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Espírito-Santo C, Guardiola FA, Ozório ROA, Magnoni LJ. Short-term induced swimming activity enhanced innate immune parameters and antioxidant status of European eel (Anguilla anguilla). Comp Biochem Physiol A Mol Integr Physiol 2024; 296:111680. [PMID: 38876440 DOI: 10.1016/j.cbpa.2024.111680] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2024] [Revised: 06/11/2024] [Accepted: 06/11/2024] [Indexed: 06/16/2024]
Abstract
The swimming activity, although an essential trait in the life cycle of fish, is still poorly understood in farmed fish. The current study aimed to investigate the impact of short-term induced swimming on the immune and antioxidant defence systems in European eel (Anguilla anguilla). Sixteen male yellow European eels (total length: 39.9 ± 0.7 cm; body weight: 108.8 ± 6.1 g) were individually placed in swimming flumes and divided into two groups: i) no swimming (n = 8); and ii) induced-swimming (n = 8) at 0.3 body lengths (BL)·s-1 for 7 h. Swimming resulted in a 2-fold lower cortisol concentration in plasma, whereas plasma glucose, lactate, and several immune-related parameters did not present variations between groups. Interestingly, swimming led to higher lysozyme, peroxidase, and protease activities in skin mucus, whereas bactericidal activity did not show differences among groups. Additionally, the gene expression of interleukin 1 beta showed an up-regulation in the skin of fish with induced swimming, while no differences were observed in the head-kidney or gills. Furthermore, modulation of the antioxidant status was observed in the liver and posterior skeletal muscle after induced swimming. Fish subjected to swimming showed lower lipid peroxidation and higher reduced glutathione levels, increasing the reduced/oxidized glutathione ratio. However, no variations in the antioxidant status were observed between groups in the anterior skeletal muscle. This study showed modulation of immune and oxidative stress markers in European eels upon short-term induced swimming compared to non-swimming fish.
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Affiliation(s)
- Carlos Espírito-Santo
- Faculty of Sciences (FCUP), University of Porto, Rua do Campo Alegre, 4069-007 Porto, Portugal; Interdisciplinary Centre of Marine and Environmental Research (CIIMAR), University of Porto, Terminal de Cruzeiros do Porto de Leixões, Av. General Norton de Matos s/n, 4450-208 Matosinhos, Portugal.
| | - Francisco A Guardiola
- Immunobiology for Aquaculture Group, Department of Cell Biology and Histology, Faculty of Biology, Campus Regional de Excelencia Internacional "Campus Mare Nostrum", University of Murcia, 30100 Murcia, Spain
| | - Rodrigo O A Ozório
- Interdisciplinary Centre of Marine and Environmental Research (CIIMAR), University of Porto, Terminal de Cruzeiros do Porto de Leixões, Av. General Norton de Matos s/n, 4450-208 Matosinhos, Portugal
| | - Leonardo J Magnoni
- The New Zealand Institute for Plant and Food Research Limited, Port Nelson, Nelson 7043, New Zealand
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Luo W, Chi S, Wang J, Yu X, Tong J. Comparative transcriptomic analyses of brain-liver-muscle in channel catfish (Ictalurus punctatus) with differential growth rate. COMPARATIVE BIOCHEMISTRY AND PHYSIOLOGY. PART D, GENOMICS & PROTEOMICS 2024; 49:101178. [PMID: 38128380 DOI: 10.1016/j.cbd.2023.101178] [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: 07/13/2023] [Revised: 12/05/2023] [Accepted: 12/07/2023] [Indexed: 12/23/2023]
Abstract
Growth is an important economically trait for aquatic animals. The popularity of farmed channel catfish (Ictalurus punctatus) in China has recently surged, prompting a need for research into the genetic mechanisms that drive growth and development to expedite the selection of fast-growing variants. In this study, the brain, liver and muscle transcriptomes of channel catfish between fast-growing and slow-growing groups were analyzed using RNA-Seq. Totally, 63, 110 and 86 differentially expressed genes (DEGs) were from brain, liver and muscle tissues. DEGs are primarily involved in growth, development, metabolism and immunity, which are related to the growth regulation of channel catfish, such as growth hormone receptor b (ghrb), fibroblast growth factor receptor 4 (fgfr4), bone morphogenetic protein 1a (bmp1a), insulin-like growth factor 2a (igf2a), collagen, type I, alpha 1a (col1a1a), acyl-CoA synthetase long chain family member 2 (acsl2) and caveolin 1 (cav1). This study advances our knowledge of the genetic mechanisms accounting for differences in growth rate and offers crucial gene resources for future growth-related molecular breeding programs in channel catfish.
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Affiliation(s)
- Weiwei Luo
- Jiangsu Union Technical Institute, Yancheng Bioengineering Branch, Yancheng Aquatic Science Research Institute, Yancheng 224001, China
| | - Shuang Chi
- Jiangsu Union Technical Institute, Yancheng Bioengineering Branch, Yancheng Aquatic Science Research Institute, Yancheng 224001, China
| | - Junru Wang
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Innovation Academy of Seed Design, The Chinese Academy of Sciences, Wuhan 430072, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Xiaomu Yu
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Innovation Academy of Seed Design, The Chinese Academy of Sciences, Wuhan 430072, China
| | - Jingou Tong
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Innovation Academy of Seed Design, The Chinese Academy of Sciences, Wuhan 430072, China; Hubei Hongshan Laboratory, Wuhan 430070, China.
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Zhang X, Wang T, Zhai D, Liu H, Xiong F, Wang Y. Transcriptome analysis and gene expression analysis related to salinity-alkalinity and low temperature adaptation of Triplophysa yarkandensis. Front Genet 2023; 13:1089274. [PMID: 36712878 PMCID: PMC9877283 DOI: 10.3389/fgene.2022.1089274] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2022] [Accepted: 12/28/2022] [Indexed: 01/14/2023] Open
Abstract
T. yarkandensis is a common species of Triplophysa, and it is distributed in Shule river of Hexi Corridor, of Gansu province in China. In order to enrich gene database resources and explore the environment adaptation of T. yarkandensis, fifteen tissues were collected from three adult T. yarkandensis for transcriptome sequencing and de novo assembly. Nine major international gene annotation databases (NR, COG, egg_NOG, TrEMBL, Pfam, KOG, Swiss prot, KEGG and Gene Ontology) were utilized to annotate unigenes. A detailed study was conducted to explore the gene expression and the differentially expressed genes among five tissues (brain, heart, kidney, liver and spleen). In addition, the current study showed that candidate genes involved in salinity-alkalinity and low temperature adaptation were differentially expressed in tissues of T. yarkandensis. Precisely, mapk1, abcc1, gpx1, gpx4, cat and aqp1 genes participated in the regulation process of salinity-alkalinity adaptation, and elovl4, acaca, fasn, acaa2, acox1 and acox3 genes were involved in fatty acid metabolism and closely associated with low temperature adaptation. On the one hand, it was found that the expression of these genes varied among different tissues, and the important pathways involved in these genes were mapped. Furthermore, we analyzed mapk1 and acox1 genes in depth to obtain the predicted gene structure and important amino acid sites. The transcriptome information in this study will be conducive to provide further understanding for the molecular level research and exploration of the environmental adaptation of T. yarkandensis.
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Affiliation(s)
- Xuejing Zhang
- Hubei Engineering Research Center for Protection and Utilization of Special Biological Resources in the Hanjiang River Basin, Jianghan University, Wuhan, China
| | - Tai Wang
- Gansu Key Laboratory of Cold Water Fishes Germplasm Resources and Genetics Breeding, Gansu Fishers Research Institute, Lanzhou, China
| | - Dongdong Zhai
- Hubei Engineering Research Center for Protection and Utilization of Special Biological Resources in the Hanjiang River Basin, Jianghan University, Wuhan, China,Hubei Key Laboratory of Environmental and Health Effects of Persistent Toxic Substances, Jianghan University, Wuhan, China
| | - Hongyan Liu
- Hubei Engineering Research Center for Protection and Utilization of Special Biological Resources in the Hanjiang River Basin, Jianghan University, Wuhan, China,Hubei Key Laboratory of Environmental and Health Effects of Persistent Toxic Substances, Jianghan University, Wuhan, China
| | - Fei Xiong
- Hubei Engineering Research Center for Protection and Utilization of Special Biological Resources in the Hanjiang River Basin, Jianghan University, Wuhan, China,Hubei Key Laboratory of Environmental and Health Effects of Persistent Toxic Substances, Jianghan University, Wuhan, China,*Correspondence: Fei Xiong, ; Ying Wang,
| | - Ying Wang
- Hubei Engineering Research Center for Protection and Utilization of Special Biological Resources in the Hanjiang River Basin, Jianghan University, Wuhan, China,Hubei Key Laboratory of Environmental and Health Effects of Persistent Toxic Substances, Jianghan University, Wuhan, China,*Correspondence: Fei Xiong, ; Ying Wang,
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Sundaray JK, Dixit S, Rather A, Rasal KD, Sahoo L. Aquaculture omics: An update on the current status of research and data analysis. Mar Genomics 2022; 64:100967. [PMID: 35779450 DOI: 10.1016/j.margen.2022.100967] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2021] [Revised: 05/26/2022] [Accepted: 06/15/2022] [Indexed: 11/28/2022]
Abstract
Aquaculture is the fast-growing agricultural sector and has the ability to meet the growing demand for protein nutritional security for future population. In future aquaculture is going to be the major source of fish proteins as capture fisheries reached at its maximum. However, several challenges need to overcome such as lack of genetically improved strains/varieties, lack of species-specific feed/functional feed, round the year availability of quality fish seed, pollution of ecosystems and increased frequencies of disease occurrence etc. In recent years, the continuous development of high throughput sequencing technology has revolutionized the biological sciences and provided necessary tools. Application of 'omics' in aquaculture research have been successfully used to resolve several productive and reproductive issues and thus ensure its sustainability and profitability. To date, high quality draft genomes of over fifty fish species have been generated and successfully used to develop large number of single nucleotide polymorphism markers (SNPs), marker panels and other genomic resources etc in several aquaculture species. Similarly, transcriptome profiling and miRNAs analysis have been used in aquaculture research to identify key transcripts and expression analysis of candidate genes/miRNAs involved in reproduction, immunity, growth, development, stress toxicology and disease. Metagenome analysis emerged as a promising scientific tool to analyze the complex genomes contained within microbial communities. Metagenomics has been successfully used in the aquaculture sector to identify novel and potential pathogens, antibiotic resistance genes, microbial roles in microcosms, microbial communities forming biofloc, probiotics etc. In the current review, we discussed application of high-throughput technologies (NGS) in the aquaculture sector.
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Affiliation(s)
- Jitendra Kumar Sundaray
- ICAR-Central Institute of Freshwater Aquaculture, Kausalyaganga, Bhubaneswar 751002, Odisha, India
| | - Sangita Dixit
- Centre for Biotechnology, School of Pharmaceutical Sciences, Siksha 'O' Anusandhan University (Deemed to be University), Bhubaneswar 751003, Odisha, India
| | - Ashraf Rather
- Division of Fish Genetics and Biotechnology, College of Fisheries, Sher-e- Kashmir University of Agricultural Science and Technology, Rangil-Ganderbal 190006, Jammu and Kashmir, India
| | - Kiran D Rasal
- Fish Genetics and Biotechnology Division, ICAR-Central Institute of Fisheries Education, Versova, Mumbai 400 061, Maharastra, India
| | - Lakshman Sahoo
- ICAR-Central Institute of Freshwater Aquaculture, Kausalyaganga, Bhubaneswar 751002, Odisha, India.
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Zhang L, Li X, Yu Y, Zhang L, Dong L, Gan J, Mao T, Liu T, Peng J, He L. Comparative analyses of liver transcriptomes reveal the effect of exercise on growth-, glucose metabolism-, and oxygen transport-related genes and signaling pathways in grass carp (Ctenopharyngodon idella). Comp Biochem Physiol A Mol Integr Physiol 2021; 262:111081. [PMID: 34536566 DOI: 10.1016/j.cbpa.2021.111081] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2021] [Revised: 08/24/2021] [Accepted: 09/13/2021] [Indexed: 12/13/2022]
Abstract
Grass carp is one of the most common farmed fish and its growth rate has been the focus of various studies. However, the impact of long-term exercise on growth rate of juvenile grass carp has not been clearly established. In this study, a four-month exercise trial and liver transcriptome analysis were performed to investigate changes in growth, liver molecular regulatory network and key genes in grass carp. When compared to the non-exercised grass carp (N-EXF), the exercised grass carp (EXF) showed a significant improvement in growth. Liver transcriptome analysis revealed 1714 significantly up-regulated and 1672 significantly down-regulated genes. These genes were enriched in various signaling pathways. These pathways included: those associated with growth, such as the PI3K-Akt and mTOR signaling pathways; those associated with glucose metabolism, such as glycolysis/gluconeogenesis, insulin and AMPK signaling pathways as well as those associated with oxygen transport, such as HIF-1, PI3K-Akt, PPAR and MAPK signaling pathways. In addition, growth-associated genes, such as ghr, igf1 and igf1r; glucose metabolism-associated genes, such as ins and insr as well as oxygen transport-associated genes, such as vhl, pdha and epo were identified. In conclusion, long-term moderate exercise improved the growth rate of grass carp. Our findings elucidate on changes in the liver molecular regulatory network and functional genes that occur during moderate exercise in fish.
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Affiliation(s)
- Lang Zhang
- Yangtze River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Wuhan, China.
| | - Xiaohui Li
- Yangtze River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Wuhan, China.
| | - Yali Yu
- Yangtze River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Wuhan, China.
| | - Lin Zhang
- Yangtze River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Wuhan, China.
| | - Lixue Dong
- Yangtze River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Wuhan, China
| | - Jinhua Gan
- Yangtze River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Wuhan, China.
| | - Tao Mao
- Yangtze River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Wuhan, China
| | - Ting Liu
- Yangtze River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Wuhan, China.
| | - Jie Peng
- Yangtze River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Wuhan, China.
| | - Li He
- Yangtze River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Wuhan, China.
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Jeffries KM, Teffer A, Michaleski S, Bernier NJ, Heath DD, Miller KM. The use of non-lethal sampling for transcriptomics to assess the physiological status of wild fishes. Comp Biochem Physiol B Biochem Mol Biol 2021; 256:110629. [PMID: 34058376 DOI: 10.1016/j.cbpb.2021.110629] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2020] [Revised: 05/19/2021] [Accepted: 05/25/2021] [Indexed: 12/14/2022]
Abstract
Fishes respond to different abiotic and biotic stressors through changes in gene expression as a part of an integrated physiological response. Transcriptomics approaches have been used to quantify gene expression patterns as a reductionist approach to understand responses to environmental stressors in animal physiology and have become more commonly used to study wild fishes. We argue that non-lethal sampling for transcriptomics should become the norm for assessing the physiological status of wild fishes, especially when there are conservation implications. Processes at the level of the transcriptome provide a "snapshot" of the cellular conditions at a given time; however, by using a non-lethal sampling protocol, researchers can connect the transcriptome profile with fitness-relevant ecological endpoints such as reproduction, movement patterns and survival. Furthermore, telemetry is a widely used approach in fisheries to understand movement patterns in the wild, and when combined with transcriptional profiling, provides arguably the most powerful use of non-lethal sampling for transcriptomics in wild fishes. In this review, we discuss the different tissues that can be successfully incorporated into non-lethal sampling strategies, which is particularly useful in the context of the emerging field of conservation transcriptomics. We briefly describe different methods for transcriptional profiling in fishes from high-throughput qPCR to whole transcriptome approaches. Further, we discuss strategies and the limitations of using transcriptomics for non-lethally studying fishes. Lastly, as 'omics' technology continues to advance, transcriptomics paired with different omics approaches to study wild fishes will provide insight into the factors that regulate phenotypic variation and the physiological responses to changing environmental conditions in the future.
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Affiliation(s)
- Ken M Jeffries
- Department of Biological Sciences, University of Manitoba, 50 Sifton Road, Winnipeg, Manitoba R3T 2N2, Canada.
| | - Amy Teffer
- Department of Environmental Conservation, University of Massachusetts Amherst, Amherst, MA 01003, United States of America
| | - Sonya Michaleski
- Department of Biological Sciences, University of Manitoba, 50 Sifton Road, Winnipeg, Manitoba R3T 2N2, Canada
| | - Nicholas J Bernier
- Department of Integrative Biology, University of Guelph, Guelph, ON N1G 2W1, Canada
| | - Daniel D Heath
- Department of Integrative Biology, Great Lakes Institute for Environmental Research, University of Windsor, Windsor, ON N9B 3P4, Canada
| | - Kristina M Miller
- Pacific Biological Station, Fisheries and Oceans Canada, 3190 Hammond Bay Rd, Nanaimo, BC V9T 6N7, Canada
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Targeting the Mild-Hypoxia Driving Force for Metabolic and Muscle Transcriptional Reprogramming of Gilthead Sea Bream ( Sparus aurata) Juveniles. BIOLOGY 2021; 10:biology10050416. [PMID: 34066667 PMCID: PMC8151949 DOI: 10.3390/biology10050416] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/25/2021] [Revised: 04/28/2021] [Accepted: 05/04/2021] [Indexed: 01/08/2023]
Abstract
Simple Summary Reduced oxygen availability generates a number of adaptive features across all the animal kingdom, and the goal of this study was targeting the mild-hypoxia driving force for metabolic and muscle transcriptional reprogramming of gilthead sea bream juveniles. Attention was focused on blood metabolic and muscle transcriptomic landmarks before and after exhaustive exercise. Our results after mild-hypoxia conditioning highlighted an increased contribution of lipid metabolism to whole energy supply to preserve the aerobic energy production, a better swimming performance regardless of changes in feed intake, as well as reduced protein turnover and improved anaerobic fitness with the restoration of normoxia. Abstract On-growing juveniles of gilthead sea bream were acclimated for 45 days to mild-hypoxia (M-HYP, 40–60% O2 saturation), whereas normoxic fish (85–90% O2 saturation) constituted two different groups, depending on if they were fed to visual satiety (control fish) or pair-fed to M-HYP fish. Following the hypoxia conditioning period, all fish were maintained in normoxia and continued to be fed until visual satiation for 3 weeks. The time course of hypoxia-induced changes was assessed by changes in blood metabolic landmarks and muscle transcriptomics before and after exhaustive exercise in a swim tunnel respirometer. In M-HYP fish, our results highlighted a higher contribution of aerobic metabolism to whole energy supply, shifting towards a higher anaerobic fitness following normoxia restoration. Despite these changes in substrate preference, M-HYP fish shared a persistent improvement in swimming performance with a higher critical speed at exercise exhaustion. The machinery of muscle contraction and protein synthesis and breakdown was also largely altered by mild-hypoxia conditioning, contributing this metabolic re-adjustment to the positive regulation of locomotion and to the catch-up growth response during the normoxia recovery period. Altogether, these results reinforce the presence of large phenotypic plasticity in gilthead sea bream, and highlights mild-hypoxia as a promising prophylactic measure to prepare these fish for predictable stressful events.
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Palstra AP, Roque A, Kruijt L, Jéhannet P, Pérez-Sánchez J, Dirks RP. Physiological Effects of Water Flow Induced Swimming Exercise in Seabream Sparus aurata. Front Physiol 2020; 11:610049. [PMID: 33364981 PMCID: PMC7750471 DOI: 10.3389/fphys.2020.610049] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2020] [Accepted: 11/17/2020] [Indexed: 11/25/2022] Open
Abstract
A longer on-land rearing period of Gilthead seabream Sparus aurata before transfer to sea-cages would allow the farmer to benefit from exercise-enhanced growth, resilience, and robustness as induced by increasing water flow in the tanks. In this study, the physiological effects of flow-conditioning were investigated by subjecting large groups of experimental fish to minimal flow or to flow regimes inducing swimming exercise at 1 or 2 body length (BL) s−1 for a period of 8 months (February–October) in 1,500 L tanks. Fish representing the three treatment groups were then used for: (1) a stress challenge netting test and plasma cortisol measurement (baseline, peaking, and recovery levels), (2) blood plasma measurements of glucose, triglycerides, lactate, cholesterol, growth hormone (GH), and insulin-like growth factor 1 (IGF1), and (3) heart and muscle gene expression of the GH and IGF1 receptors and the muscle transcriptome by deep RNA sequencing (RNAseq). Fish size after 8 months of flow conditioning was 92 ± 27 g body weight (BW) for fish under minimal flow, 106 ± 24 g BW (+15%) at 1 BL s−1, and 125 ± 27 g BW (+36%) at 2 BL s−1. Flow conditioning at 1 BL s−1 provided optimal conditions for growth and uniformity, but also stress (lowest baseline plasma cortisol), robustness (higher condition factor and larger hearts), and energy mobilization (increased plasma glucose). Although flow enhanced growth linearly with swimming speed, also the percentage of lordotic fish increased with exercise, particularly high for swimming at 2 BL s−1. The absence of important differences in plasma GH and IGF1, and expression levels of their receptors in heart and white skeletal muscle, indicated that other factors may be involved in growth enhancement. RNAseq of the white skeletal muscle showed upregulated expression of genes involved in muscle contraction, muscle development and its molecular regulation, and immune genes that may play a role in the muscle repair mechanism. An exercise regime of swimming at 1 BL s−1 can be considered as optimal for farming robust seabream although the increase of skeletal deformities should be avoided.
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Affiliation(s)
- Arjan P Palstra
- Wageningen University & Research Animal Breeding and Genomics, Wageningen Livestock Research, Wageningen, Netherlands
| | - Ana Roque
- IRTA-SCR, Sant Carles de la Rapita, Spain
| | - Leo Kruijt
- Wageningen University & Research Animal Breeding and Genomics, Wageningen Livestock Research, Wageningen, Netherlands
| | - Pauline Jéhannet
- Wageningen University & Research Animal Breeding and Genomics, Wageningen Livestock Research, Wageningen, Netherlands
| | - Jaume Pérez-Sánchez
- Nutrigenomics and Fish Growth Endocrinology Group, Institute of Aquaculture Torre de la Sal (CSIC), Castellon, Spain
| | - Ron P Dirks
- Future Genomics Technologies B.V., Leiden, Netherlands
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Identification of mRNA Degradome Variation Dependent on Divergent Muscle Mass in Different Pig Breeds. ANNALS OF ANIMAL SCIENCE 2020. [DOI: 10.2478/aoas-2020-0065] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Abstract
The search is still on for the molecular processes associated with the development and metabolism of skeletal muscles. Selection conducted in farm animals is focused on high muscle mass because it delivers higher economic profit. The present study aimed to shed light on mRNA degradome signals that could be characteristic for molecular processes associated with an abundance of muscle mass and to identify miRNA regulatory networks controlling these processes in pigs applying next-generation-sequencing (NGS). In the study, over 10,000 degraded transcripts were identified per sample, with the highest abundance for genes encoding mitochondrial proteins (COXs, NDs, CYTB, ATP6 and ATP8). Moreover, only 26% of the miRNA targets were found within this degraded transcript pool, which suggested for miRNAs other molecular mechanism at different level of gene expression than mRNA degradation. On the other hand, a small share of the identified degraded transcripts associated with miRNA regulation suggests a different mechanism of mRNA degradation for identified degraded transcropts. Subsequently, most of the miRNA gene degraded targets, such as ENO3, CKM, CRYAB and ADAM19 encode proteins involved in the muscle mass control. The present study showed an interesting dependence between miRNAs and their targets. Nevertheless, the complete view of the miRNA regulatory network could be a subject of further advanced research, which would employ a miRNA transfection procedure in skeletal muscle cell cultures.
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Luo W, Wang J, Yu X, Zhou Y, Tong J. Comparative transcriptome analyses and identification of candidate genes involved in vertebral abnormality of bighead carp Hypophthalmichthys nobilis. COMPARATIVE BIOCHEMISTRY AND PHYSIOLOGY D-GENOMICS & PROTEOMICS 2020; 36:100752. [PMID: 33126027 DOI: 10.1016/j.cbd.2020.100752] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/03/2020] [Revised: 10/07/2020] [Accepted: 10/10/2020] [Indexed: 10/23/2022]
Abstract
Body deformity occurs both in wild and farmed fishes, which is one of the most challenging problems for aquaculture industry. In most cases, such body deformities are linked to skeletal deformities. Currently, very limited information is available on skeletal deformities of farmed fish species which may be caused by genetic factor. In this study, we performed muscle and vertebra transcriptome analyses in body deformity and normality of bighead carp Hypophthalmichthys nobilis (from one meiotic gynogenesis family) using RNA-Seq. A total of 43,923 and 44,416 unigenes were predicted in muscles and vertebrae, respectively. Based on these data, we further explored the gene expression profiles in gynogenetic normal and abnormal bighead carp. No differentially expressed gene (DEG) was found in transcriptome data of muscles. Totally, 20 key DEGs were identified in transcriptome data of vertebrae, such as low density lipoprotein-related protein 2 (lrp2), bone morphogenetic protein 2B (bmp2b) and collagen alpha-1(IV) (col4a1). 12 potential pathways were also identified in vertebra transcriptome data, which were mainly involved in development, growth, cytoskeleton and energy metabolism, such as MAPK signaling pathway, regulation of actin cytoskeleton and TGF-beta signaling pathway. Results of this study will be informative for the understanding of genetic mechanisms for body shape formation and also provide potential candidate genes for selection program involved in body shape and skeletal development in H. nobilis.
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Affiliation(s)
- Weiwei Luo
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, The Innovation Academy of Seed Design, The Chinese Academy of Sciences, Wuhan 430072, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Junru Wang
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, The Innovation Academy of Seed Design, The Chinese Academy of Sciences, Wuhan 430072, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Xiaomu Yu
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, The Innovation Academy of Seed Design, The Chinese Academy of Sciences, Wuhan 430072, China.
| | - Ying Zhou
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, The Innovation Academy of Seed Design, The Chinese Academy of Sciences, Wuhan 430072, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Jingou Tong
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, The Innovation Academy of Seed Design, The Chinese Academy of Sciences, Wuhan 430072, China.
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11
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Guan WZ, Qiu GF. Transcriptome analysis of the growth performance of hybrid mandarin fish after food conversion. PLoS One 2020; 15:e0240308. [PMID: 33035258 PMCID: PMC7546499 DOI: 10.1371/journal.pone.0240308] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2020] [Accepted: 09/24/2020] [Indexed: 11/18/2022] Open
Abstract
During recent years, China has become a hotspot for the domestication of mandarin fish, and this is of great commercial value. Although the food preference of domesticated mandarin fish has been studied, little is known about genes regulating their growth. We raised hybrid mandarin fish on artificial feed for 3 months, the results showed that the survival rate of hybrid mandarin fish was 60.00%. Their total length and body weight were 18.34 ±0.43 cm and 100.44 ±4.87 g. The absolute length and weight gain rates were 0.14 cm/d and 1.08 g/d, respectively. Finally, RNA sequencing (RNA-Seq) was performed to identify potential genes and pathways activated in response to growth performance. The transcriptome analysis generated 68, 197 transcripts and 45,871 unigenes. Among them, 1025 genes were up-regulated and 593 genes were down-regulated between the fast- and slow-growth fish. Finally, we obtained 32 differentially expressed genes, which were mainly related to fatty acid biosynthesis (e.g. FASN and ACACB), collecting duct acid secretion (e.g. ATP6E and KCC4), cell cycle (e.g. CDC20 and CCNB), and the insulin-like growth factor (IGF) system (IGFBP1). These pathways might be related to the growth of hybrid mandarin fish. In addition, more potential single nucleotide polymorphisms (SNPs) were detected in the fast-growth fish than in the slow-growth fish. The results suggest that the interaction of metabolism and abundant alleles might determine the growth of hybrid mandarin fish after food conversion.
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Affiliation(s)
- Wen-Zhi Guan
- Key Laboratory of Freshwater Aquatic Genetic Resources, Ministry of Agriculture, National Demonstration Center for Experimental Fisheries Science Education, Shanghai Engineering Research Center of Aquaculture, Shanghai Ocean University, Shanghai, China
- Shanghai Fisheries Research Institute, Shanghai Fisheries Technical Extension Station, Shanghai, China
| | - Gao-Feng Qiu
- Key Laboratory of Freshwater Aquatic Genetic Resources, Ministry of Agriculture, National Demonstration Center for Experimental Fisheries Science Education, Shanghai Engineering Research Center of Aquaculture, Shanghai Ocean University, Shanghai, China
- * E-mail: (GFQ); (FL)
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12
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Liu X, Zeng S, Liu S, Wang G, Lai H, Zhao X, Bi S, Guo D, Chen X, Yi H, Su Y, Zhang Y, Li G. Identifying the Related Genes of Muscle Growth and Exploring the Functions by Compensatory Growth in Mandarin Fish ( Siniperca chuatsi). Front Physiol 2020; 11:553563. [PMID: 33117188 PMCID: PMC7552573 DOI: 10.3389/fphys.2020.553563] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2020] [Accepted: 08/31/2020] [Indexed: 01/16/2023] Open
Abstract
How organisms display many different biochemical, physiological processes through genes expression and regulatory mechanisms affecting muscle growth is a central issue in growth and development. In Siniperca chuatsi, the growth-related genes and underlying relevant mechanisms are poorly understood, especially for difference of body sizes and compensatory growth performance. Muscle from 3-month old individuals of different sizes was used for transcriptome analysis. Results showed that 8,942 different expression genes (DEGs) were identified after calculating the RPKM. The DEGs involved in GH-IGF pathways, protein synthesis, ribosome synthesis and energy metabolisms, which were expressed significantly higher in small individuals (S) than large fish (L). In repletion feeding and compensatory growth experiments, eight more significant DEGs were used for further research (GHR2, IGFR1, 4ebp, Mhc, Mlc, Myf6, MyoD, troponin). When food was plentiful, eight genes participated in and promoted growth and muscle synthesis, respectively. Starvation can be shown to inhibit the expression of Mhc, Mlc and troponin, and high expression of GHR2, IGFR1, and 4ebp inhibited growth. Fasting promoted the metabolic actions of GHR2, IGFR1, and 4ebp rather than the growth-promoting actions. MyoD can sense and regulate the hunger, which also worked with Mhc and Mlc to accelerate the compensatory growth of S. chuatsi. This study is helpful to understand the regulation mechanisms of muscle growth-related genes. The elected genes will contribute to the selective breeding in future as candidate genes.
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Affiliation(s)
- Xuange Liu
- Guangdong Province Key Laboratory for Aquatic Economic Animals, School of Life Sciences, Sun Yat-sen University, Guangzhou, China.,Guangdong Provincial Engineering Technology Research Center for Healthy Breeding of Important Economic Fish, Guangzhou, China.,Southern Marine Science and Engineering Guangdong Laboratory, Zhuhai, China
| | - Shuang Zeng
- Guangdong Province Key Laboratory for Aquatic Economic Animals, School of Life Sciences, Sun Yat-sen University, Guangzhou, China.,Guangdong Provincial Engineering Technology Research Center for Healthy Breeding of Important Economic Fish, Guangzhou, China.,Southern Marine Science and Engineering Guangdong Laboratory, Zhuhai, China
| | - Shuang Liu
- Guangdong Province Key Laboratory for Aquatic Economic Animals, School of Life Sciences, Sun Yat-sen University, Guangzhou, China.,Guangdong Provincial Engineering Technology Research Center for Healthy Breeding of Important Economic Fish, Guangzhou, China.,Southern Marine Science and Engineering Guangdong Laboratory, Zhuhai, China
| | - Gongpei Wang
- Guangdong Province Key Laboratory for Aquatic Economic Animals, School of Life Sciences, Sun Yat-sen University, Guangzhou, China.,Guangdong Provincial Engineering Technology Research Center for Healthy Breeding of Important Economic Fish, Guangzhou, China.,Southern Marine Science and Engineering Guangdong Laboratory, Zhuhai, China
| | - Han Lai
- Guangdong Province Key Laboratory for Aquatic Economic Animals, School of Life Sciences, Sun Yat-sen University, Guangzhou, China.,Guangdong Provincial Engineering Technology Research Center for Healthy Breeding of Important Economic Fish, Guangzhou, China.,Southern Marine Science and Engineering Guangdong Laboratory, Zhuhai, China
| | - Xiaopin Zhao
- Guangdong Province Key Laboratory for Aquatic Economic Animals, School of Life Sciences, Sun Yat-sen University, Guangzhou, China.,Guangdong Provincial Engineering Technology Research Center for Healthy Breeding of Important Economic Fish, Guangzhou, China.,Southern Marine Science and Engineering Guangdong Laboratory, Zhuhai, China
| | - Sheng Bi
- Guangdong Province Key Laboratory for Aquatic Economic Animals, School of Life Sciences, Sun Yat-sen University, Guangzhou, China.,Guangdong Provincial Engineering Technology Research Center for Healthy Breeding of Important Economic Fish, Guangzhou, China.,Southern Marine Science and Engineering Guangdong Laboratory, Zhuhai, China
| | - Dingli Guo
- Guangdong Province Key Laboratory for Aquatic Economic Animals, School of Life Sciences, Sun Yat-sen University, Guangzhou, China.,Guangdong Provincial Engineering Technology Research Center for Healthy Breeding of Important Economic Fish, Guangzhou, China.,Southern Marine Science and Engineering Guangdong Laboratory, Zhuhai, China
| | - Xiaoli Chen
- Guangdong Province Key Laboratory for Aquatic Economic Animals, School of Life Sciences, Sun Yat-sen University, Guangzhou, China.,Guangdong Provincial Engineering Technology Research Center for Healthy Breeding of Important Economic Fish, Guangzhou, China.,Southern Marine Science and Engineering Guangdong Laboratory, Zhuhai, China
| | - Huadong Yi
- Guangdong Province Key Laboratory for Aquatic Economic Animals, School of Life Sciences, Sun Yat-sen University, Guangzhou, China.,Guangdong Provincial Engineering Technology Research Center for Healthy Breeding of Important Economic Fish, Guangzhou, China.,Southern Marine Science and Engineering Guangdong Laboratory, Zhuhai, China
| | - Yuqin Su
- Guangdong Province Key Laboratory for Aquatic Economic Animals, School of Life Sciences, Sun Yat-sen University, Guangzhou, China.,Guangdong Provincial Engineering Technology Research Center for Healthy Breeding of Important Economic Fish, Guangzhou, China.,Southern Marine Science and Engineering Guangdong Laboratory, Zhuhai, China
| | - Yong Zhang
- Guangdong Province Key Laboratory for Aquatic Economic Animals, School of Life Sciences, Sun Yat-sen University, Guangzhou, China.,Guangdong Provincial Engineering Technology Research Center for Healthy Breeding of Important Economic Fish, Guangzhou, China.,Southern Marine Science and Engineering Guangdong Laboratory, Zhuhai, China
| | - Guifeng Li
- Guangdong Province Key Laboratory for Aquatic Economic Animals, School of Life Sciences, Sun Yat-sen University, Guangzhou, China.,Guangdong Provincial Engineering Technology Research Center for Healthy Breeding of Important Economic Fish, Guangzhou, China.,Southern Marine Science and Engineering Guangdong Laboratory, Zhuhai, China
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13
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Anderson AP, Rose E, Flanagan SP, Jones AG. The Estrogen-Responsive Transcriptome of Female Secondary Sexual Traits in the Gulf Pipefish. J Hered 2020; 111:294-306. [PMID: 32124926 DOI: 10.1093/jhered/esaa008] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2019] [Accepted: 02/24/2020] [Indexed: 01/01/2023] Open
Abstract
Sexual dimorphism often results from hormonally regulated trait differences between the sexes. In sex-role-reversed vertebrates, females often have ornaments used in mating competition that are expected to be under hormonal control. Males of the sex-role-reversed Gulf pipefish (Syngnathus scovelli) develop female-typical traits when they are exposed to estrogens. We aimed to identify genes whose expression levels changed during the development and maintenance of female-specific ornaments. We performed RNA-sequencing on skin and muscle tissue in male Gulf pipefish with and without exposure to estrogen to investigate the transcriptome of the sexually dimorphic ornament of vertical iridescent bands found in females and estrogen-exposed males. We further compared differential gene expression patterns between males and females to generate a list of genes putatively involved in the female secondary sex traits of bands and body depth. A detailed analysis of estrogen-receptor binding sites demonstrates that estrogen-regulated genes tend to have nearby cis-regulatory elements. Our results identified a number of genes that differed between the sexes and confirmed that many of these were estrogen-responsive. These estrogen-regulated genes may be involved in the arrangement of chromatophores for color patterning, as well as in the growth of muscles to achieve the greater body depth typical of females in this species. In addition, anaerobic respiration and adipose tissue could be involved in the rigors of female courtship and mating competition. Overall, this study generates a number of interesting hypotheses regarding the genetic basis of a female ornament in a sex-role-reversed pipefish.
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Affiliation(s)
| | - Emily Rose
- Department of Biology, University of Tampa, Tampa, FL
| | - Sarah P Flanagan
- School of Biological Sciences, University of Canterbury, Christchurch, New Zealand
| | - Adam G Jones
- Department of Biological Sciences, University of Idaho, Moscow, ID
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14
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Pengam M, Moisan C, Simon B, Guernec A, Inizan M, Amérand A. Training protocols differently affect AMPK-PGC-1α signaling pathway and redox state in trout muscle. Comp Biochem Physiol A Mol Integr Physiol 2020; 243:110673. [PMID: 32044445 DOI: 10.1016/j.cbpa.2020.110673] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2019] [Revised: 01/29/2020] [Accepted: 02/06/2020] [Indexed: 01/04/2023]
Abstract
Beneficial effects of physical exercise training are in part related to enhancement of muscle mitochondrial performance. The effects of two different trainings were investigated on transcripts and proteins of the AMPK-PGC-1α signaling pathway, the mitochondrial functioning (citrate synthase (CS), oxidative phosphorylation complexes, uncoupling proteins (UCP)) and the antioxidant defenses (superoxide dismutase (SOD), glutathione peroxidase (GPx), catalase) in rainbow trout red and white skeletal muscles. One group of trouts swam for 10 days at a moderate intensity (approximately 57% Ucrit or 2.0 body lengths/s, 23.5 h/day) and another group at a high intensity (approximately 90% Ucrit or 3.2 body lengths/s, 2 h/day). In the red muscle, the increase of Cs mRNA levels was significantly correlated with the transcripts of Ampkα1, Ampkα2, Pgc-1α, the oxidative phosphorylation complexes, Ucp2α, Ucp2β, Sod1, Sod2 and Gpx1. After 10 days of training, high intensity training (HIT) stimulates more the transcription of genes involved in this aerobic pathway than moderate intensity training (MIT) in the skeletal muscles, and mainly in the red oxidative muscle. However, no changes in CS, cytochrome c oxidase (COX) and antioxidant defenses activities and in oxidative stress marker (isoprostane plasmatic levels) were observed. The transcriptomic responses are fiber- and training-type dependent when proteins were not yet expressed after 10 days of training. As in mammals, our results suggest that HIT could promote benefit effects in fish.
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Affiliation(s)
- Morgane Pengam
- Université de Brest, EA 4324 ORPHY, UFR Sciences et Techniques, 6 avenue Victor Le Gorgeu, F-29200 Brest, France
| | - Christine Moisan
- Université de Brest, EA 4324 ORPHY, UFR Sciences et Techniques, 6 avenue Victor Le Gorgeu, F-29200 Brest, France
| | - Bernard Simon
- Université de Brest, EA 4324 ORPHY, UFR Sciences et Techniques, 6 avenue Victor Le Gorgeu, F-29200 Brest, France
| | - Anthony Guernec
- Université de Brest, EA 4324 ORPHY, UFR Sciences et Techniques, 6 avenue Victor Le Gorgeu, F-29200 Brest, France
| | - Manon Inizan
- Université de Brest, EA 4324 ORPHY, UFR Sciences et Techniques, 6 avenue Victor Le Gorgeu, F-29200 Brest, France
| | - Aline Amérand
- Université de Brest, EA 4324 ORPHY, UFR Sciences et Techniques, 6 avenue Victor Le Gorgeu, F-29200 Brest, France.
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15
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Raffini F, Schneider RF, Franchini P, Kautt AF, Meyer A. Diving into divergence: Differentiation in swimming performances, physiology and gene expression between locally‐adapted sympatric cichlid fishes. Mol Ecol 2019; 29:1219-1234. [DOI: 10.1111/mec.15304] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2019] [Revised: 10/24/2019] [Accepted: 11/08/2019] [Indexed: 12/25/2022]
Affiliation(s)
- Francesca Raffini
- Lehrstuhl für Zoologie und Evolutionsbiologie Department of Biology University of Konstanz Konstanz Germany
- International Max Planck Research School (IMPRS) for Organismal Biology Max‐Planck‐Institut für Ornithologie Radolfzell Germany
- Max Planck Institute for Ornithology Radolfzell Germany
| | - Ralf F. Schneider
- Lehrstuhl für Zoologie und Evolutionsbiologie Department of Biology University of Konstanz Konstanz Germany
- International Max Planck Research School (IMPRS) for Organismal Biology Max‐Planck‐Institut für Ornithologie Radolfzell Germany
| | - Paolo Franchini
- Lehrstuhl für Zoologie und Evolutionsbiologie Department of Biology University of Konstanz Konstanz Germany
| | - Andreas F. Kautt
- Lehrstuhl für Zoologie und Evolutionsbiologie Department of Biology University of Konstanz Konstanz Germany
| | - Axel Meyer
- Lehrstuhl für Zoologie und Evolutionsbiologie Department of Biology University of Konstanz Konstanz Germany
- International Max Planck Research School (IMPRS) for Organismal Biology Max‐Planck‐Institut für Ornithologie Radolfzell Germany
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16
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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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17
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Aedo JE, Zuloaga R, Boltaña S, Molina A, Valdés JA. Membrane-initiated cortisol action modulates early pyruvate dehydrogenase kinase 2 (pdk2) expression in fish skeletal muscle. Comp Biochem Physiol A Mol Integr Physiol 2019; 233:24-29. [DOI: 10.1016/j.cbpa.2019.03.022] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2018] [Revised: 02/27/2019] [Accepted: 03/25/2019] [Indexed: 10/27/2022]
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18
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Gomes F, Watanabe L, Vianez J, Nunes M, Cardoso J, Lima C, Schneider H, Sampaio I. Comparative analysis of the transcriptome of the Amazonian fish species Colossoma macropomum (tambaqui) and hybrid tambacu by next generation sequencing. PLoS One 2019; 14:e0212755. [PMID: 30802266 PMCID: PMC6388931 DOI: 10.1371/journal.pone.0212755] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2018] [Accepted: 02/10/2019] [Indexed: 12/13/2022] Open
Abstract
Background The C. macropomum is a characiform fish from the Amazon basin that has been hybridized with other pacu species to produce commercial hybrids, such as the tambacu. However, little is known of the functional genomics of the parental species or these hybrid forms. The transcriptome of C. macropomum and tambacu were sequenced using 454 Roche platform (pyrosequencing) techniques to characterize the domains of Gene Ontology (GO) and to evaluate the levels of gene expression in the two organisms. Results The 8,188,945 reads were assembled into 400,845 contigs. A total of 58,322 contigs were annotated with a predominance of biological processes for both organisms, as determined by Gene Ontology (GO). Similar numbers of metabolic pathways were identified in both the C. macropomum and the tambacu, with the metabolism category presenting the largest number of transcripts. The BUSCO analysis indicated that our assembly was more than 40% complete. We identified 21,986 genes for the two fishes. The P and Log2FC values indicated significant differences in the levels of gene expression, with a total of 600 up-regulated genes. Conclusion In spite of the lack of a reference genome, the functional annotation was successful, and confirmed a considerable difference in the specificity and levels of gene expression between the two organisms. This report provides a comprehensive baseline for the genetic management of these commercially important fishes, in particular for the identification of specific genes that may represent markers involved in the immunity, growth, and fertility of these organisms, with potential practical applications in aquaculture management.
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Affiliation(s)
- Fátima Gomes
- Institute of Coastal Studies, Laboratory of Genetics and Molecular Biology, Universidade Federal do Pará, Campus de Bragança, Alameda Leandro Ribeiro, Bragança, PA, Brazil
- * E-mail:
| | - Luciana Watanabe
- Institute of Coastal Studies, Laboratory of Genetics and Molecular Biology, Universidade Federal do Pará, Campus de Bragança, Alameda Leandro Ribeiro, Bragança, PA, Brazil
| | - João Vianez
- Center for Technological Innovation, Evandro Chagas Institute, Ministry of Health, Ananindeua, PA, Brazil
| | - Márcio Nunes
- Center for Technological Innovation, Evandro Chagas Institute, Ministry of Health, Ananindeua, PA, Brazil
| | - Jedson Cardoso
- Center for Technological Innovation, Evandro Chagas Institute, Ministry of Health, Ananindeua, PA, Brazil
- Postgraduate Program in Virology (PPGV), Evandro Chagas Institute, Ministry of Health, Ananindeua, PA, Brazil
| | - Clayton Lima
- Center for Technological Innovation, Evandro Chagas Institute, Ministry of Health, Ananindeua, PA, Brazil
| | - Horacio Schneider
- Institute of Coastal Studies, Laboratory of Genetics and Molecular Biology, Universidade Federal do Pará, Campus de Bragança, Alameda Leandro Ribeiro, Bragança, PA, Brazil
| | - Iracilda Sampaio
- Institute of Coastal Studies, Laboratory of Genetics and Molecular Biology, Universidade Federal do Pará, Campus de Bragança, Alameda Leandro Ribeiro, Bragança, PA, Brazil
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19
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Exercise improves growth, alters physiological performance and gene expression in common carp (Cyprinus carpio). Comp Biochem Physiol A Mol Integr Physiol 2018; 226:38-48. [DOI: 10.1016/j.cbpa.2018.08.007] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2018] [Revised: 08/04/2018] [Accepted: 08/13/2018] [Indexed: 01/09/2023]
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20
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Watanabe L, Gomes F, Vianez J, Nunes M, Cardoso J, Lima C, Schneider H, Sampaio I. De novo transcriptome based on next-generation sequencing reveals candidate genes with sex-specific expression in Arapaima gigas (Schinz, 1822), an ancient Amazonian freshwater fish. PLoS One 2018; 13:e0206379. [PMID: 30372461 PMCID: PMC6205615 DOI: 10.1371/journal.pone.0206379] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2018] [Accepted: 10/11/2018] [Indexed: 12/24/2022] Open
Abstract
Background The Arapaima (Arapaima gigas) is one of the world's largest freshwater bony fish, and is found in the rivers of the Amazon basin. This species is a potential aquaculture resource, although reproductive management in captivity is limited in particular due to the lack of external sexual dimorphism. In this study, using the 454 Roche platform (pyrosequencing) techniques, we evaluated a major portion of the transcriptome of this important Amazonian species. Results Four libraries obtained from the liver and skin tissue of juvenile specimens (representing males and females separately) were sequenced, yielding 5,453,919 high-quality reads. The de novo transcriptome assembly resulted in 175,792 contigs, with 51,057 significant blast hits. A total of 38,586 transcripts were mapped by Gene Ontology using Blast2GO. We identified 20,219 genes in the total transcriptome (9,551 in the liver and 16,818 in the skin). The gene expression analyses indicated 105 genes in the liver and 204 in the skin with differentiated expression profiles, with 95 being over-expressed in the females and 214 in the males. The log2 Fold Change and heatmap based on Reads Per Kilobase per Million mapped reads (RPKM) revealed that the gene expression in the skin is highly differentiated between male and female arapaima, while the levels of expression in the liver are similar between the sexes. Conclusion Transcriptome analysis based on pyrosequencing proved to be a reliable tool for the identification of genes with differentiated expression profiles between male and female arapaima. These results provide useful insights into the molecular pathways of sexual dimorphism in this important Amazonian species, and for comparative analyses with other teleosts.
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Affiliation(s)
- Luciana Watanabe
- Laboratório de Genética e Biologia Molecular, Instituto de Estudos Costeiros (IECOS), Universidade Federal do Pará, Campus de Bragança, Pará, Brazil
- * E-mail:
| | - Fátima Gomes
- Laboratório de Genética e Biologia Molecular, Instituto de Estudos Costeiros (IECOS), Universidade Federal do Pará, Campus de Bragança, Pará, Brazil
| | - João Vianez
- Centro de Inovações Tecnológicas (CIT), Instituto Evandro Chagas (IEC), Ananindeua, Pará, Brazil
| | - Márcio Nunes
- Centro de Inovações Tecnológicas (CIT), Instituto Evandro Chagas (IEC), Ananindeua, Pará, Brazil
| | - Jedson Cardoso
- Centro de Inovações Tecnológicas (CIT), Instituto Evandro Chagas (IEC), Ananindeua, Pará, Brazil
| | - Clayton Lima
- Centro de Inovações Tecnológicas (CIT), Instituto Evandro Chagas (IEC), Ananindeua, Pará, Brazil
| | - Horacio Schneider
- Laboratório de Genética e Biologia Molecular, Instituto de Estudos Costeiros (IECOS), Universidade Federal do Pará, Campus de Bragança, Pará, Brazil
| | - Iracilda Sampaio
- Laboratório de Genética e Biologia Molecular, Instituto de Estudos Costeiros (IECOS), Universidade Federal do Pará, Campus de Bragança, Pará, Brazil
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Palstra AP, Kals J, Blanco Garcia A, Dirks RP, Poelman M. Immunomodulatory Effects of Dietary Seaweeds in LPS Challenged Atlantic Salmon Salmo salar as Determined by Deep RNA Sequencing of the Head Kidney Transcriptome. Front Physiol 2018; 9:625. [PMID: 29910738 PMCID: PMC5992350 DOI: 10.3389/fphys.2018.00625] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2018] [Accepted: 05/09/2018] [Indexed: 02/03/2023] Open
Abstract
Seaweeds may represent immuno-stimulants that could be used as health-promoting fish feed components. This study was performed to gain insights into the immunomodulatory effects of dietary seaweeds in Atlantic salmon. Specifically tested were 10% inclusion levels of Laminaria digitata (SW1) and a commercial blend of seaweeds (Oceanfeed®) (SW2) against a fishmeal based control diet (FMC). Differences between groups were assessed in growth, feed conversion ratio and blood parameters hematocrit and hemoglobin. After a LPS challenge of fish representing each of the three groups, RNAseq was performed on the head kidney as major immune organ to determine transcriptomic differences in response to the immune activation. Atlantic salmon fed with dietary seaweeds did not show major differences in performance in comparison with fishmeal fed fish. RNAseq resulted in ∼154 million reads which were mapped against a NCBI Salmo salar reference and against a de novo assembled S. salar reference for analyses of expression of immune genes and ontology of immune processes among the 87,600 cDNA contigs. The dietary seaweeds provoked a more efficient immune response which involved more efficient identification of the infection site, and processing and presentation of antigens. More specifically, chemotaxis and the chemokine-mediated signaling were improved and therewith the defense response to Gram-positive bacterium reduced. Specific Laminaria digitata effects included reduction of the interferon-gamma-mediated signaling. Highly upregulated and specific for this diet was the expression of major histocompatibility complex class I-related gene protein. The commercial blend of seaweeds caused more differential expression than Laminaria digitata and improved immune processes such as receptor-mediated endocytosis and cell adhesion, and increased the expression of genes involved in response to lipopolysaccharide and inflammatory response. Particularly, expression of many important immune receptors was up-regulated illustrating increased responsiveness. NF-kappa-B inhibitor alpha is an important gene that marked the difference between both seaweed diets as Laminaria digitata inhibits the expression for this cytokine while the blend of seaweeds stimulates it. It can be concluded that the inclusion of seaweeds such as Laminaria digitata can have important modulatory effects on the immune capacity of Atlantic salmon resulting in a more efficient immune response.
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Affiliation(s)
- Arjan P Palstra
- Wageningen Marine Research, Wageningen University & Research, Yerseke, Netherlands.,Department of Animal Breeding and Genomics, Wageningen Livestock Research, Wageningen University & Research, Wageningen, Netherlands
| | - Jeroen Kals
- Wageningen Marine Research, Wageningen University & Research, Yerseke, Netherlands.,Department of Animal Nutrition, Wageningen Livestock Research, Wageningen University & Research, Wageningen, Netherlands
| | - Ainhoa Blanco Garcia
- Wageningen Marine Research, Wageningen University & Research, Yerseke, Netherlands
| | | | - Marnix Poelman
- Wageningen Marine Research, Wageningen University & Research, Yerseke, Netherlands
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23
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Jacobson G, Muncaster S, Mensink K, Forlenza M, Elliot N, Broomfield G, Signal B, Bird S. Omics and cytokine discovery in fish: Presenting the Yellowtail kingfish (Seriola lalandi) as a case study. DEVELOPMENTAL AND COMPARATIVE IMMUNOLOGY 2017; 75:63-76. [PMID: 28416435 DOI: 10.1016/j.dci.2017.04.001] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/09/2017] [Revised: 04/01/2017] [Accepted: 04/01/2017] [Indexed: 06/07/2023]
Abstract
A continued programme of research is essential to overcome production bottlenecks in any aquacultured fish species. Since the introduction of genetic and molecular techniques, the quality of immune research undertaken in fish has greatly improved. Thousands of species specific cytokine genes have been discovered, which can be used to conduct more sensitive studies to understand how fish physiology is affected by aquaculture environments or disease. Newly available transcriptomic technologies, make it increasingly easier to study the immunogenetics of farmed species for which little data exists. This paper reviews how the application of transcriptomic procedures such as RNA Sequencing (RNA-Seq) can advance fish research. As a case study, we present some preliminary findings using RNA-Seq to identify cytokine related genes in Seriola lalandi. These will allow in-depth investigations to understand the immune responses of these fish in response to environmental change or disease and help in the development of therapeutic approaches.
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Affiliation(s)
- Gregory Jacobson
- Molecular Genetics, Department of Biological Sciences, School of Science and Engineering, University of Waikato, Private Bag 3105, Hamilton 3240, New Zealand
| | - Simon Muncaster
- School Applied Science, Bay of Plenty Polytechnic, 70 Windermere Dr, Poike, Tauranga 3112, New Zealand
| | - Koen Mensink
- Cell Biology and Immunology Group, Department of Animal Sciences, Wageningen University, Wageningen, The Netherlands
| | - Maria Forlenza
- Cell Biology and Immunology Group, Department of Animal Sciences, Wageningen University, Wageningen, The Netherlands
| | - Nick Elliot
- Molecular Genetics, Department of Biological Sciences, School of Science and Engineering, University of Waikato, Private Bag 3105, Hamilton 3240, New Zealand
| | - Grant Broomfield
- Molecular Genetics, Department of Biological Sciences, School of Science and Engineering, University of Waikato, Private Bag 3105, Hamilton 3240, New Zealand
| | - Beth Signal
- Molecular Genetics, Department of Biological Sciences, School of Science and Engineering, University of Waikato, Private Bag 3105, Hamilton 3240, New Zealand
| | - Steve Bird
- Molecular Genetics, Department of Biological Sciences, School of Science and Engineering, University of Waikato, Private Bag 3105, Hamilton 3240, New Zealand.
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Trans-omics approaches used to characterise fish nutritional biorhythms in leopard coral grouper (Plectropomus leopardus). Sci Rep 2017; 7:9372. [PMID: 28839183 PMCID: PMC5570933 DOI: 10.1038/s41598-017-09531-4] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2017] [Accepted: 07/14/2017] [Indexed: 01/21/2023] Open
Abstract
Aquaculture is now a major supplier of fish, and has the potential to be a major source of protein in the future. Leopard coral groupers are traded in Asian markets as superior fish, and production via aquaculture has commenced. As feeding efficiency is of great concern in aquaculture, we sought to examine the metabolism of leopard coral groupers using trans-omics approaches. Metabolic mechanisms were comprehensively analysed using transcriptomic and metabolomic techniques. This study focused on the dynamics of muscular metabolites and gene expression. The omics data were discussed in light of circadian rhythms and fasting/feeding. The obtained data suggest that branched-chain amino acids played a role in energy generation in the fish muscle tissues during fasting. Moreover, glycolysis, TCA cycles, and purine metabolic substances exhibited circadian patterns, and gene expression also varied. This study is the first step to understanding the metabolic mechanisms of the leopard coral grouper.
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Genetic architecture of gene transcription in two Atlantic salmon (Salmo salar) populations. Heredity (Edinb) 2017; 119:117-124. [PMID: 28467401 DOI: 10.1038/hdy.2017.24] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2016] [Revised: 03/26/2017] [Accepted: 04/05/2017] [Indexed: 01/19/2023] Open
Abstract
Gene expression regulation has an important role in short-term acclimation and long-term adaptation to changing environments. However, the genetic architecture of gene expression has received much less attention than that of traditional phenotypic traits. In this study, we used a 5 × 5 full-factorial breeding design within each of two Atlantic salmon (Salmo salar) populations to characterize the genetic architecture of gene transcription. The two populations (LaHave and Sebago) are being used for reintroduction efforts into Lake Ontario, Canada. We used high-throughput quantitative real-time PCR to measure gene transcription levels for 22 genes in muscle tissue of Atlantic salmon fry. We tested for population differences in gene transcription and partitioned the transcription variance into additive genetic, non-additive genetic and maternal effects within each population. Interestingly, average additive genetic effects for gene transcription were smaller than those reported for traditional phenotypic traits in salmonids, suggesting that the evolutionary potential of gene transcription is lower than that of traditional traits. Contrary to expectations for early life stage traits, maternal effects were small. In general, the LaHave population had higher additive genetic effects for gene transcription than the Sebago population had, indicating that the LaHave fish have a higher adaptive potential to respond to the novel selection pressures associated with reintroduction into a novel environment. This study highlights not only the profound variation in gene transcription possible among salmonid populations but also the among-population variation in the underlying genetic architecture of such traits.
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Analysis of Gene Expression in an Inbred Line of Soft-Shell Clams ( Mya arenaria) Displaying Growth Heterosis: Regulation of Structural Genes and the NOD2 Pathway. Int J Genomics 2016; 2016:6720947. [PMID: 27822466 PMCID: PMC5086354 DOI: 10.1155/2016/6720947] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2016] [Revised: 08/11/2016] [Accepted: 08/25/2016] [Indexed: 12/19/2022] Open
Abstract
Mya arenaria is a bivalve mollusk of commercial and economic importance, currently impacted by ocean warming, acidification, and invasive species. In order to inform studies on the growth of M. arenaria, we selected and inbred a population of soft-shell clams for a fast-growth phenotype. This population displayed significantly faster growth (p < 0.0001), as measured by 35.4% greater shell size. To assess the biological basis of this growth heterosis, we characterized the complete transcriptomes of six individuals and identified differentially expressed genes by RNAseq. Pathways differentially expressed included structural gene pathways. Also differentially expressed was the nucleotide-binding oligomerization domain 2 (NOD2) receptor pathway that contributes to determination of growth, immunity, apoptosis, and proliferation. NOD2 pathway members that were upregulated included a subset of isoforms of RIPK2 (mean 3.3-fold increase in expression), ERK/MAPK14 (3.8-fold), JNK/MAPK8 (4.1-fold), and NFκB (4.08-fold). These transcriptomes will be useful resources for both the aquaculture community and researchers with an interest in mollusks and growth heterosis.
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Jeffries KM, Connon RE, Davis BE, Komoroske LM, Britton MT, Sommer T, Todgham AE, Fangue NA. Effects of high temperatures on threatened estuarine fishes during periods of extreme drought. J Exp Biol 2016; 219:1705-16. [DOI: 10.1242/jeb.134528] [Citation(s) in RCA: 63] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2015] [Accepted: 03/15/2016] [Indexed: 12/17/2022]
Abstract
ABSTRACT
Climate change and associated increases in water temperatures may impact physiological performance in ectotherms and exacerbate endangered species declines. We used an integrative approach to assess the impact of elevated water temperature on two fishes of immediate conservation concern in a large estuary system, the threatened longfin smelt (Spirinchus thaleichthys) and endangered delta smelt (Hypomesus transpacificus). Abundances have reached record lows in California, USA, and these populations are at imminent risk of extirpation. California is currently impacted by a severe drought, resulting in high water temperatures, conditions that will become more common as a result of climate change. We exposed fish to environmentally relevant temperatures (14°C and 20°C) and used RNA sequencing to examine the transcriptome-wide responses to elevated water temperature in both species. Consistent with having a lower temperature tolerance, longfin smelt exhibited a pronounced cellular stress response, with an upregulation of heat shock proteins, after exposure to 20°C that was not observed in delta smelt. We detected an increase in metabolic rate in delta smelt at 20°C and increased expression of genes involved in metabolic processes and protein synthesis, patterns not observed in longfin smelt. Through examination of responses across multiple levels of biological organization, and by linking these responses to habitat distributions in the wild, we demonstrate that longfin smelt may be more susceptible than delta smelt to increases in temperatures, and they have little room to tolerate future warming in California. Understanding the species-specific physiological responses of sensitive species to environmental stressors is crucial for conservation efforts and managing aquatic systems globally.
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Affiliation(s)
- Ken M. Jeffries
- Anatomy, Physiology & Cell Biology, School of Veterinary Medicine, University of California, Davis, One Shields Avenue, Davis, CA 95616, USA
- Wildlife, Fish & Conservation Biology, University of California, Davis, One Shields Avenue, Davis, CA 95616, USA
| | - Richard E. Connon
- Anatomy, Physiology & Cell Biology, School of Veterinary Medicine, University of California, Davis, One Shields Avenue, Davis, CA 95616, USA
| | - Brittany E. Davis
- Wildlife, Fish & Conservation Biology, University of California, Davis, One Shields Avenue, Davis, CA 95616, USA
- Department of Animal Science, University of California, Davis, One Shields Avenue, Davis, CA 95616, USA
| | - Lisa M. Komoroske
- Anatomy, Physiology & Cell Biology, School of Veterinary Medicine, University of California, Davis, One Shields Avenue, Davis, CA 95616, USA
- Wildlife, Fish & Conservation Biology, University of California, Davis, One Shields Avenue, Davis, CA 95616, USA
| | - Monica T. Britton
- Bioinformatics Core Facility, Genome Center, University of California, Davis, One Shields Avenue, Davis, CA 95616, USA
| | - Ted Sommer
- California Department of Water Resources, Division of Environmental Services, P.O. Box 942836, Sacramento, CA 94236, USA
| | - Anne E. Todgham
- Department of Animal Science, University of California, Davis, One Shields Avenue, Davis, CA 95616, USA
| | - Nann A. Fangue
- Wildlife, Fish & Conservation Biology, University of California, Davis, One Shields Avenue, Davis, CA 95616, USA
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Nagasawa K, Sarropoulou E, Edvardsen V, Fernandes JMO. Substantial Downregulation of Myogenic Transcripts in Skeletal Muscle of Atlantic Cod during the Spawning Period. PLoS One 2016; 11:e0148374. [PMID: 26844771 PMCID: PMC4742245 DOI: 10.1371/journal.pone.0148374] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2015] [Accepted: 01/18/2016] [Indexed: 11/19/2022] Open
Abstract
Gonadal maturation is an extremely energy consuming process for batch spawners and it is associated with a significant decrease in growth and seasonal deterioration in flesh quality. Our knowledge about the molecular mechanisms linking sexual maturation and muscle growth is still limited. In the present study, we performed RNA-Seq using 454 GS-FLX pyrosequencing in fast skeletal muscle sampled from two-year-old Atlantic cod (Gadus morhua) at representative time points throughout the reproductive cycle (August, March and May). In total, 126,937 good quality reads were obtained, with 546 nucleotide length and 52% GC content on average. RNA-Seq analysis using the CLC Genomics Workbench with the Atlantic cod reference UniGene cDNA data revealed 59,581 (46.9%) uniquely annotated reads. Pairwise comparison for expression levels identified 153 differentially expressed UniGenes between time points. Notably, we found a significant suppression of myh13 and myofibrillar gene isoforms in fast skeletal muscle during the spawning season. This study uncovered a large number of differentially expressed genes that may be influenced by gonadal maturation, thus representing a significant contribution to our limited understanding of the molecular mechanisms regulating muscle wasting and regeneration in batch spawners during their reproductive cycle.
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Affiliation(s)
- Kazue Nagasawa
- Marine Genomics Group, Faculty of Biosciences and Aquaculture, Nord University, 8049 Bodø, Norway
| | - Elena Sarropoulou
- Institute of Marine Biology, Biotechnology and Aquaculture, Hellenic Centre for Marine Research, 71003 Heraklion, Greece
| | - Vigdis Edvardsen
- Marine Genomics Group, Faculty of Biosciences and Aquaculture, Nord University, 8049 Bodø, Norway
| | - Jorge M. O. Fernandes
- Marine Genomics Group, Faculty of Biosciences and Aquaculture, Nord University, 8049 Bodø, Norway
- * E-mail:
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Evaluation of potential candidate genes involved in salinity tolerance in striped catfish (Pangasianodon hypophthalmus) using an RNA-Seq approach. Mar Genomics 2015; 25:75-88. [PMID: 26653845 DOI: 10.1016/j.margen.2015.11.010] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2015] [Revised: 11/21/2015] [Accepted: 11/21/2015] [Indexed: 12/19/2022]
Abstract
Increasing salinity levels in freshwater and coastal environments caused by sea level rise linked to climate change is now recognized to be a major factor that can impact fish growth negatively, especially for freshwater teleost species. Striped catfish (Pangasianodon hypophthalmus) is an important freshwater teleost that is now widely farmed across the Mekong River Delta in Vietnam. Understanding the basis for tolerance and adaptation to raised environmental salinity conditions can assist the regional culture industry to mitigate predicted impacts of climate change across this region. Attempt of next generation sequencing using the ion proton platform results in more than 174 million raw reads from three tissue libraries (gill, kidney and intestine). Reads were filtered and de novo assembled using a variety of assemblers and then clustered together to generate a combined reference transcriptome. Downstream analysis resulted in a final reference transcriptome that contained 60,585 transcripts with an N50 of 683 bp. This resource was further annotated using a variety of bioinformatics databases, followed by differential gene expression analysis that resulted in 3062 transcripts that were differentially expressed in catfish samples raised under two experimental conditions (0 and 15 ppt). A number of transcripts with a potential role in salinity tolerance were then classified into six different functional gene categories based on their gene ontology assignments. These included; energy metabolism, ion transportation, detoxification, signal transduction, structural organization and detoxification. Finally, we combined the data on functional salinity tolerance genes into a hypothetical schematic model that attempted to describe potential relationships and interactions among target genes to explain the molecular pathways that control adaptive salinity responses in P. hypophthalmus. Our results indicate that P. hypophthalmus exhibit predictable plastic regulatory responses to elevated salinity by means of characteristic gene expression patterns, providing numerous candidate genes for future investigations.
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Aedo JE, Maldonado J, Aballai V, Estrada JM, Bastias-Molina M, Meneses C, Gallardo-Escarate C, Silva H, Molina A, Valdés JA. mRNA-seq reveals skeletal muscle atrophy in response to handling stress in a marine teleost, the red cusk-eel (Genypterus chilensis). BMC Genomics 2015; 16:1024. [PMID: 26626593 PMCID: PMC4667402 DOI: 10.1186/s12864-015-2232-7] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2015] [Accepted: 11/19/2015] [Indexed: 01/07/2023] Open
Abstract
Background Fish reared under intensive conditions are repeatedly exposed to stress, which negatively impacts growth. Although most fish follow a conserved pattern of stress response, with increased concentrations of cortisol, each species presents specificities in the cell response and stress tolerance. Therefore, culturing new species requires a detailed knowledge of these specific responses. The red cusk-eel (Genypterus chilensis) is a new economically important marine species for the Chilean aquaculture industry. However, there is no information on the stress- and cortisol-induced mechanisms that decrease skeletal muscle growth in this teleost. Results Using Illumina RNA-seq technology, skeletal muscle sequence reads for G. chilensis were generated under control and handling stress conditions. Reads were mapped onto a reference transcriptome, resulting in the in silico identification of 785 up-regulated and 167 down-regulated transcripts. Gene ontology enrichment analysis revealed a significant up-regulation of catabolic genes associated with skeletal muscle atrophy. These results were validated by RT-qPCR analysis for ten candidates genes involved in ubiquitin-mediated proteolysis, autophagy and skeletal muscle growth. Additionally, using a primary culture of fish skeletal muscle cells, the effect of cortisol was evaluated in relation to red cusk-eel skeletal muscle atrophy. Conclusions The present data demonstrated that handling stress promotes skeletal muscle atrophy in the marine teleost G. chilensis through the expression of components of the ubiquitin-proteasome and autophagy-lysosome systems. Furthermore, cortisol was a powerful inductor of skeletal muscle atrophy in fish myotubes. This study is an important step towards understanding the atrophy system in non-model teleost species and provides novel insights on the cellular and molecular mechanisms that control skeletal muscle growth in early vertebrates. Electronic supplementary material The online version of this article (doi:10.1186/s12864-015-2232-7) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Jorge E Aedo
- Laboratorio de Biotecnología Molecular, Facultad de Ciencias Biológicas, Universidad Andrés Bello, Santiago, Chile
| | - Jonathan Maldonado
- Departamento de Producción Agrícola, Laboratorio de Genómica Funcional & Bioinformática, Universidad de Chile, Facultad de Ciencias Agronómicas, Av. Santa Rosa 11315, La Pintana, 8820808, Santiago, Chile
| | - Víctor Aballai
- Laboratorio de Biotecnología Molecular, Facultad de Ciencias Biológicas, Universidad Andrés Bello, Santiago, Chile
| | - Juan M Estrada
- Centro de Investigación Marina Quintay (CIMARQ), Universidad Andrés Bello, Quintay, Chile
| | - Macarena Bastias-Molina
- Centro de Biotecnología Vegetal, Facultad Ciencias Biológicas, Universidad Andrés Bello, Santiago, Chile
| | - Claudio Meneses
- Centro de Biotecnología Vegetal, Facultad Ciencias Biológicas, Universidad Andrés Bello, Santiago, Chile
| | - Cristian Gallardo-Escarate
- Laboratory of Biotechnology and Aquatic Genomics, Universidad de Concepción, Concepción, Chile.,Interdisciplinary Center for Aquaculture Research (INCAR), P.O. Box 160-C, Concepción, Chile
| | - Herman Silva
- Departamento de Producción Agrícola, Laboratorio de Genómica Funcional & Bioinformática, Universidad de Chile, Facultad de Ciencias Agronómicas, Av. Santa Rosa 11315, La Pintana, 8820808, Santiago, Chile
| | - Alfredo Molina
- Laboratorio de Biotecnología Molecular, Facultad de Ciencias Biológicas, Universidad Andrés Bello, Santiago, Chile.,Interdisciplinary Center for Aquaculture Research (INCAR), P.O. Box 160-C, Concepción, Chile.,Centro de Investigación Marina Quintay (CIMARQ), Universidad Andrés Bello, Quintay, Chile
| | - Juan A Valdés
- Laboratorio de Biotecnología Molecular, Facultad de Ciencias Biológicas, Universidad Andrés Bello, Santiago, Chile. .,Interdisciplinary Center for Aquaculture Research (INCAR), P.O. Box 160-C, Concepción, Chile. .,Centro de Investigación Marina Quintay (CIMARQ), Universidad Andrés Bello, Quintay, Chile.
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Valenzuela CA, Escobar D, Perez L, Zuloaga R, Estrada JM, Mercado L, Valdés JA, Molina A. Transcriptional dynamics of immune, growth and stress related genes in skeletal muscle of the fine flounder (Paralichthys adpersus) during different nutritional statuses. DEVELOPMENTAL AND COMPARATIVE IMMUNOLOGY 2015; 53:145-157. [PMID: 26165160 DOI: 10.1016/j.dci.2015.06.007] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/22/2015] [Revised: 06/09/2015] [Accepted: 06/10/2015] [Indexed: 06/04/2023]
Abstract
The effects of stress on immune activity and growth in early vertebrates have not been studied in detail. The present study used fine flounder (Paralichthys adspersus) skeletal muscle as a model to evaluate molecules involved in the stress response, including the glucocorticoid receptors, foxo1/3, and the target genes of these. Additionally, immune markers (il-1β and tnfα) and effector molecules of atrophy (bnip3, caspase-3, and lc3) were assessed. These molecules were analyzed during periods of long-term fasting and refeeding. During fasting, gene expression related to the stress response and atrophy increased; whereas immune markers were down-regulated. During refeeding, atrophy- and stress-related gene expression significantly decreased. In contrast, immune markers were up-regulated. These results provide novel insight on the control of growth in the skeletal muscle of a non-mammalian species under a stressful condition, suggesting that growth, stress, and immune activity in muscle are closely related and coordinated by orchestrated transcriptional dynamics.
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Affiliation(s)
- Cristián A Valenzuela
- Laboratorio de Biotecnología Molecular, Departamento de Ciencias Biológicas, Facultad Ciencias Biológicas, Universidad Andrés Bello, Av. Republica 217, Santiago, Chile; Interdisciplinary Center for Aquaculture Research (INCAR), Víctor Lamas 1290, PO Box 160-C, Concepción, Chile; Centro de Investigación Marina de Quintay (CIMARQ), Valparaiso, Chile
| | - Daniela Escobar
- Laboratorio de Biotecnología Molecular, Departamento de Ciencias Biológicas, Facultad Ciencias Biológicas, Universidad Andrés Bello, Av. Republica 217, Santiago, Chile
| | - Lorena Perez
- Laboratorio de Biotecnología Molecular, Departamento de Ciencias Biológicas, Facultad Ciencias Biológicas, Universidad Andrés Bello, Av. Republica 217, Santiago, Chile
| | - Rodrigo Zuloaga
- Laboratorio de Biotecnología Molecular, Departamento de Ciencias Biológicas, Facultad Ciencias Biológicas, Universidad Andrés Bello, Av. Republica 217, Santiago, Chile; Interdisciplinary Center for Aquaculture Research (INCAR), Víctor Lamas 1290, PO Box 160-C, Concepción, Chile; Centro de Investigación Marina de Quintay (CIMARQ), Valparaiso, Chile
| | | | - Luis Mercado
- Laboratorio de Genética e Inmunología Molecular, Grupo de Marcadores Inmunológicos, Pontificia Universidad Católica de Valparaíso, Av. Universidad No 330, Placilla Sector Curauma, Valparaíso, Chile
| | - Juan Antonio Valdés
- Laboratorio de Biotecnología Molecular, Departamento de Ciencias Biológicas, Facultad Ciencias Biológicas, Universidad Andrés Bello, Av. Republica 217, Santiago, Chile; Interdisciplinary Center for Aquaculture Research (INCAR), Víctor Lamas 1290, PO Box 160-C, Concepción, Chile; Centro de Investigación Marina de Quintay (CIMARQ), Valparaiso, Chile.
| | - Alfredo Molina
- Laboratorio de Biotecnología Molecular, Departamento de Ciencias Biológicas, Facultad Ciencias Biológicas, Universidad Andrés Bello, Av. Republica 217, Santiago, Chile; Interdisciplinary Center for Aquaculture Research (INCAR), Víctor Lamas 1290, PO Box 160-C, Concepción, Chile; Centro de Investigación Marina de Quintay (CIMARQ), Valparaiso, Chile.
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RNA-seq transcriptome analysis of extensor digitorum longus and soleus muscles in large white pigs. Mol Genet Genomics 2015; 291:687-701. [DOI: 10.1007/s00438-015-1138-z] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2015] [Accepted: 10/17/2015] [Indexed: 10/24/2022]
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Transcriptome and Molecular Pathway Analysis of the Hepatopancreas in the Pacific White Shrimp Litopenaeus vannamei under Chronic Low-Salinity Stress. PLoS One 2015; 10:e0131503. [PMID: 26147449 PMCID: PMC4492601 DOI: 10.1371/journal.pone.0131503] [Citation(s) in RCA: 50] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2015] [Accepted: 06/03/2015] [Indexed: 11/29/2022] Open
Abstract
The Pacific white shrimp Litopenaeus vannamei is a euryhaline penaeid species that shows ontogenetic adaptations to salinity, with its larvae inhabiting oceanic environments and postlarvae and juveniles inhabiting estuaries and lagoons. Ontogenetic adaptations to salinity manifest in L. vannamei through strong hyper-osmoregulatory and hypo-osmoregulatory patterns and an ability to tolerate extremely low salinity levels. To understand this adaptive mechanism to salinity stress, RNA-seq was used to compare the transcriptomic response of L. vannamei to changes in salinity from 30 (control) to 3 practical salinity units (psu) for 8 weeks. In total, 26,034 genes were obtained from the hepatopancreas tissue of L. vannamei using the Illumina HiSeq 2000 system, and 855 genes showed significant changes in expression under salinity stress. Eighteen top Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways were significantly involved in physiological responses, particularly in lipid metabolism, including fatty-acid biosynthesis, arachidonic acid metabolism and glycosphingolipid and glycosaminoglycan metabolism. Lipids or fatty acids can reduce osmotic stress in L. vannamei by providing additional energy or changing the membrane structure to allow osmoregulation in relevant organs, such as the gills. Steroid hormone biosynthesis and the phosphonate and phosphinate metabolism pathways were also involved in the adaptation of L. vannamei to low salinity, and the differential expression patterns of 20 randomly selected genes were validated by quantitative real-time PCR (qPCR). This study is the first report on the long-term adaptive transcriptomic response of L. vannamei to low salinity, and the results will further our understanding of the mechanisms underlying osmoregulation in euryhaline crustaceans.
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García-Ortega LF, Martínez O. How Many Genes Are Expressed in a Transcriptome? Estimation and Results for RNA-Seq. PLoS One 2015; 10:e0130262. [PMID: 26107654 PMCID: PMC4479379 DOI: 10.1371/journal.pone.0130262] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2015] [Accepted: 05/19/2015] [Indexed: 01/02/2023] Open
Abstract
RNA-seq experiments estimate the number of genes expressed in a transcriptome as well as their relative frequencies. However, an undetermined number of genes can remain undetected due to their low expression relative to the sample size (sequence depth). Estimation of the true number of genes expressed in a transcriptome is essential in order to determine which genes are exclusively expressed in specific tissues or under particular conditions. A reliable estimate of the true number of expressed genes is also required to accurately measure transcriptome changes and to predict the sequencing depth needed to increase the proportion of detected genes. This problem is analogous to ecological sampling problems such as estimating the number of species at a given site. Here we present a non-parametric estimator for the number of undetected genes as well as for the extra sample size needed to detect a given proportion of the undetected genes. Our estimators are superior to ones already published by having smaller standard errors and biases. We applied our method to a set of 32 publicly available RNA-seq experiments, including the evaluation of 311 individually sequenced libraries. We found that in the majority of the cases more than one thousand genes are undetected, and that on average approximately 6% of the expressed genes per accession remain undetected. This figure increases to approximately 10% if individual sequencing libraries are analyzed. Our method is also applicable to metagenomic experiments. Using our method, the number of undetected genes as well as the sample size needed to detect them can be calculated, leading to more accurate and complete gene expression studies.
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Affiliation(s)
- Luis Fernando García-Ortega
- Laboratorio Nacional de Genómica para la Biodiversidad (Langebio), Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional (Cinvestav-IPN), Irapuato, Guanajuato, México
| | - Octavio Martínez
- Laboratorio Nacional de Genómica para la Biodiversidad (Langebio), Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional (Cinvestav-IPN), Irapuato, Guanajuato, México
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De novo assembly and comprehensive characterization of the skeletal muscle transcriptomes of the European anchovy (Engraulis encrasicolus). Mar Genomics 2015; 20:7-9. [DOI: 10.1016/j.margen.2015.01.001] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2014] [Revised: 01/05/2015] [Accepted: 01/07/2015] [Indexed: 11/17/2022]
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36
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He L, Pei Y, Jiang Y, Li Y, Liao L, Zhu Z, Wang Y. Global gene expression patterns of grass carp following compensatory growth. BMC Genomics 2015; 16:184. [PMID: 25887225 PMCID: PMC4374334 DOI: 10.1186/s12864-015-1427-2] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2014] [Accepted: 03/02/2015] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Compensatory growth is accelerated compared with normal growth and occurs when growth-limiting conditions are overcome. Most animals, especially fish, are capable of compensatory growth, but the mechanisms remain unclear. Further investigation of the mechanism of compensatory growth in fish is needed to improve feeding efficiency, reduce cost, and explore growth-related genes. RESULTS In the study, grass carp, an important farmed fish in China, were subjected to a compensatory growth experiment followed by transcriptome analysis by RNA-sequencing. Samples of fish from starved and re-feeding conditions were compared with the control. Under starved conditions, 4061 and 1988 differentially expressed genes (DEGs) were detected in muscle and liver tissue when compared the experimental group with control group, respectively. After re-feeding, 349 and 247 DEGs were identified in muscle and liver when the two groups were compared. Moreover, when samples from experimental group in starved and re-feeding conditions were compared, 4903 and 2444 DEGs were found in muscle and liver. Most of these DEGs were involved in metabolic processes, or encoded enzymes or proteins with catalytic activity or binding functions, or involved in metabolic and biosynthetic pathways. A number of the more significant DEGs were subjected to further analysis. Under fasting conditions, many up-regulated genes were associated with protein ubiquitination or degradation, whereas many down-regulated genes were involved in the metabolism of glucose and fatty acids. Under re-feeding conditions, genes participating in muscle synthesis and fatty acid metabolism were up-regulated significantly, and genes related to protein ubiquitination or degradation were down-regulated. Moreover, Several DEGs were random selected for confirmation by real-time quantitative PCR. CONCLUSIONS Global gene expression patterns of grass carp during compensatory growth were determined. To our knowledge, this is a first reported for a teleost fish. The results will enhance our understanding of the mechanism of compensatory growth in teleost fish.
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Affiliation(s)
- Libo He
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, China.
| | - Yongyan Pei
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, China. .,University of Chinese Academy of Sciences, Beijing, 100049, China.
| | - Yao Jiang
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, China. .,University of Chinese Academy of Sciences, Beijing, 100049, China.
| | - Yongming Li
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, China.
| | - Lanjie Liao
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, China.
| | - Zuoyan Zhu
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, China.
| | - Yaping Wang
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, China.
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Mareco EA, Garcia de la Serrana D, Johnston IA, Dal-Pai-Silva M. Characterization of the transcriptome of fast and slow muscle myotomal fibres in the pacu (Piaractus mesopotamicus). BMC Genomics 2015; 16:182. [PMID: 25886905 PMCID: PMC4372171 DOI: 10.1186/s12864-015-1423-6] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2014] [Accepted: 02/28/2015] [Indexed: 12/19/2022] Open
Abstract
BACKGROUND The Pacu (Piaractus mesopotamicus) is a member of the Characiform family native to the Prata Basin (South America) and a target for the aquaculture industry. A limitation for the development of a selective breeding program for this species is a lack of available genetic information. The primary objectives of the present study were 1) to increase the genetic resources available for the species, 2) to exploit the anatomical separation of myotomal fibres types to compare the transcriptomes of slow and fast muscle phenotypes and 3) to systematically investigate the expression of Ubiquitin Specific Protease (USP) family members in fast and slow muscle in response to fasting and refeeding. RESULTS We generated 0.6 Tb of pair-end reads from slow and fast skeletal muscle libraries. Over 665 million reads were assembled into 504,065 contigs with an average length of 1,334 bp and N50 = 2,772 bp. We successfully annotated nearly 47% of the transcriptome and identified around 15,000 unique genes and over 8000 complete coding sequences. 319 KEGG metabolic pathways were also annotated and 380 putative microsatellites were identified. 956 and 604 genes were differentially expressed between slow and fast skeletal muscle, respectively. 442 paralogues pairs arising from the teleost-specific whole genome duplication were identified, with the majority showing different expression patterns between fibres types (301 in slow and 245 in fast skeletal muscle). 45 members of the USP family were identified in the transcriptome. Transcript levels were quantified by qPCR in a separate fasting and refeeding experiment. USP genes in fast muscle showed a similar transient increase in expression with fasting as the better characterized E3 ubiquitin ligases. CONCLUSION We have generated a 53-fold coverage transcriptome for fast and slow myotomal muscle in the pacu (Piaractus mesopotamicus) significantly increasing the genetic resources available for this important aquaculture species. We describe significant differences in gene expression between muscle fibre types for fundamental components of general metabolism, the Pi3k/Akt/mTor network and myogenesis, including detailed analysis of paralogue expression. We also provide a comprehensive description of USP family member expression between muscle fibre types and with changing nutritional status.
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Affiliation(s)
- Edson A Mareco
- Institute of Biosciences of Botucatu, São Paulo State University - UNESP, Botucatu, 18618-970, São Paulo, Brazil. .,School of Biology, Scottish Oceans Institute, University of St Andrews, St Andrews, KY16 8LB, Scotland, UK.
| | | | - Ian A Johnston
- School of Biology, Scottish Oceans Institute, University of St Andrews, St Andrews, KY16 8LB, Scotland, UK.
| | - Maeli Dal-Pai-Silva
- Institute of Biosciences of Botucatu, São Paulo State University - UNESP, Botucatu, 18618-970, São Paulo, Brazil.
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Zhang X, Wang S, Chen S, Chen Y, Liu Y, Shao C, Wang Q, Lu Y, Gong G, Ding S, Sha Z. Transcriptome analysis revealed changes of multiple genes involved in immunity in Cynoglossus semilaevis during Vibrio anguillarum infection. FISH & SHELLFISH IMMUNOLOGY 2015; 43:209-218. [PMID: 25543033 DOI: 10.1016/j.fsi.2014.11.018] [Citation(s) in RCA: 85] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/23/2014] [Revised: 11/15/2014] [Accepted: 11/16/2014] [Indexed: 06/04/2023]
Abstract
Half-smooth tongue sole (Cynoglossus semilaevis) is one of the most valuable marine aquatic species in Northern China. Given to the rapid development of aquaculture industry, the C. semilaevis was subjected to disease-causing bacteria Vibrio anguillarum. It therefore is indispensable and urgent to understand the mechanism of C. semilaevis host defense against V. anguillarum infection. In the present study, the extensively analysis at the transcriptome level for V. Anguillarum disease in tongue sole was carried out. In total, 94,716 high quality contigs were generated from 75,884,572 clean reads in three libraries (HOSG, NOSG, and CG). 22,746 unigenes were identified when compared with SwissProt, an NR protein database and NT nucleotide database. 954 genes exhibiting the differentially expression at least one pair of comparison in all three libraries were identified. GO enrichment for these genes revealed gene response to biotic stimulus, immune system regulation, and immune response and cytokine production. Further, the pathways such as complement and coagulation cascades and Vibrio cholerae infection pathways were enriched in defensing of pathogen. Besides, 13,428 SSRs and 118,239 SNPs were detected in tongue sole, providing further support for genetic variation and marker-assisted selection in future. In summary, this study identifies several putative immune pathways and candidate genes deserving further investigation in the context of development of therapeutic regimens and lays the foundation for selecting resistant lines of C. semilaevis against V. anguillarum.
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Affiliation(s)
- Xiang Zhang
- Key Laboratory for Sustainable Utilization of Marine Fisheries Resources, Ministry of Agriculture, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao 266071, Shandong, China; Laboratory of Marine Biodiversity and Global Change, College of Oceanography and Environmental Science, Xiamen University, 182 Daxue Road, Xiamen 361005, Fujian, China
| | - Shaolin Wang
- Department of Psychiatry & Neurobiology Science, University of Virginia, 1670 Discovery Drive, Suite 110, Charlottesville 22911, VA, USA
| | - Songlin Chen
- Key Laboratory for Sustainable Utilization of Marine Fisheries Resources, Ministry of Agriculture, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao 266071, Shandong, China
| | - Yadong Chen
- Key Laboratory for Sustainable Utilization of Marine Fisheries Resources, Ministry of Agriculture, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao 266071, Shandong, China
| | - Yang Liu
- College of Fisheries and Life Science, Dalian Ocean University, Dalian 116023, China
| | - Changwei Shao
- Key Laboratory for Sustainable Utilization of Marine Fisheries Resources, Ministry of Agriculture, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao 266071, Shandong, China
| | - Qilong Wang
- Key Laboratory for Sustainable Utilization of Marine Fisheries Resources, Ministry of Agriculture, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao 266071, Shandong, China
| | - Yang Lu
- Key Laboratory for Sustainable Utilization of Marine Fisheries Resources, Ministry of Agriculture, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao 266071, Shandong, China
| | - Guangye Gong
- Key Laboratory for Sustainable Utilization of Marine Fisheries Resources, Ministry of Agriculture, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao 266071, Shandong, China
| | - Shaoxiong Ding
- Laboratory of Marine Biodiversity and Global Change, College of Oceanography and Environmental Science, Xiamen University, 182 Daxue Road, Xiamen 361005, Fujian, China
| | - Zhenxia Sha
- Key Laboratory for Sustainable Utilization of Marine Fisheries Resources, Ministry of Agriculture, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao 266071, Shandong, China.
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Palstra AP, Mes D, Kusters K, Roques JAC, Flik G, Kloet K, Blonk RJW. Forced sustained swimming exercise at optimal speed enhances growth of juvenile yellowtail kingfish (Seriola lalandi). Front Physiol 2015; 5:506. [PMID: 25620933 PMCID: PMC4287099 DOI: 10.3389/fphys.2014.00506] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2014] [Accepted: 12/04/2014] [Indexed: 01/28/2023] Open
Abstract
Swimming exercise at optimal speed may optimize growth performance of yellowtail kingfish in a recirculating aquaculture system. Therefore, optimal swimming speeds (Uopt in m s−1 or body lengths s−1, BL s−1) were assessed and then applied to determine the effects of long-term forced and sustained swimming at Uopt on growth performance of juvenile yellowtail kingfish. Uopt was quantified in Blazka-type swim-tunnels for 145, 206, and 311 mm juveniles resulting in values of: (1) 0.70 m s−1 or 4.83 BL s−1, (2) 0.82 m s−1 or 3.25 BL s−1, and (3) 0.85 m s−1 or 2.73 BL s−1. Combined with literature data from larger fish, a relation of Uopt (BL s−1) = 234.07(BL)−0.779 (R2 = 0.9909) was established for this species. Yellowtail kingfish, either forced to perform sustained swimming exercise at an optimal speed of 2.46 BL s−1 (“swimmers”) or allowed to perform spontaneous activity at low water flow (“resters”) in a newly designed 3600 L oval flume (with flow created by an impeller driven by an electric motor), were then compared. At the start of the experiment, ten fish were sampled representing the initial condition. After 18 days, swimmers (n = 23) showed a 92% greater increase in BL and 46% greater increase in BW as compared to resters (n = 23). As both groups were fed equal rations, feed conversion ratio (FCR) for swimmers was 1.21 vs. 1.74 for resters. Doppler ultrasound imaging showed a statistically significant higher blood flow (31%) in the ventral aorta of swimmers vs. resters (44 ± 3 vs. 34 ± 3 mL min−1, respectively, under anesthesia). Thus, growth performance can be rapidly improved by optimal swimming, without larger feed investments.
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Affiliation(s)
- Arjan P Palstra
- Institute for Marine Resources and Ecosystem Studies, Wageningen Aquaculture†, Wageningen University and Research Centre Yerseke, Netherlands
| | - Daan Mes
- Institute for Marine Resources and Ecosystem Studies, Wageningen Aquaculture†, Wageningen University and Research Centre Yerseke, Netherlands
| | - Kasper Kusters
- Institute for Marine Resources and Ecosystem Studies, Wageningen Aquaculture†, Wageningen University and Research Centre Yerseke, Netherlands
| | - Jonathan A C Roques
- Department of Animal physiology, Institute for Water and Wetland Research, Radboud University Nijmegen Nijmegen, Netherlands
| | - Gert Flik
- Department of Animal physiology, Institute for Water and Wetland Research, Radboud University Nijmegen Nijmegen, Netherlands
| | | | - Robbert J W Blonk
- Institute for Marine Resources and Ecosystem Studies, Wageningen Aquaculture†, Wageningen University and Research Centre Yerseke, Netherlands
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Morash AJ, Vanderveken M, McClelland GB. Muscle metabolic remodeling in response to endurance exercise in salmonids. Front Physiol 2014; 5:452. [PMID: 25484869 PMCID: PMC4240067 DOI: 10.3389/fphys.2014.00452] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2014] [Accepted: 11/03/2014] [Indexed: 11/13/2022] Open
Abstract
Phenotypic plasticity of skeletal muscle is relevant to swimming performance and metabolism in fishes, especially those that undergo extreme locomotory feats, such as seasonal migration. However, the influence of endurance exercise and the molecular mechanisms coordinating this remodeling are not well understood. The present study examines muscle metabolic remodeling associated with endurance exercise in fed rainbow trout as compared to migrating salmon. Trout were swum for 4 weeks at 1.5 BL/s, a speed similar to that of migrating salmon and red and white muscles were sampled after each week. We quantified changes in key enzymes in aerobic and carbohydrate metabolism [citrate synthase (CS), β-hydroxyacyl-CoA dehydrogenase (HOAD), hexokinase (HK)] and changes in mRNA expression of major regulators of metabolic phenotype (AMPK, PPARs) and lipid (carnitine palmitoyltransferase, CPT I), protein (aspartate aminotransferase, AST) and carbohydrate (HK) oxidation pathways. After 1 week of swimming substantial increases were seen in AMPK and PPARα mRNA expression and of their downstream target genes, CPTI and HK in red muscle. However, significant changes in CS and HK activity occurred only after 4 weeks. In contrast, there were few changes in mRNA expression and enzyme activities in white muscle over the 4-weeks. Red muscle results mimic those found in migrating salmon suggesting a strong influence of exercise on red muscle phenotype. In white muscle, only changes in AMPK and PPAR expression were similar to that seen with migrating salmon. However, in contrast to exercise alone, in natural migration HK decreased while AST increased suggesting that white muscle plays a role in supplying fuel and intermediates possibly through tissue breakdown during prolonged fasting. Dissecting individual and potentially synergistic effects of multiple stressors will enable us to determine major drivers of the metabolic phenotype and their impacts on whole animal performance.
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Affiliation(s)
- Andrea J Morash
- Department of Biology, McMaster University Hamilton, ON, Canada ; Institute for Marine and Antarctic Studies, University of Tasmania Hobart, TAS, Australia
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Díaz N, Ribas L, Piferrer F. Effects of changes in food supply at the time of sex differentiation on the gonadal transcriptome of juvenile fish. Implications for natural and farmed populations. PLoS One 2014; 9:e111304. [PMID: 25340342 PMCID: PMC4207807 DOI: 10.1371/journal.pone.0111304] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2014] [Accepted: 09/30/2014] [Indexed: 01/18/2023] Open
Abstract
Background Food supply is a major factor influencing growth rates in animals. This has important implications for both natural and farmed fish populations, since food restriction may difficult reproduction. However, a study on the effects of food supply on the development of juvenile gonads has never been transcriptionally described in fish. Methods and Findings This study investigated the consequences of growth on gonadal transcriptome of European sea bass in: 1) 4-month-old sexually undifferentiated fish, comparing the gonads of fish with the highest vs. the lowest growth, to explore a possible link between transcriptome and future sex, and 2) testis from 11-month-old juveniles where growth had been manipulated through changes in food supply. The four groups used were: i) sustained fast growth, ii) sustained slow growth, iii) accelerated growth, iv) decelerated growth. The transcriptome of undifferentiated gonads was not drastically affected by initial natural differences in growth. Further, changes in the expression of genes associated with protein turnover were seen, favoring catabolism in slow-growing fish and anabolism in fast-growing fish. Moreover, while fast-growing fish took energy from glucose, as deduced from the pathways affected and the analysis of protein-protein interactions examined, in slow-growing fish lipid metabolism and gluconeogenesis was favored. Interestingly, the highest transcriptomic differences were found when forcing initially fast-growing fish to decelerate their growth, while accelerating growth of initially slow-growing fish resulted in full transcriptomic convergence with sustained fast-growing fish. Conclusions Food availability during sex differentiation shapes the juvenile testis transcriptome, as evidenced by adaptations to different energy balances. Remarkably, this occurs in absence of major histological changes in the testis. Thus, fish are able to recover transcriptionally their testes if they are provided with enough food supply during sex differentiation; however, an initial fast growth does not represent any advantage in terms of transcriptional fitness if later food becomes scarce.
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Affiliation(s)
- Noelia Díaz
- Institut de Ciències del Mar, Consejo Superior de Investigaciones Científicas (CSIC), Barcelona, Spain
| | - Laia Ribas
- Institut de Ciències del Mar, Consejo Superior de Investigaciones Científicas (CSIC), Barcelona, Spain
| | - Francesc Piferrer
- Institut de Ciències del Mar, Consejo Superior de Investigaciones Científicas (CSIC), Barcelona, Spain
- * E-mail:
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Calduch-Giner JA, Echasseriau Y, Crespo D, Baron D, Planas JV, Prunet P, Pérez-Sánchez J. Transcriptional assessment by microarray analysis and large-scale meta-analysis of the metabolic capacity of cardiac and skeletal muscle tissues to cope with reduced nutrient availability in Gilthead Sea Bream (Sparus aurata L.). MARINE BIOTECHNOLOGY (NEW YORK, N.Y.) 2014; 16:423-435. [PMID: 24626932 DOI: 10.1007/s10126-014-9562-3] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/18/2013] [Accepted: 01/06/2014] [Indexed: 06/03/2023]
Abstract
The effects of nutrient availability on the transcriptome of cardiac and skeletal muscle tissues were assessed in juvenile gilthead sea bream fed with a standard diet at two feeding levels: (1) full ration size and (2) 70 % satiation followed by a finishing phase at the maintenance ration. Microarray analysis evidenced a characteristic transcriptomic profile for each muscle tissue following changes in oxidative capacity (heart > red skeletal muscle > white skeletal muscle). The transcriptome of heart and secondly that of red skeletal muscle were highly responsive to nutritional changes, whereas that of glycolytic white skeletal muscle showed less ability to respond. The highly expressed and nutritionally regulated genes of heart were mainly related to signal transduction and transcriptional regulation. In contrast, those of white muscle were enriched in gene ontology (GO) terms related to proteolysis and protein ubiquitination. Microarray meta-analysis using the bioinformatic tool Fish and Chips ( http://fishandchips.genouest.org/index.php ) showed the close association of a representative cluster of white skeletal muscle with some of cardiac and red skeletal muscle, and many GO terms related to mitochondrial function appeared to be common links between them. A second round of cluster comparisons revealed that mitochondria-related GOs also linked differentially expressed genes of heart with those of liver from cortisol-treated gilthead sea bream. These results show that mitochondria are among the first responders to environmental and nutritional stress stimuli in gilthead sea bream, and functional phenotyping of this cellular organelle is highly promising to obtain reliable markers of growth performance and well-being in this fish species.
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Affiliation(s)
- Josep A Calduch-Giner
- Nutrigenomics and Fish Growth Endocrinology Group, Instituto de Acuicultura Torre de la Sal (IATS-CSIC), Castellón, Spain
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Wang S, Furmanek T, Kryvi H, Krossøy C, Totland GK, Grotmol S, Wargelius A. Transcriptome sequencing of Atlantic salmon (Salmo salar L.) notochord prior to development of the vertebrae provides clues to regulation of positional fate, chordoblast lineage and mineralisation. BMC Genomics 2014; 15:141. [PMID: 24548379 PMCID: PMC3943441 DOI: 10.1186/1471-2164-15-141] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2013] [Accepted: 02/13/2014] [Indexed: 11/26/2022] Open
Abstract
Background In teleosts such as Atlantic salmon (Salmo salar L.), segmentation and subsequent mineralisation of the notochord during embryonic stages are essential for normal vertebrae formation. However, the molecular mechanisms leading to segmentation and mineralisation of the notochord are poorly understood. The aim of this study was to identify genes/pathways acting in gradients over time and along the anterior-posterior axis during notochord segmentation and immediately prior to mineralisation of the vertebral bodies in Atlantic salmon. Results Notochord samples were collected from unsegmented, pre-segmented and segmented developmental stages. In each stage, the cellular core of the notochord was cut into three pieces along the longitudinal axis (anterior, mid, posterior). RNA was sequenced (22 million pair-end 100 bp/ library) and mapped to the salmon genome. 66569 transcripts were predicted and 55775 were annotated. In order to identify possible gradients leading to segmentation of the notochord, all 71 notochord-expressed hox genes were investigated, most of them displaying a typical anterior-posterior expression pattern along the notochord axis. The clustering of hox genes revealed a pattern that could be related to notochord segmentation. We further investigated how mineralisation is initiated in the notochord, and several factors related to chondrogenic lineage were identified (sox9, sox5, sox6, tgfb3, ihhb and col2a1), suggesting a cartilage-like character of the notochord. KEGG analysis of differentially expressed genes between stages revealed down-regulation of pathways associated with ECM, cell division, metabolism and development at onset of notochord segmentation. This implies that inhibitory signals produce segmentation of the notochord. One such potential inhibitory signal was identified, col11a2, which was detected in segments of non-mineralising notochord. Conclusions An incomplete salmon genome was successfully used to analyse RNA-seq data from the cellular core of the Atlantic salmon notochord. In transcriptome we found; hox gene patterns possibly linked to segmentation; down-regulation of pathways in the notochord at onset of segmentation; segmented expression of col11a2 in non-mineralised segments of the notochord; and a chondroblast-like footprint in the notochord.
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RNA-seq analysis of early hepatic response to handling and confinement stress in rainbow trout. PLoS One 2014; 9:e88492. [PMID: 24558395 PMCID: PMC3928254 DOI: 10.1371/journal.pone.0088492] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2013] [Accepted: 01/07/2014] [Indexed: 12/02/2022] Open
Abstract
Fish under intensive rearing conditions experience various stressors which have negative impacts on survival, growth, reproduction and fillet quality. Identifying and characterizing the molecular mechanisms underlying stress responses will facilitate the development of strategies that aim to improve animal welfare and aquaculture production efficiency. In this study, we used RNA-seq to identify transcripts which are differentially expressed in the rainbow trout liver in response to handling and confinement stress. These stressors were selected due to their relevance in aquaculture production. Total RNA was extracted from the livers of individual fish in five tanks having eight fish each, including three tanks of fish subjected to a 3 hour handling and confinement stress and two control tanks. Equal amount of total RNA of six individual fish was pooled by tank to create five RNA-seq libraries which were sequenced in one lane of Illumina HiSeq 2000. Three sequencing runs were conducted to obtain a total of 491,570,566 reads which were mapped onto the previously generated stress reference transcriptome to identify 316 differentially expressed transcripts (DETs). Twenty one DETs were selected for qPCR to validate the RNA-seq approach. The fold changes in gene expression identified by RNA-seq and qPCR were highly correlated (R2 = 0.88). Several gene ontology terms including transcription factor activity and biological process such as glucose metabolic process were enriched among these DETs. Pathways involved in response to handling and confinement stress were implicated by mapping the DETs to reference pathways in the KEGG database. Accession Numbers Raw RNA-seq reads have been submitted to the NCBI Short Read Archive under accession number SRP022881. Customized Perl Scripts All customized scripts described in this paper are available from Dr. Guangtu Gao or the corresponding author.
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Magnoni LJ, Palstra AP, Planas JV. Fueling the engine: induction of AMP-activated protein kinase in trout skeletal muscle by swimming. ACTA ACUST UNITED AC 2014; 217:1649-52. [PMID: 24526729 DOI: 10.1242/jeb.099192] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
AMP-activated protein kinase (AMPK) is well known to be induced by exercise and to mediate important metabolic changes in the skeletal muscle of mammals. Despite the physiological importance of exercise as a modulator of energy use by locomotory muscle, the regulation of this enzyme by swimming has not been investigated in fish. We found that sustained swimming (40 days at 0.75 body lengths s(-1)) increased AMPK activity in red and white trout skeletal muscle (3.9- and 2.2-fold, respectively) as well as the expression of AMPK target genes involved in energy use: lipoprotein lipase and citrate synthase in red and white muscle and CPT1β1b and PGC-1α in red muscle. Furthermore, electrical pulse stimulation of cultured trout myotubes increased AMPK activity and glucose uptake (1.9- and 1.2-fold, respectively) in an AMPK-dependent manner. These results suggest that AMPK may play an important mediatory role in the metabolic adaptation to swimming in fish skeletal muscle.
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Affiliation(s)
- Leonardo J Magnoni
- Departament de Fisiologia i Immunologia, Facultat de Biologia, Universitat de Barcelona, Institut de Biomedicina de la Universitat de Barcelona (IBUB), 08028 Barcelona, Spain
| | - Arjan P Palstra
- Departament de Fisiologia i Immunologia, Facultat de Biologia, Universitat de Barcelona, Institut de Biomedicina de la Universitat de Barcelona (IBUB), 08028 Barcelona, Spain
| | - Josep V Planas
- Departament de Fisiologia i Immunologia, Facultat de Biologia, Universitat de Barcelona, Institut de Biomedicina de la Universitat de Barcelona (IBUB), 08028 Barcelona, Spain
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Qian X, Ba Y, Zhuang Q, Zhong G. RNA-Seq technology and its application in fish transcriptomics. OMICS-A JOURNAL OF INTEGRATIVE BIOLOGY 2013; 18:98-110. [PMID: 24380445 DOI: 10.1089/omi.2013.0110] [Citation(s) in RCA: 177] [Impact Index Per Article: 16.1] [Reference Citation Analysis] [Abstract] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
High-throughput sequencing technologies, also known as next-generation sequencing (NGS) technologies, have revolutionized the way that genomic research is advancing. In addition to the static genome, these state-of-art technologies have been recently exploited to analyze the dynamic transcriptome, and the resulting technology is termed RNA sequencing (RNA-seq). RNA-seq is free from many limitations of other transcriptomic approaches, such as microarray and tag-based sequencing method. Although RNA-seq has only been available for a short time, studies using this method have completely changed our perspective of the breadth and depth of eukaryotic transcriptomes. In terms of the transcriptomics of teleost fishes, both model and non-model species have benefited from the RNA-seq approach and have undergone tremendous advances in the past several years. RNA-seq has helped not only in mapping and annotating fish transcriptome but also in our understanding of many biological processes in fish, such as development, adaptive evolution, host immune response, and stress response. In this review, we first provide an overview of each step of RNA-seq from library construction to the bioinformatic analysis of the data. We then summarize and discuss the recent biological insights obtained from the RNA-seq studies in a variety of fish species.
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Affiliation(s)
- Xi Qian
- 1 Department of Animal Science, University of Vermont , Burlington, Vermont
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Abstract
In this review, we present an overview of the recent advances of genomic technologies applied to studies of fish species belonging to the superclass of Osteichthyes (bony fish) with a major emphasis on the infraclass of Teleostei, also called teleosts. This superclass that represents more than 50% of all known vertebrate species has gained considerable attention from genome researchers in the last decade. We discuss many examples that demonstrate that this highly deserved attention is currently leading to new opportunities for answering important biological questions on gene function and evolutionary processes. In addition to giving an overview of the technologies that have been applied for studying various fish species we put the recent advances in genome research on the model species zebrafish and medaka in the context of its impact for studies of all fish of the superclass of Osteichthyes. We thereby want to illustrate how the combined value of research on model species together with a broad angle perspective on all bony fish species will have a huge impact on research in all fields of fundamental science and will speed up applications in many societally important areas such as the development of new medicines, toxicology test systems, environmental sensing systems and sustainable aquaculture strategies.
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