHYSIOLOGY AND BIOCHEMISTRY 2020; 46:1255-1277. [PMID: 32162151 DOI: 10.1007/s10695-020-00786-9] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/09/2019] [Accepted: 03/02/2020] [Indexed: 06/10/2023]
Abstract
Salinity is a major ecological factor in the marine environment, and extremely important for the survival, development, and growth of fish. In this study, gill transcriptomes were examined by high-throughput sequencing at three different salinities (12 ppt as low salinity, 22 ppt as control salinity, and 32 ppt as high salinity) in an importantly economical fish silvery pomfret. A total of 187 genes were differentially expressed, including 111 up-regulated and 76 down-regulated transcripts in low-salinity treatment group and 107 genes differentially expressed, including 74 up-regulated and 33 down-regulated transcripts in high-salinity treatment group compared with the control group, respectively. Some pathways including NOD-like receptor signaling pathway, cytokine-cytokine receptor interaction, Toll-like receptor pathway, cardiac muscle contraction, and vascular smooth muscle contraction were significantly enriched. qPCR analysis further confirmed that mRNA expression levels of immune (HSP90A, IL-1β, TNFα, TLR2, IP-10, MIG, CCL19, and IL-11) and ion transport-related genes (WNK2, NPY2R, CFTR, and SLC4A2) significantly changed under salinity stress. Low salinity stress caused more intensive expression changes of immune-related genes than high salinity. These results imply that salinity stress may affect immune function in addition to regulating osmotic pressure in silvery pomfret.
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Affiliation(s)
- Juan Li
- College of Marine Science, Ningbo University, 169 Qixing South Road, Meishan Bonded Port, Ningbo, 315832, Zhejiang, People's Republic of China
| | - Liangyi Xue
- College of Marine Science, Ningbo University, 169 Qixing South Road, Meishan Bonded Port, Ningbo, 315832, Zhejiang, People's Republic of China.
- Collaborative Innovation Center for Zhejiang Marine High-Efficiency and Healthy Aquaculture, Ningbo University, Ningbo, Zhejiang, People's Republic of China.
| | - Mingyue Cao
- College of Marine Science, Ningbo University, 169 Qixing South Road, Meishan Bonded Port, Ningbo, 315832, Zhejiang, People's Republic of China
| | - Yu Zhang
- College of Marine Science, Ningbo University, 169 Qixing South Road, Meishan Bonded Port, Ningbo, 315832, Zhejiang, People's Republic of China
| | - Yajun Wang
- College of Marine Science, Ningbo University, 169 Qixing South Road, Meishan Bonded Port, Ningbo, 315832, Zhejiang, People's Republic of China
| | - Shanliang Xu
- College of Marine Science, Ningbo University, 169 Qixing South Road, Meishan Bonded Port, Ningbo, 315832, Zhejiang, People's Republic of China
| | - Baoxiao Zheng
- College of Marine Science, Ningbo University, 169 Qixing South Road, Meishan Bonded Port, Ningbo, 315832, Zhejiang, People's Republic of China
| | - Zhengjia Lou
- College of Marine Science, Ningbo University, 169 Qixing South Road, Meishan Bonded Port, Ningbo, 315832, Zhejiang, People's Republic of China
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