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Kumar PV, Rasal KD, Acharya A, Dey D, Sonwane AA, Reang D, Rajeshkannan R, Pawar SS, Kurade NP, Bhendarkar MP, Krishnani KK, Nagpure NS, Brahmane MP. Muscle Transcriptome Sequencing Revealed Thermal Stress-Responsive Regulatory Genes in Farmed Rohu, Labeo rohita (Hamilton, 1822). MARINE BIOTECHNOLOGY (NEW YORK, N.Y.) 2023; 25:1057-1075. [PMID: 37878212 DOI: 10.1007/s10126-023-10259-8] [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: 08/16/2023] [Accepted: 10/09/2023] [Indexed: 10/26/2023]
Abstract
Rohu, Labeo rohita, is one of the most important aquaculture species in the Indian subcontinent. Understanding the molecular-level physiological responses to thermal stress or climate change is essential. In the present work, transcriptome sequencing was carried out in the muscle tissue of the rohu in response to heat stress (35 °C) in comparison with the control (28 °C). A total of 125 Gb of sequence data was generated, and the raw-reads were filtered and trimmed, which resulted in 484 million quality reads. Reference-based assembly of reads was performed using L. rohita genome, and a total of 90.17% of reads were successfully mapped. A total of 37,462 contigs were assembled with an N50 value of 1854. The differential expression analysis revealed a total of 107 differentially expressed genes (DEGs) (15 up-, 37 down-, and 55 neutrally regulated) as compared to the control group (Log2FC > 2, P < 0.05). Gene enrichment analysis of DEGs indicates that transcripts were associated with molecular, biological, and cellular activities. The randomly selected differentially expressed transcripts were validated by RT-qPCR and found consistent expression patterns in line with the RNA-seq data. Several transcripts such as SERPINE1(HSP47), HSP70, HSP90alpha, Rano class II histocompatibility A beta, PGC-1 and ERR-induced regulator, proto-oncogene c-Fos, myozenin2, alpha-crystallin B chain-like protein, angiopoietin-like protein 8, and acetyl-CoA carboxylases have been identified in muscle tissue of rohu that are associated with stress/immunity. This study identified the key biomarker SERPINE1 (HSP47), which showed significant upregulation (~ 2- to threefold) in muscle tissue of rohu exposed to high temperature. This study can pave a path for the identification of stress-responsive biomarkers linked with thermal adaptations in the farmed carps.
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Affiliation(s)
- Pokanti Vinay Kumar
- ICAR - Central Institute of Fisheries Education, Mumbai, Maharashtra, 400061, India
| | - Kiran D Rasal
- ICAR - Central Institute of Fisheries Education, Mumbai, Maharashtra, 400061, India
| | - Arpit Acharya
- ICAR - Central Institute of Fisheries Education, Mumbai, Maharashtra, 400061, India
| | - Diganta Dey
- ICAR - Central Institute of Fisheries Education, Mumbai, Maharashtra, 400061, India
| | - Arvind A Sonwane
- ICAR - Central Institute of Fisheries Education, Mumbai, Maharashtra, 400061, India
| | - Dhalongsaih Reang
- ICAR - Central Institute of Fisheries Education, Mumbai, Maharashtra, 400061, India
| | - R Rajeshkannan
- ICAR - Central Institute of Fisheries Education, Mumbai, Maharashtra, 400061, India
| | - Sachin S Pawar
- School of Atmospheric Stress Management, ICAR - National Institute of Abiotic Stress Management, Baramati, Pune, Maharashtra, 413115, India
| | - Nitin P Kurade
- School of Atmospheric Stress Management, ICAR - National Institute of Abiotic Stress Management, Baramati, Pune, Maharashtra, 413115, India
| | - Mukesh P Bhendarkar
- School of Atmospheric Stress Management, ICAR - National Institute of Abiotic Stress Management, Baramati, Pune, Maharashtra, 413115, India
| | - Kishore K Krishnani
- ICAR - Central Institute of Fisheries Education, Mumbai, Maharashtra, 400061, India
- School of Atmospheric Stress Management, ICAR - National Institute of Abiotic Stress Management, Baramati, Pune, Maharashtra, 413115, India
| | - Naresh S Nagpure
- ICAR - Central Institute of Fisheries Education, Mumbai, Maharashtra, 400061, India
| | - Manoj P Brahmane
- ICAR - Central Institute of Fisheries Education, Mumbai, Maharashtra, 400061, India.
- School of Atmospheric Stress Management, ICAR - National Institute of Abiotic Stress Management, Baramati, Pune, Maharashtra, 413115, India.
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Liu Z, Zhou T, Gao D. Genetic and epigenetic regulation of growth, reproduction, disease resistance and stress responses in aquaculture. Front Genet 2022; 13:994471. [PMID: 36406125 PMCID: PMC9666392 DOI: 10.3389/fgene.2022.994471] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2022] [Accepted: 10/20/2022] [Indexed: 11/25/2022] Open
Abstract
Major progress has been made with genomic and genetic studies in aquaculture in the last decade. However, research on epigenetic regulation of aquaculture traits is still at an early stage. It is apparent that most, if not all, aquaculture traits are regulated at both genetic and epigenetic levels. This paper reviews recent progress in understanding of genetic and epigenetic regulation of important aquaculture traits such as growth, reproduction, disease resistance, and stress responses. Although it is challenging to make generalized statements, DNA methylation is mostly correlated with down-regulation of gene expression, especially when at promoters and enhancers. As such, methylation of growth factors and their receptors is negatively correlated with growth; hypomethylation of genes important for stress tolerance is correlated with increased stress tolerance; hypomethylation of genes important for male or female sex differentiation leads to sex differentiation into males or females, respectively. It is apparent that environmental regulation of aquaculture traits is mediated at the level of epigenetic regulation, and such environment-induced epigenetic changes appeared to be intergenerationally inherited, but evidences for transgenerational inheritance are still limited.
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Affiliation(s)
- Zhanjiang Liu
- Department of Biology, College of Arts and Sciences, Syracuse University, Syracuse, NY, United States,*Correspondence: Zhanjiang Liu,
| | - Tao Zhou
- Fujian Key Laboratory of Genetics and Breeding of Marine Organisms, College of Ocean and Earth Sciences, Xiamen University, Xiamen, China
| | - Dongya Gao
- Department of Biology, College of Arts and Sciences, Syracuse University, Syracuse, NY, United States
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Ignatz EH, Hori TS, Kumar S, Benfey TJ, Braden LM, Runighan CD, Westcott JD, Rise ML. RNA-Seq Analysis of the Growth Hormone Transgenic Female Triploid Atlantic Salmon (Salmo salar) Hepatic Transcriptome Reveals Broad Temperature-Mediated Effects on Metabolism and Other Biological Processes. Front Genet 2022; 13:852165. [PMID: 35677560 PMCID: PMC9168996 DOI: 10.3389/fgene.2022.852165] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2022] [Accepted: 05/02/2022] [Indexed: 12/13/2022] Open
Abstract
This study examined the impact of rearing temperature (10.5, 13.5 or 16.5°C) on the hepatic transcriptome of AquAdvantage Salmon (growth hormone transgenic female triploid Atlantic salmon) at an average weight of 800 g. Six stranded PE libraries were Illumina-sequenced from each temperature group, resulting in an average of over 100 M raw reads per individual fish. RNA-sequencing (RNA-seq) results showed the greatest difference in the number of differentially expressed transcripts (1750 DETs), as revealed by both DESeq2 and edgeR (q < 0.05; fold-change > |1.5|), was between the 10.5 and 16.5°C temperature groups. In contrast, 172 and 52 DETs were found in the 10.5 vs. 13.5°C and the 13.5 vs. 16.5°C comparisons, respectively. Considering the DETs between the 10.5 and 16.5°C groups, 282 enriched gene ontology (GO) terms were identified (q < 0.05), including “response to stress”, “immune system process”, “lipid metabolic process”, “oxidation-reduction process”, and “cholesterol metabolic process”, suggesting elevated temperature elicited broad effects on multiple biological systems. Pathway analysis using ClueGO showed additional impacts on amino acid and lipid metabolism. There was a significant positive correlation between RNA-seq and real-time quantitative polymerase chain reaction (RT-qPCR) results for 8 of 9 metabolic-related transcripts tested. RT-qPCR results also correlated to changes in fillet tissue composition previously reported in these salmon (e.g., methionine and lysine concentrations positively correlated with hsp90ab1 transcript expression), suggesting that rearing temperature played a significant role in mediating metabolic/biosynthetic pathways of AquAdvantage Salmon. Many transcripts related to lipid/fatty acid metabolism (e.g., elovl2, fabpi, hacd2, mgll, s27a2, thrsp) were downregulated at 16.5°C compared to both other temperature groups. Additionally, enrichment of stress-, apoptosis- and catabolism-relevant GO terms at 16.5°C suggests that this temperature may not be ideal for commercial production when using freshwater recirculating aquaculture systems (RAS). This study relates phenotypic responses to transcript-specific findings and therefore aids in the determination of an optimal rearing temperature for AquAdvantage Salmon. With approval to grow and sell AquAdvantage Salmon in the United States and Canada, the novel insights provided by this research can help industry expansion by promoting optimal physiological performance and health.
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Affiliation(s)
- Eric H. Ignatz
- Department of Ocean Sciences, Memorial University of Newfoundland and Labrador, St. John’s, NL, Canada
- *Correspondence: Eric H. Ignatz, ; Matthew L. Rise,
| | | | - Surendra Kumar
- Department of Ocean Sciences, Memorial University of Newfoundland and Labrador, St. John’s, NL, Canada
| | - Tillmann J. Benfey
- Department of Biology, University of New Brunswick, Fredericton, NB, Canada
| | - Laura M. Braden
- AquaBounty Canada, Inc., Souris, PE, Canada
- Department of Pathology and Microbiology, Atlantic Veterinary College, University of Prince Edward Island, Charlottetown, PE, Canada
| | | | - Jillian D. Westcott
- Fisheries and Marine Institute, Memorial University of Newfoundland and Labrador, St. John’s, NL, Canada
| | - Matthew L. Rise
- Department of Ocean Sciences, Memorial University of Newfoundland and Labrador, St. John’s, NL, Canada
- *Correspondence: Eric H. Ignatz, ; Matthew L. Rise,
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Lai Z, Zhao W, Lu Y, Wu L, Yang C, Wang Q. Characterization of transcription factor activator pretein-1 (AP-1) and its association with cold tolerance in Pinctada fucata martensii. FISH & SHELLFISH IMMUNOLOGY 2022; 124:572-578. [PMID: 35483598 DOI: 10.1016/j.fsi.2022.04.014] [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: 12/28/2021] [Revised: 04/06/2022] [Accepted: 04/11/2022] [Indexed: 06/14/2023]
Abstract
AP-1 is an important transcription factor for cell proliferation/differentiation and animal immunity/development; however, its role in research in shellfish is poorly understood. Here, the cDNA of AP-1 gene from Pinctada fucata martensii was characterized. Its expression was detected in all six examined tissues, and a high level was observed in the gill and hepatopancreas. Analysis of the developmental transcriptomes showed that the PmAP-1 gene expression levels were high during D-stage larval and spat stages. The gene also exhibited a significantly high expression under cold tolerance stress. SNP analysis of the exon region and 5' flanking region of PmAP-1 revealed 19 SNPs of which 8 showed significant differences between cold tolerance selection line and base stock. Furthermore, three haplotypes generated by the SNPs of PmAP-1 were significantly associated with cold tolerance, respectively.These results suggest that the PmAP-1 gene plays an important role in the response of P. f. martensii to low temperature stress. These SNPs and haplotypes of PmAP-1 may be related to the cold tolerance of P. f. martensii, and could be candidate markers potentially for further selective breeding.
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Affiliation(s)
- Zhuoxin Lai
- Fisheries College, Guangdong Ocean University, Zhanjiang, 524088, China
| | - Wei Zhao
- BGI Genomics, BGI-Shenzhen, Shenzhen, 518083, China
| | - Yingying Lu
- Fisheries College, Guangdong Ocean University, Zhanjiang, 524088, China
| | - Lingjun Wu
- Fisheries College, Guangdong Ocean University, Zhanjiang, 524088, China
| | - Chuangye Yang
- Fisheries College, Guangdong Ocean University, Zhanjiang, 524088, China; Guangdong Science and Innovation Center for Pearl Culture, Zhanjiang, 524088, China; Guangdong Provincial Engineering Laboratory for Mariculture Organism Breeding, Zhanjiang, 524088, China; Guangdong Provincial Key Laboratory of Pathogenic Biology and Epidemiology for Aquatic Economic Animals, Zhanjiang, 524088, China
| | - Qingheng Wang
- Fisheries College, Guangdong Ocean University, Zhanjiang, 524088, China; Guangdong Science and Innovation Center for Pearl Culture, Zhanjiang, 524088, China; Guangdong Provincial Engineering Laboratory for Mariculture Organism Breeding, Zhanjiang, 524088, China; Guangdong Provincial Key Laboratory of Pathogenic Biology and Epidemiology for Aquatic Economic Animals, Zhanjiang, 524088, China.
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Pandey A, Rajesh M, Baral P, Sarma D, Tripathi PH, Akhtar MS, Ciji A, Dubey MK, Pande V, Sharma P, Kamalam BS. Concurrent changes in thermal tolerance thresholds and cellular heat stress response reveals novel molecular signatures and markers of high temperature acclimation in rainbow trout. J Therm Biol 2021; 102:103124. [PMID: 34863487 DOI: 10.1016/j.jtherbio.2021.103124] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2021] [Revised: 10/27/2021] [Accepted: 10/30/2021] [Indexed: 01/31/2023]
Abstract
The objective of this study was to better understand the molecular mechanisms which regulate acclimatory responses and thermal safety margins of rainbow trout (Oncorhynchus mykiss) at temperatures above physiological optimum. For this, we investigated the time course of changes in critical thermal tolerance thresholds and associated hepatic and renal transcript abundance of molecular markers related to cellular stress response, during high temperature acclimation. The experimental fish were initially acclimated to 17 °C and later exposed to a gradually raised elevated temperature regime (22 °C) for a period of 30 days. CTmax, CTmin and mRNA expression of candidate markers were examined before the thermal challenge (T0) and over the time-course (days) of high temperature exposure (T1, T3, T7, T15 and T30). With respect to organismal response, CTmax was significantly elevated at T3, but the degree of gain in heat tolerance was not persistent. Contrarily, we observed a gradual loss in cold tolerance with highest CTmin estimate at T30. Based on the time-course of mRNA expression, the studied markers could be categorized into those which were persistently elevated (hsp70a, hsp70b, hspa5, hsp90a, hsp90b, stip1 and serpinh1 in kidney and hsp90b in liver); those which concurred with changes in CTmin (hspbp1, hsp90b, stip1, gr1, hif1a, hyou1, tnfa and tlr5 in kidney); and those which concurred with changes in CTmax (hsp90a, serpinh1, tlr5 and lmo2 in liver). Apparently, transcriptional changes in kidney and liver reflected CTmin and CTmax trend, respectively. Expression profile of stip1 and tlr5 suggest that they are potential novel markers which could reflect thermal limits in rainbow trout. Hepatic metabolic markers were either initially elevated (alt, glud, g6pase1) or down-regulated at different time-points (ast2, gls1, fas, cpt1b, mtor), linked to gluconeogenesis and metabolic depression, respectively. Whereas, growth-axis markers showed no significant differences. Overall, this time-course analysis has revealed potential associations in organismal and tissue-specific cellular response to high temperature acclimation in a thermally sensitive coldwater ectotherm.
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Affiliation(s)
- Anupam Pandey
- ICAR-Directorate of Coldwater Fisheries Research, Bhimtal, 263136, Uttarakhand, India; Department of Biotechnology, Kumaun University, Bhimtal, 263136, Uttarakhand, India
| | - Manchi Rajesh
- ICAR-Directorate of Coldwater Fisheries Research, Bhimtal, 263136, Uttarakhand, India
| | - Pratibha Baral
- ICAR-Directorate of Coldwater Fisheries Research, Bhimtal, 263136, Uttarakhand, India
| | - Debajit Sarma
- ICAR-Directorate of Coldwater Fisheries Research, Bhimtal, 263136, Uttarakhand, India
| | - Priyanka H Tripathi
- ICAR-Directorate of Coldwater Fisheries Research, Bhimtal, 263136, Uttarakhand, India; Department of Biotechnology, Kumaun University, Bhimtal, 263136, Uttarakhand, India
| | - Md Shahbaz Akhtar
- ICAR-Directorate of Coldwater Fisheries Research, Bhimtal, 263136, Uttarakhand, India
| | - Alexander Ciji
- ICAR-Directorate of Coldwater Fisheries Research, Bhimtal, 263136, Uttarakhand, India
| | - Maneesh Kumar Dubey
- ICAR-Directorate of Coldwater Fisheries Research, Bhimtal, 263136, Uttarakhand, India
| | - Veena Pande
- Department of Biotechnology, Kumaun University, Bhimtal, 263136, Uttarakhand, India
| | - Prakash Sharma
- ICAR-Directorate of Coldwater Fisheries Research, Bhimtal, 263136, Uttarakhand, India
| | - Biju Sam Kamalam
- ICAR-Directorate of Coldwater Fisheries Research, Bhimtal, 263136, Uttarakhand, India.
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Cooper RD, Shaffer HB. Allele-specific expression and gene regulation help explain transgressive thermal tolerance in non-native hybrids of the endangered California tiger salamander (Ambystoma californiense). Mol Ecol 2021; 30:987-1004. [PMID: 33338297 DOI: 10.1111/mec.15779] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2019] [Revised: 11/30/2020] [Accepted: 12/11/2020] [Indexed: 01/26/2023]
Abstract
Hybridization between native and non-native species is an ongoing global conservation threat. Hybrids that exhibit traits and tolerances that surpass parental values are of particular concern, given their potential to outperform native species. Effective management of hybrid populations requires an understanding of both physiological performance and the underlying mechanisms that drive transgressive hybrid traits. Here, we explore several aspects of the hybridization between the endangered California tiger salamander (Ambystoma californiense; CTS) and the introduced barred tiger salamander (Ambystoma mavortium; BTS). We assayed critical thermal maximum (CTMax) to compare the ability of CTS, BTS and F1 hybrids to tolerate acute thermal stress, and found that hybrids exhibit a wide range of CTMax values, with 33% (4/12) able to tolerate temperatures greater than either parent. We then quantified the genomic response, measured at the RNA transcript level, of each salamander, to explore the mechanisms underlying thermal tolerance strategies. We found that CTS and BTS have strikingly different values and tissue-specific patterns of overall gene expression, with hybrids expressing intermediate values. F1 hybrids display abundant and variable degrees of allele-specific expression (ASE), likely arising from extensive compensatory evolution in gene regulatory mechanisms between CTS and BTS. We found evidence that the proportion of genes with allelic imbalance in individual hybrids correlates with their CTMax, suggesting a link between ASE and expanded thermal tolerance that may contribute to the success of hybrid salamanders in California. Future climate change may further complicate management of CTS if hybrid salamanders are better equipped to deal with rising temperatures.
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Affiliation(s)
- Robert D Cooper
- Department of Ecology and Evolutionary Biology, University of California, Los Angeles, CA, USA.,La Kretz Center for California Conservation Science, Institute of the Environment and Sustainability, University of California, Los Angeles, CA, USA
| | - H Bradley Shaffer
- Department of Ecology and Evolutionary Biology, University of California, Los Angeles, CA, USA.,La Kretz Center for California Conservation Science, Institute of the Environment and Sustainability, University of California, Los Angeles, CA, USA
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Comparative Analysis of the Transcriptome and Distribution of Putative SNPs in Two Rainbow Trout ( Oncorhynchus mykiss) Breeding Strains by Using Next-Generation Sequencing. Genes (Basel) 2020; 11:genes11080841. [PMID: 32722051 PMCID: PMC7464081 DOI: 10.3390/genes11080841] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2020] [Revised: 07/22/2020] [Accepted: 07/23/2020] [Indexed: 11/24/2022] Open
Abstract
Selective breeding can significantly improve the establishment of sustainable and profitable aquaculture fish farming. For rainbow trout (Oncorhynchus mykiss), one of the main aquaculture coldwater species in Europe, a variety of selected hatchery strains are commercially available. In this study, we investigated the genetic variation between the local Born strain, selected for survival, and the commercially available Silver Steelhead strain, selected for growth. We sequenced the transcriptome of six tissues (gills, head kidney, heart, liver, spleen, and white muscle) from eight healthy individuals per strain, using RNA-seq technology to identify strain-specific gene-expression patterns and single nucleotide polymorphisms (SNPs). In total, 1760 annotated genes were differentially expressed across all tissues. Pathway analysis assigned them to different gene networks. We also identified a set of SNPs, which are heterozygous for one of the two breeding strains: 1229 of which represent polymorphisms over all tissues and individuals. Our data indicate a strong genetic differentiation between Born and Silver Steelhead trout, despite the relatively short time of evolutionary separation of the two breeding strains. The results most likely reflect their specifically adapted genotypes and might contribute to the understanding of differences regarding their robustness toward high stress and pathogenic challenge described in former studies.
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Aedo JE, Zuloaga R, Bastías-Molina M, Meneses C, Boltaña S, Molina A, Valdés JA. Early transcriptomic responses associated with the membrane-initiated action of cortisol in the skeletal muscle of rainbow trout (Oncorhynchus mykiss). Physiol Genomics 2019; 51:596-606. [DOI: 10.1152/physiolgenomics.00042.2019] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Cortisol is a critical neuroendocrine regulator of the stress response in fish. Cortisol practically affects all tissues by interacting with an intracellular receptor and modulating target gene expression. However, cortisol also interacts with components of the plasma membrane in a nongenomic process that activates rapid signaling. Until now, the implication of this novel cortisol signaling for the global transcriptional response has not been explored. In the present work, we evaluated the effects of the membrane-initiated actions of cortisol on the in vivo transcriptome of rainbow trout ( Oncorhynchus mykiss) skeletal muscle. RNA-Seq analyses were performed to examine the transcriptomic changes in rainbow trout stimulated by physiological concentrations of cortisol and cortisol coupled with bovine serum albumin (cortisol-BSA), a membrane-impermeable analog of cortisol. A total of 660 million paired-ends reads were generated. Reads mapped onto the reference genome revealed that 1,737; 897; and 1,012 transcripts were differentially expressed after 1, 3, and 9 h of cortisol-BSA treatment, respectively. Gene Ontology analysis showed that this novel action of cortisol modulates several biological processes, such as mRNA processing, ubiquitin-dependent protein catabolic processes, and transcription regulation. In addition, a KEGG analysis revealed that focal adhesion was the main signaling pathway that was upregulated at all the times tested. Taking these results together, we propose that the membrane-initiated cortisol action contributes significantly in the regulation of stress-mediated gene expression.
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Affiliation(s)
- Jorge E. Aedo
- Universidad Andrés Bello, Departamento Ciencias Biológicas, Facultad de Ciencias de la Vida, Santiago, Chile
- Interdisciplinary Center for Aquaculture Research (INCAR), Concepción, Chile
| | - Rodrigo Zuloaga
- Universidad Andrés Bello, Departamento Ciencias Biológicas, Facultad de Ciencias de la Vida, Santiago, Chile
| | - Macarena Bastías-Molina
- Universidad Andrés Bello, Centro de Biotecnología Vegetal, FONDAP Center for Genome Regulation, Facultad de Ciencias de la Vida, Santiago, Chile
| | - Claudio Meneses
- Universidad Andrés Bello, Centro de Biotecnología Vegetal, FONDAP Center for Genome Regulation, Facultad de Ciencias de la Vida, Santiago, Chile
| | - Sebastián Boltaña
- Interdisciplinary Center for Aquaculture Research (INCAR), Concepción, Chile
- Universidad de Concepción, ThermoFish Lab, Biotechnology Center, Concepción, Chile
| | - Alfredo Molina
- Universidad Andrés Bello, Departamento Ciencias Biológicas, Facultad de Ciencias de la Vida, Santiago, Chile
- Universidad de Concepción, ThermoFish Lab, Biotechnology Center, Concepción, Chile
| | - Juan Antonio Valdés
- Universidad Andrés Bello, Departamento Ciencias Biológicas, Facultad de Ciencias de la Vida, Santiago, Chile
- Universidad de Concepción, ThermoFish Lab, Biotechnology Center, Concepción, Chile
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Transcriptome Analysis of Yamame ( Oncorhynchus masou) in Normal Conditions after Heat Stress. BIOLOGY 2019; 8:biology8020021. [PMID: 30934851 PMCID: PMC6628215 DOI: 10.3390/biology8020021] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/07/2019] [Revised: 03/25/2019] [Accepted: 03/25/2019] [Indexed: 12/18/2022]
Abstract
Understanding the mechanism of high-temperature tolerance in cold-freshwater fish is crucial for predicting how certain species will cope with global warming. In this study, we investigated temperature tolerance in masu salmon (Oncorhynchus masou, known in Japan as ‘yamame’), an important aquaculture species. By selective breeding, we developed a group of yamame (F2) with high-temperature tolerance. This group was subjected to a high-temperature tolerance test and divided into two groups: High-temperature tolerant (HT) and non-high-temperature tolerant (NT). RNA was extracted from the gill and adipose fin tissues of each group, and the mRNA expression profiles were analyzed using RNA sequencing. A total of 2893 differentially expressed genes (DEGs) from the gill and 836 from the adipose fin were identified by comparing the HT and NT groups. Functional analyses were then performed to identify associated gene ontology (GO) terms and the Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways. The HT group showed a high expression of heat shock protein 70 (HSP70) gene and enriched gene expression in the extracellular matrix (ECM), cell junction, and adhesion pathways in gill tissues compared to the NT group. The HT group also exhibited highly expressed genes in glycolysis and showed lower expression of the genes in the p53 signaling pathway in adipose fin tissues. Taken together, the difference of expression of some genes in the normal condition may be responsible for the difference in heat tolerance between the HT and NT yamame in the heat stress condition.
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Identification and characterization of microRNAs in the liver of rainbow trout in response to heat stress by high-throughput sequencing. Gene 2018; 679:274-281. [DOI: 10.1016/j.gene.2018.09.012] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2017] [Revised: 08/30/2018] [Accepted: 09/06/2018] [Indexed: 01/30/2023]
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Huang J, Li Y, Liu Z, Kang Y, Wang J. Transcriptomic responses to heat stress in rainbow trout Oncorhynchus mykiss head kidney. FISH & SHELLFISH IMMUNOLOGY 2018; 82:32-40. [PMID: 30077801 DOI: 10.1016/j.fsi.2018.08.002] [Citation(s) in RCA: 56] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/17/2018] [Revised: 07/24/2018] [Accepted: 08/01/2018] [Indexed: 05/20/2023]
Abstract
Rainbow trout (Oncorhynchus mykiss) are widely cultured throughout the word for commercial aquaculture. However, as a cold-water species, rainbow trout are highly susceptible to heat stress, which may cause pathological signs or diseases by alleviating the immune roles and then lead to mass mortality. Understanding the molecular mechanisms that occur in the rainbow trout in response to heat stress will be useful to decrease heat stress-related morbidity and mortality in trout aquaculture. In the present study, we conducted transcriptome analysis of head kidney tissue in rainbow trout under heat-stress (24 °C) and control (18 °C) conditions, to identify heat stress-induced genes and pathways. More than 281 million clean reads were generated from six head kidney libraries. Using an adjusted P-value of P < 0.05 as the threshold, a total of 443 differentially expressed genes (DEGs) were identified, including members of the HSP90, HSP70, HSP60, and HSP40 family and several cofactors or cochaperones. The RNA-seq results were confirmed by RT-qPCR. Gene ontology and Kyoto Encyclopedia of Genes and Genomes enrichment analysis of DEGs were performed. Many genes involved in maintaining homeostasis or adapting to stress and stimuli were highly induced in response to high temperature. The most significantly enriched pathway was "Protein processing in endoplasmic reticulum (ER)", a quality control system that ensures correct protein folding or degradation of misfolded polypeptides by ER-associated degradation. Other signaling pathways involved in regulation of immune system and post-transcriptional regulation of spliceosome were also critical for thermal adaptation. These findings improve our understanding of the molecular mechanisms of heat stress responses and are useful to develop strategies for the improvement of rainbow trout survival rate during summer high-temperature period.
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Affiliation(s)
- Jinqiang Huang
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, 730070, China
| | - Yongjuan Li
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, 730070, China; College of Science, Gansu Agricultural University, Lanzhou, 730070, China
| | - Zhe Liu
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, 730070, China.
| | - Yujun Kang
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, 730070, China
| | - Jianfu Wang
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, 730070, China
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Danion M, Le Floch S, Cabon J, Louboutin L, Morin T. Transchem project - Part II: Transgenerational effects of long-term exposure to pendimethalin at environmental concentrations on the early development and viral pathogen susceptibility of rainbow trout (Oncorhynchus mykiss). AQUATIC TOXICOLOGY (AMSTERDAM, NETHERLANDS) 2018; 202:126-135. [PMID: 30025381 DOI: 10.1016/j.aquatox.2018.07.003] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/22/2018] [Revised: 06/27/2018] [Accepted: 07/03/2018] [Indexed: 06/08/2023]
Abstract
In the Transchem project, rainbow trout genitors were exposed to environmental concentrations of pendimethalin over a period of 18 months and two new first generations of offspring, F1_2013 and F1_2014, were obtained. We investigated the impact of direct chemical exposure on juveniles as well as the potential cumulative transgenerational and direct effects on the larval development and on the pathogen susceptibility of offspring. Depending on the chemical treatment or not of the adults, their offspring were distributed in the tanks of our experimental system, in two batches i.e. juveniles from the control genitors (G-) and others from the contaminated ones (G+), and then, half of the tanks were exposed daily to pendimethalin (Off+) while the others were used as controls (Off-). Viral challenges were performed on the offspring, before and after three months of direct chemical exposure, with strains of infectious hematopoietic necrosis virus (IHNV), viral haemorrhagic septicemia virus (VHSV) and sleeping disease alphavirus (SDV). Direct and transgenerational macroscopic effects were observed on offspring, with a percentage of abnormalities in offspring derived from the genitors exposed to pendimethalin (G+) significantly higher compared to those from the genitors from non-exposed group (G-). Before the direct chemical exposure, similar kinetics of mortality was observed between the offspring from the contaminated or control genitors after VHSV infection. With IHNV, the G+ group died in a slightly larger proportion compared to the G- group and seroconversion was greater for the G- group. For the SDV challenge, the mortality was delayed for the G+ offspring compared to the G- and seroconversion reached 65% in the G+ group compared to 45% in the G-, with similar antibody titres. After three months of direct chemical exposure, kinetics of mortality induced by IHNV infection were similar for all groups studied. Infection with SDV resulted in a cumulative mortality of 40% for the G- groups (Off- and Off+), significantly higher than those observed from the contaminated genitors G+. Proportion of seropositivity for SDV varied from 24 to 47% depending on the group, with very low quantities of secreted antibodies. Lastly, the direct exposure of offspring could impact the capacity of fish to adapt their haematological parameters to environmental and physiological changes, and underlines the potential toxic effects on the next generations.
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Affiliation(s)
- Morgane Danion
- French Agency for Food, Environmental and Occupational Health & Safety (ANSES), Ploufragan-Plouzané Laboratory, Fish Viral Pathology Unit, Technopôle Brest-Iroise, 29280 Plouzané, France; European University of Brittany, France.
| | - Stéphane Le Floch
- Centre of Documentation, Research and Experimentation on Accidental Water Pollution (CEDRE), 715 Rue Alain Colas, 29200 Brest, France
| | - Joelle Cabon
- French Agency for Food, Environmental and Occupational Health & Safety (ANSES), Ploufragan-Plouzané Laboratory, Fish Viral Pathology Unit, Technopôle Brest-Iroise, 29280 Plouzané, France; European University of Brittany, France
| | - Lénaïg Louboutin
- French Agency for Food, Environmental and Occupational Health & Safety (ANSES), Ploufragan-Plouzané Laboratory, Fish Viral Pathology Unit, Technopôle Brest-Iroise, 29280 Plouzané, France; European University of Brittany, France
| | - Thierry Morin
- French Agency for Food, Environmental and Occupational Health & Safety (ANSES), Ploufragan-Plouzané Laboratory, Fish Viral Pathology Unit, Technopôle Brest-Iroise, 29280 Plouzané, France; European University of Brittany, France
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Chen Z, Farrell AP, Matala A, Narum SR. Mechanisms of thermal adaptation and evolutionary potential of conspecific populations to changing environments. Mol Ecol 2018; 27:659-674. [PMID: 29290103 DOI: 10.1111/mec.14475] [Citation(s) in RCA: 43] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2017] [Revised: 11/26/2017] [Accepted: 12/05/2017] [Indexed: 01/01/2023]
Abstract
Heterogeneous and ever-changing thermal environments drive the evolution of populations and species, especially when extreme conditions increase selection pressure for traits influencing fitness. However, projections of biological diversity under scenarios of climate change rarely consider evolutionary adaptive potential of natural species. In this study, we tested for mechanistic evidence of evolutionary thermal adaptation among ecologically divergent redband trout populations (Oncorhynchus mykiss gairdneri) in cardiorespiratory function, cellular response and genomic variation. In a common garden environment, fish from an extreme desert climate had significantly higher critical thermal maximum (p < .05) and broader optimum thermal window for aerobic scope (>3°C) than fish from cooler montane climate. In addition, the desert population had the highest maximum heart rate during warming (20% greater than montane populations), indicating improved capacity to deliver oxygen to internal tissues. In response to acute heat stress, distinct sets of cardiac genes were induced among ecotypes, which helps to explain the differences in cardiorespiratory function. Candidate genomic markers and genes underlying these physiological adaptations were also pinpointed, such as genes involved in stress response and metabolic activity (hsp40, ldh-b and camkk2). These markers were developed into a multivariate model that not only accurately predicted critical thermal maxima, but also evolutionary limit of thermal adaptation in these specific redband trout populations relative to the expected limit for the species. This study demonstrates mechanisms and limitations of an aquatic species to evolve under changing environments that can be incorporated into advanced models to predict ecological consequences of climate change for natural organisms.
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Affiliation(s)
- Zhongqi Chen
- Department of Zoology, The University of British Columbia, Vancouver, BC, Canada
| | - Anthony P Farrell
- Department of Zoology, The University of British Columbia, Vancouver, BC, Canada.,Faculty of Land and Food Systems, The University of British Columbia, Vancouver, BC, Canada
| | - Amanda Matala
- Columbia River Inter-Tribal Fish Commission, Hagerman, ID, USA
| | - Shawn R Narum
- Columbia River Inter-Tribal Fish Commission, Hagerman, ID, USA
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Li Y, Huang J, Liu Z, Zhou Y, Xia B, Wang Y, Kang Y, Wang J. Transcriptome analysis provides insights into hepatic responses to moderate heat stress in the rainbow trout ( Oncorhynchus mykiss ). Gene 2017; 619:1-9. [DOI: 10.1016/j.gene.2017.03.041] [Citation(s) in RCA: 61] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2017] [Revised: 03/26/2017] [Accepted: 03/28/2017] [Indexed: 01/20/2023]
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Chatchaiphan S, Srisapoome P, Kim JH, Devlin RH, Na-Nakorn U. De Novo Transcriptome Characterization and Growth-Related Gene Expression Profiling of Diploid and Triploid Bighead Catfish (Clarias macrocephalus Günther, 1864). MARINE BIOTECHNOLOGY (NEW YORK, N.Y.) 2017; 19:36-48. [PMID: 28181037 DOI: 10.1007/s10126-017-9730-3] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/18/2016] [Accepted: 12/31/2016] [Indexed: 06/06/2023]
Abstract
To enhance understanding of triploid gene expression, the transcriptome information from bighead catfish (Clarias macrocephalus Günther, 1864) was studied using the paired-end Illumina HiSeq™ 2000 sequencing platform. In total, 68,227,832 raw reads were generated from liver tissues and 53,149 unigenes were assembled, with an average length of 765 bp and N50 length of 1283 bp. Of these unigenes, 33,428 (62.89%) could be annotated according to their homology with matches in the NCBI non-redundant (Nr), NCBI nucleotide (Nt), Swiss-Prot, Clusters of Orthologous Groups (COG), gene ontology (GO), or Kyoto Encyclopedia of Genes and Genomes (KEGG) databases. Relative expression of liver genes between diploid and triploid bighead catfish revealed more than 90% of the annotated unigenes similarly expressed, regardless of ploidy, whereas 362 upregulated and 83 downregulated with at least a twofold change in triploid relative to diploid. Quantitative real-time PCR of 15 differentially expressed growth-related genes showed consistency between the expression profiles of those genes with the results from RNA-seq analysis. Our results showed that genes in C. macrocephalus liver responded independently to triploidy with the majority showing similar expression levels between diploid and triploid (a dosage compensation phenomenon). The underlying mechanism of the varying gene expression patterns was discussed. Notably, 5 of the top 20 upregulated genes associated with stress response and thus may reflect stress caused by triploidy. The present study adds a substantial contribution to the sequence data available for C. macrocephalus and hence provides valuable resources for further studies. Furthermore, it gives information that may enhance understanding of triploid physiology.
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Affiliation(s)
- Satid Chatchaiphan
- Graduate Program in Aquaculture, The Graduate School, Kasetsart University, Chatuchak, Bangkok, 10900, Thailand
| | - Prapansak Srisapoome
- Department of Aquaculture, Faculty of Fisheries, Kasetsart University, Chatuchak, Bangkok, 10900, Thailand
| | - Jin-Hyoung Kim
- Division of Life Sciences, Korea Polar Research Institute, Incheon, 21990, South Korea
| | - Robert H Devlin
- Fisheries and Oceans Canada, Centre for Aquaculture and Environmental Research, West Vancouver, BC, V7V1N6, Canada
| | - Uthairat Na-Nakorn
- Department of Aquaculture, Faculty of Fisheries, Kasetsart University, Chatuchak, Bangkok, 10900, Thailand.
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