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Ryder D, Stone D, Minardi D, Riley A, Avant J, Cross L, Soeffker M, Davidson D, Newman A, Thomson P, Darby C, van Aerle R. De novo assembly and annotation of the Patagonian toothfish (Dissostichus eleginoides) genome. BMC Genomics 2024; 25:233. [PMID: 38438840 PMCID: PMC10910785 DOI: 10.1186/s12864-024-10141-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2023] [Accepted: 02/19/2024] [Indexed: 03/06/2024] Open
Abstract
BACKGROUND Patagonian toothfish (Dissostichus eleginoides) is an economically and ecologically important fish species in the family Nototheniidae. Juveniles occupy progressively deeper waters as they mature and grow, and adults have been caught as deep as 2500 m, living on or in just above the southern shelves and slopes around the sub-Antarctic islands of the Southern Ocean. As apex predators, they are a key part of the food web, feeding on a variety of prey, including krill, squid, and other fish. Despite its importance, genomic sequence data, which could be used for more accurate dating of the divergence between Patagonian and Antarctic toothfish, or establish whether it shares adaptations to temperature with fish living in more polar or equatorial climes, has so far been limited. RESULTS A high-quality D. eleginoides genome was generated using a combination of Illumina, PacBio and Omni-C sequencing technologies. To aid the genome annotation, the transcriptome derived from a variety of toothfish tissues was also generated using both short and long read sequencing methods. The final genome assembly was 797.8 Mb with a N50 scaffold length of 3.5 Mb. Approximately 31.7% of the genome consisted of repetitive elements. A total of 35,543 putative protein-coding regions were identified, of which 50% have been functionally annotated. Transcriptomics analysis showed that approximately 64% of the predicted genes (22,617 genes) were found to be expressed in the tissues sampled. Comparative genomics analysis revealed that the anti-freeze glycoprotein (AFGP) locus of D. eleginoides does not contain any AFGP proteins compared to the same locus in the Antarctic toothfish (Dissostichus mawsoni). This is in agreement with previously published results looking at hybridization signals and confirms that Patagonian toothfish do not possess AFGP coding sequences in their genome. CONCLUSIONS We have assembled and annotated the Patagonian toothfish genome, which will provide a valuable genetic resource for ecological and evolutionary studies on this and other closely related species.
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Affiliation(s)
- David Ryder
- Centre for Environment, Fisheries and Aquaculture Science (Cefas), Lowestoft, Suffolk, UK.
| | - David Stone
- Centre for Environment, Fisheries and Aquaculture Science (Cefas), Lowestoft, Suffolk, UK
| | - Diana Minardi
- Centre for Environment, Fisheries and Aquaculture Science (Cefas), Lowestoft, Suffolk, UK
| | - Ainsley Riley
- Centre for Environment, Fisheries and Aquaculture Science (Cefas), Lowestoft, Suffolk, UK
| | - Justin Avant
- Centre for Environment, Fisheries and Aquaculture Science (Cefas), Lowestoft, Suffolk, UK
| | - Lisa Cross
- Centre for Environment, Fisheries and Aquaculture Science (Cefas), Lowestoft, Suffolk, UK
| | - Marta Soeffker
- Centre for Environment, Fisheries and Aquaculture Science (Cefas), Lowestoft, Suffolk, UK
- Collaborative Centre for Sustainable Use of the Seas, University of East Anglia, Norwich, UK
| | | | | | | | - Chris Darby
- Centre for Environment, Fisheries and Aquaculture Science (Cefas), Lowestoft, Suffolk, UK
| | - Ronny van Aerle
- Centre for Environment, Fisheries and Aquaculture Science (Cefas), Lowestoft, Suffolk, UK
- Centre for Sustainable Aquaculture Futures , University of Exeter, Exeter, UK
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O’Brien KM, Oldham CA, Sarrimanolis J, Fish A, Castellini L, Vance J, Lekanof H, Crockett EL. Warm acclimation alters antioxidant defences but not metabolic capacities in the Antarctic fish, Notothenia coriiceps. CONSERVATION PHYSIOLOGY 2022; 10:coac054. [PMID: 35935168 PMCID: PMC9346567 DOI: 10.1093/conphys/coac054] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/10/2022] [Revised: 06/14/2022] [Accepted: 07/19/2022] [Indexed: 06/15/2023]
Abstract
The Southern Ocean surrounding the Western Antarctic Peninsula region is rapidly warming. Survival of members of the dominant suborder of Antarctic fishes, the Notothenioidei, will likely require thermal plasticity and adaptive capacity in key traits delimiting thermal tolerance. Herein, we have assessed the thermal plasticity of several cellular and biochemical pathways, many of which are known to be associated with thermal tolerance in notothenioids, including mitochondrial function, activities of aerobic and anaerobic enzymes, antioxidant defences, protein ubiquitination and degradation in cardiac, oxidative skeletal muscles and gill of Notothenia coriiceps warm acclimated to 4°C for 22 days or 5°C for 42 days. Levels of triacylglycerol (TAG) were measured in liver and oxidative and glycolytic skeletal muscles, and glycogen in liver and glycolytic muscle to assess changes in energy stores. Metabolic pathways displayed minimal thermal plasticity, yet antioxidant defences were lower in heart and oxidative skeletal muscles of warm-acclimated animals compared with animals held at ambient temperature. Despite higher metabolic rates at elevated temperature, energy storage depots of TAG and glycogen increase in liver and remain unchanged in muscle with warm acclimation. Overall, our studies reveal that N. coriiceps displays thermal plasticity in some key traits that may contribute to their survival as the Southern Ocean continues to warm.
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Affiliation(s)
- Kristin M O’Brien
- Institute of Arctic Biology, University of Alaska, Fairbanks, AK 99775 USA
| | - Corey A Oldham
- Institute of Arctic Biology, University of Alaska, Fairbanks, AK 99775 USA
| | - Jon Sarrimanolis
- Institute of Arctic Biology, University of Alaska, Fairbanks, AK 99775 USA
| | - Autumn Fish
- Institute of Arctic Biology, University of Alaska, Fairbanks, AK 99775 USA
| | - Luke Castellini
- Institute of Arctic Biology, University of Alaska, Fairbanks, AK 99775 USA
| | - Jenna Vance
- Department of Biological Sciences, Ohio University, Athens, OH 45701 USA
| | - Hayley Lekanof
- Institute of Arctic Biology, University of Alaska, Fairbanks, AK 99775 USA
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O'Brien KM, Joyce W, Crockett EL, Axelsson M, Egginton S, Farrell AP. Resilience of cardiac performance in Antarctic notothenioid fishes in a warming climate. J Exp Biol 2021; 224:268390. [PMID: 34042975 DOI: 10.1242/jeb.220129] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Warming in the region of the Western Antarctic Peninsula is occurring at an unprecedented rate, which may threaten the survival of Antarctic notothenioid fishes. Herein, we review studies characterizing thermal tolerance and cardiac performance in notothenioids - a group that includes both red-blooded species and the white-blooded, haemoglobinless icefishes - as well as the relevant biochemistry associated with cardiac failure during an acute temperature ramp. Because icefishes do not feed in captivity, making long-term acclimation studies unfeasible, we focus only on the responses of red-blooded notothenioids to warm acclimation. With acute warming, hearts of the white-blooded icefish Chaenocephalus aceratus display persistent arrhythmia at a lower temperature (8°C) compared with those of the red-blooded Notothenia coriiceps (14°C). When compared with the icefish, the enhanced cardiac performance of N. coriiceps during warming is associated with greater aerobic capacity, higher ATP levels, less oxidative damage and enhanced membrane integrity. Cardiac performance can be improved in N. coriiceps with warm acclimation to 5°C for 6-9 weeks, accompanied by an increase in the temperature at which cardiac failure occurs. Also, both cardiac mitochondrial and microsomal membranes are remodelled in response to warm acclimation in N. coriiceps, displaying homeoviscous adaptation. Overall, cardiac performance in N. coriiceps is malleable and resilient to warming, yet thermal tolerance and plasticity vary among different species of notothenioid fishes; disruptions to the Antarctic ecosystem driven by climate warming and other anthropogenic activities endanger the survival of notothenioids, warranting greater protection afforded by an expansion of marine protected areas.
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Affiliation(s)
- Kristin M O'Brien
- Institute of Arctic Biology , University of Alaska Fairbanks, Fairbanks, AK 99775-7000, USA
| | - William Joyce
- Department of Biology - Zoophysiology, Aarhus University, 8000 Aarhus C, Denmark
| | | | - Michael Axelsson
- Department of Biological and Environmental Sciences, University of Gothenburg, 40530 Gothenburg, Sweden
| | - Stuart Egginton
- School of Biomedical Sciences , University of Leeds, Leeds LS2 9JT, UK
| | - Anthony P Farrell
- Department of Zoology, and Faculty of Land and Food Systems, University of British Columbia, Vancouver, BC, Canada, V6T 1Z4
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Ansaloni F, Gerdol M, Torboli V, Fornaini NR, Greco S, Giulianini PG, Coscia MR, Miccoli A, Santovito G, Buonocore F, Scapigliati G, Pallavicini A. Cold Adaptation in Antarctic Notothenioids: Comparative Transcriptomics Reveals Novel Insights in the Peculiar Role of Gills and Highlights Signatures of Cobalamin Deficiency. Int J Mol Sci 2021; 22:ijms22041812. [PMID: 33670421 PMCID: PMC7918649 DOI: 10.3390/ijms22041812] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2021] [Revised: 02/04/2021] [Accepted: 02/08/2021] [Indexed: 01/13/2023] Open
Abstract
Far from being devoid of life, Antarctic waters are home to Cryonotothenioidea, which represent one of the fascinating cases of evolutionary adaptation to extreme environmental conditions in vertebrates. Thanks to a series of unique morphological and physiological peculiarities, which include the paradigmatic case of loss of hemoglobin in the family Channichthyidae, these fish survive and thrive at sub-zero temperatures. While some of the distinctive features of such adaptations have been known for decades, our knowledge of their genetic and molecular bases is still limited. We generated a reference de novo assembly of the icefish Chionodraco hamatus transcriptome and used this resource for a large-scale comparative analysis among five red-blooded Cryonotothenioidea, the sub-Antarctic notothenioid Eleginops maclovinus and seven temperate teleost species. Our investigation targeted the gills, a tissue of primary importance for gaseous exchange, osmoregulation, ammonia excretion, and its role in fish immunity. One hundred and twenty genes were identified as significantly up-regulated in Antarctic species and surprisingly shared by red- and white-blooded notothenioids, unveiling several previously unreported molecular players that might have contributed to the evolutionary success of Cryonotothenioidea in Antarctica. In particular, we detected cobalamin deficiency signatures and discussed the possible biological implications of this condition concerning hematological alterations and the heavy parasitic loads typically observed in all Cryonotothenioidea.
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Affiliation(s)
- Federico Ansaloni
- Department of Life Sciences, University of Trieste, 34127 Trieste, Italy; (F.A.); (V.T.); (N.R.F.); (S.G.); (P.G.G.); (A.P.)
- International School for Advanced Studies, 34136 Trieste, Italy
| | - Marco Gerdol
- Department of Life Sciences, University of Trieste, 34127 Trieste, Italy; (F.A.); (V.T.); (N.R.F.); (S.G.); (P.G.G.); (A.P.)
- Correspondence:
| | - Valentina Torboli
- Department of Life Sciences, University of Trieste, 34127 Trieste, Italy; (F.A.); (V.T.); (N.R.F.); (S.G.); (P.G.G.); (A.P.)
| | - Nicola Reinaldo Fornaini
- Department of Life Sciences, University of Trieste, 34127 Trieste, Italy; (F.A.); (V.T.); (N.R.F.); (S.G.); (P.G.G.); (A.P.)
- Department of Cell Biology, Charles University, 12800 Prague, Czech Republic
| | - Samuele Greco
- Department of Life Sciences, University of Trieste, 34127 Trieste, Italy; (F.A.); (V.T.); (N.R.F.); (S.G.); (P.G.G.); (A.P.)
| | - Piero Giulio Giulianini
- Department of Life Sciences, University of Trieste, 34127 Trieste, Italy; (F.A.); (V.T.); (N.R.F.); (S.G.); (P.G.G.); (A.P.)
| | - Maria Rosaria Coscia
- Institute of Biochemistry and Cell Biology, National Research Council of Italy, 80131 Naples, Italy;
| | - Andrea Miccoli
- Department for Innovation in Biological, Agro-Food and Forest Systems, University of Tuscia, 01100 Viterbo, Italy; (A.M.); (F.B.); (G.S.)
| | | | - Francesco Buonocore
- Department for Innovation in Biological, Agro-Food and Forest Systems, University of Tuscia, 01100 Viterbo, Italy; (A.M.); (F.B.); (G.S.)
| | - Giuseppe Scapigliati
- Department for Innovation in Biological, Agro-Food and Forest Systems, University of Tuscia, 01100 Viterbo, Italy; (A.M.); (F.B.); (G.S.)
| | - Alberto Pallavicini
- Department of Life Sciences, University of Trieste, 34127 Trieste, Italy; (F.A.); (V.T.); (N.R.F.); (S.G.); (P.G.G.); (A.P.)
- Anton Dohrn Zoological Station, 80122 Naples, Italy
- National Institute of Oceanography and Experimental Geophysics, 34010 Trieste, Italy
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Giordano D, Corti P, Coppola D, Altomonte G, Xue J, Russo R, di Prisco G, Verde C. Regulation of globin expression in Antarctic fish under thermal and hypoxic stress. Mar Genomics 2020; 57:100831. [PMID: 33250437 DOI: 10.1016/j.margen.2020.100831] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2020] [Revised: 11/18/2020] [Accepted: 11/18/2020] [Indexed: 01/27/2023]
Abstract
In the freezing waters of the Southern Ocean, Antarctic teleost fish, the Notothenioidei, have developed unique adaptations to cope with cold, including, at the extreme, the loss of hemoglobin in icefish. As a consequence, icefish are thought to be the most vulnerable of the Antarctic fish species to ongoing ocean warming. Some icefish also fail to express myoglobin but all appear to retain neuroglobin, cytoglobin-1, cytoglobin-2, and globin-X. Despite the lack of the inducible heat shock response, Antarctic notothenioid fish are endowed with physiological plasticity to partially compensate for environmental changes, as shown by numerous physiological and genomic/transcriptomic studies over the last decade. However, the regulatory mechanisms that determine temperature/oxygen-induced changes in gene expression remain largely unexplored in these species. Proteins such as globins are susceptible to environmental changes in oxygen levels and temperature, thus playing important roles in mediating Antarctic fish adaptations. In this study, we sequenced the full-length transcripts of myoglobin, neuroglobin, cytoglobin-1, cytoglobin-2, and globin-X from the Antarctic red-blooded notothenioid Trematomus bernacchii and the white-blooded icefish Chionodraco hamatus and evaluated transcripts levels after exposure to high temperature and low oxygen levels. Basal levels of globins are similar in the two species and both stressors affect the expression of Antarctic fish globins in brain, retina and gills. Temperature up-regulates globin expression more effectively in white-blooded than in red-blooded fish while hypoxia strongly up-regulates globins in red-blooded fish, particularly in the gills. These results suggest globins function as regulators of temperature and hypoxia tolerance. This study provides the first insights into globin transcriptional changes in Antarctic fish.
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Affiliation(s)
- Daniela Giordano
- Institute of Biosciences and BioResources (IBBR), CNR, Via Pietro Castellino 111, Napoli 80131, Italy; Department of Marine Biotechnology, Stazione Zoologica Anton Dohrn (SZN), Villa Comunale, Napoli 80121, Italy.
| | - Paola Corti
- Heart, Lung, Blood, and Vascular Medicine Institute, University of Pittsburgh, Pittsburgh, PA 15213, USA; Division of Cardiology, Department of Medicine, University of Pittsburgh, Pittsburgh, PA 15213, USA
| | - Daniela Coppola
- Institute of Biosciences and BioResources (IBBR), CNR, Via Pietro Castellino 111, Napoli 80131, Italy; Department of Marine Biotechnology, Stazione Zoologica Anton Dohrn (SZN), Villa Comunale, Napoli 80121, Italy
| | - Giovanna Altomonte
- Institute of Biosciences and BioResources (IBBR), CNR, Via Pietro Castellino 111, Napoli 80131, Italy; Department of Science, Roma Tre University, Viale Guglielmo Marconi 446, Roma I-00146, Italy
| | - Jianmin Xue
- Heart, Lung, Blood, and Vascular Medicine Institute, University of Pittsburgh, Pittsburgh, PA 15213, USA
| | - Roberta Russo
- Institute of Biosciences and BioResources (IBBR), CNR, Via Pietro Castellino 111, Napoli 80131, Italy
| | - Guido di Prisco
- Institute of Biosciences and BioResources (IBBR), CNR, Via Pietro Castellino 111, Napoli 80131, Italy
| | - Cinzia Verde
- Institute of Biosciences and BioResources (IBBR), CNR, Via Pietro Castellino 111, Napoli 80131, Italy; Department of Marine Biotechnology, Stazione Zoologica Anton Dohrn (SZN), Villa Comunale, Napoli 80121, Italy
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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: 12] [Impact Index Per Article: 3.0] [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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7
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Yang S, Zhao T, Ma A, Huang Z, Liu Z, Cui W, Zhang J, Zhu C, Guo X, Yuan C. Metabolic responses in Scophthalmus maximus kidney subjected to thermal stress. FISH & SHELLFISH IMMUNOLOGY 2020; 103:37-46. [PMID: 32278112 DOI: 10.1016/j.fsi.2020.04.003] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/19/2019] [Revised: 04/01/2020] [Accepted: 04/02/2020] [Indexed: 06/11/2023]
Abstract
Turbot (Scophthalmus maximus) is an economically important marine fish cultured in China. In this study, fish in the experimental group were exposed to four temperatures: 15, 20, 25 and 28 °C. Metabolomics analysis and quantitative real-time PCR were used to assess changes in metabolic profiling and gene expression associated with thermal stress. The results showed the levels of heat shock protein 70 (HSP70), heat shock protein 90 (HSP90), blood creatinine and cortisol in S. maximus were all significantly upregulated (P < 0.05), indicating a stress response at 25 °C or higher. Challenge with thermal stress significantly increased expression levels of succinate dehydrogenase (SDH), fructose-1, 6-bisphosphatase (FBPase), malate dehydrogenase (MDH), cytosolic phosphoenolpyruvate carboxykinase (cPEPCK), glucose-6-phosphatase (G6Pase) and aspartate aminotransferase (AST) (P < 0.05). However, there was no effect on the expression levels of lactate dehydrogenase (LDH), alanine aminotransferase (ALT) and mitochondrial phosphoenolpyruvate carboxykinase (mPEPCK). Moreover, high temperature decreased levels of glycogenic amino acids, including histidine, threonine, glutamine, phenylalanine, arginine, serine, tyrosine, methionine and isoleucine. These findings suggest a significant correlation between gene expression and regulation of carbohydrate and amino acid metabolism in heat-stressed S. maximus kidney. In addition, the maintenance of aerobic metabolism and activation of gluconeogenesis appeared to be a critical metabolic strategy in combating heat stress in turbot kidney.
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Affiliation(s)
- Shuangshuang Yang
- Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Shandong Key Laboratory of Marine Fisheries Biotechnology and Genetic Breeding, Qingdao Key Laboratory for Marine Fish Breeding and Biotechnology, Qingdao, 266071, China; Laboratory for Marine Biology and Biotechnology, Pilot National Laboratory for Marine Science and Technology (Qingdao), Qingdao, 266237, China
| | - Tingting Zhao
- Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Shandong Key Laboratory of Marine Fisheries Biotechnology and Genetic Breeding, Qingdao Key Laboratory for Marine Fish Breeding and Biotechnology, Qingdao, 266071, China; Laboratory for Marine Biology and Biotechnology, Pilot National Laboratory for Marine Science and Technology (Qingdao), Qingdao, 266237, China; College of Fisheries and Life Science, Shanghai Ocean University, Shanghai, 201306, China
| | - Aijun Ma
- Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Shandong Key Laboratory of Marine Fisheries Biotechnology and Genetic Breeding, Qingdao Key Laboratory for Marine Fish Breeding and Biotechnology, Qingdao, 266071, China; Laboratory for Marine Biology and Biotechnology, Pilot National Laboratory for Marine Science and Technology (Qingdao), Qingdao, 266237, China.
| | - Zhihui Huang
- Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Shandong Key Laboratory of Marine Fisheries Biotechnology and Genetic Breeding, Qingdao Key Laboratory for Marine Fish Breeding and Biotechnology, Qingdao, 266071, China; Laboratory for Marine Biology and Biotechnology, Pilot National Laboratory for Marine Science and Technology (Qingdao), Qingdao, 266237, China
| | - Zhifeng Liu
- Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Shandong Key Laboratory of Marine Fisheries Biotechnology and Genetic Breeding, Qingdao Key Laboratory for Marine Fish Breeding and Biotechnology, Qingdao, 266071, China; Laboratory for Marine Biology and Biotechnology, Pilot National Laboratory for Marine Science and Technology (Qingdao), Qingdao, 266237, China
| | - Wenxiao Cui
- Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Shandong Key Laboratory of Marine Fisheries Biotechnology and Genetic Breeding, Qingdao Key Laboratory for Marine Fish Breeding and Biotechnology, Qingdao, 266071, China; Laboratory for Marine Biology and Biotechnology, Pilot National Laboratory for Marine Science and Technology (Qingdao), Qingdao, 266237, China; College of Fisheries and Life Science, Shanghai Ocean University, Shanghai, 201306, China
| | - Jinsheng Zhang
- Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Shandong Key Laboratory of Marine Fisheries Biotechnology and Genetic Breeding, Qingdao Key Laboratory for Marine Fish Breeding and Biotechnology, Qingdao, 266071, China; Laboratory for Marine Biology and Biotechnology, Pilot National Laboratory for Marine Science and Technology (Qingdao), Qingdao, 266237, China; College of Fisheries and Life Science, Shanghai Ocean University, Shanghai, 201306, China
| | - Chunyue Zhu
- Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Shandong Key Laboratory of Marine Fisheries Biotechnology and Genetic Breeding, Qingdao Key Laboratory for Marine Fish Breeding and Biotechnology, Qingdao, 266071, China; Laboratory for Marine Biology and Biotechnology, Pilot National Laboratory for Marine Science and Technology (Qingdao), Qingdao, 266237, China; College of Fisheries and Life Science, Shanghai Ocean University, Shanghai, 201306, China
| | - Xiaoli Guo
- Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Shandong Key Laboratory of Marine Fisheries Biotechnology and Genetic Breeding, Qingdao Key Laboratory for Marine Fish Breeding and Biotechnology, Qingdao, 266071, China; Laboratory for Marine Biology and Biotechnology, Pilot National Laboratory for Marine Science and Technology (Qingdao), Qingdao, 266237, China; College of Fisheries and Life Science, Shanghai Ocean University, Shanghai, 201306, China
| | - Chenhao Yuan
- Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Shandong Key Laboratory of Marine Fisheries Biotechnology and Genetic Breeding, Qingdao Key Laboratory for Marine Fish Breeding and Biotechnology, Qingdao, 266071, China; Laboratory for Marine Biology and Biotechnology, Pilot National Laboratory for Marine Science and Technology (Qingdao), Qingdao, 266237, China
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8
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Vasadia DJ, Zippay ML, Place SP. Characterization of thermally sensitive miRNAs reveals a central role of the FoxO signaling pathway in regulating the cellular stress response of an extreme stenotherm, Trematomus bernacchii. Mar Genomics 2019; 48:100698. [PMID: 31307923 DOI: 10.1016/j.margen.2019.100698] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2019] [Revised: 06/21/2019] [Accepted: 06/25/2019] [Indexed: 01/20/2023]
Abstract
Despite the lack of an inducible heat shock response (HSR), the Antarctic notothenioid fish, Trematomus bernacchii, has retained a level of physiological plasticity that can at least partially compensate for the effects of acute heat stress. Over the last decade, both physiological and transcriptomic studies have signaled these fish can mitigate the effects of acute heat stress by employing other aspects of the cellular stress response (CSR) that help confer thermotolerance as well as drive homeostatic mechanisms during long-term thermal acclimations. However, the regulatory mechanisms that determine temperature-induced changes in gene expression remain largely unexplored in this species. Therefore, this study utilized next generation sequencing coupled with an in silico approach to explore the regulatory role of microRNAs in governing the transcriptomic level response observed in this Antarctic notothenioid with respect to the CSR. Using RNAseq, we characterized the expression of 125 distinct miRNA orthologues in T. bernacchii gill tissue. Additionally, we identified 12 miRNAs that appear to be thermally responsive based on differential expression (DE) analyses performed between fish acclimated to control (-1.5 °C) and an acute heat stress (+4 °C). We further characterized the functional role of these DE miRNAs using bioinformatics pipelines to identify putative gene targets of the DE miRNAs and subsequent gene set enrichment analyses, which together suggest these miRNAs are involved in regulating diverse aspects of the CSR in T. bernacchii.
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Affiliation(s)
- Dipali J Vasadia
- Sonoma State University, Department of Biology, Rohnert Park, CA 94928, United States of America
| | - Mackenzie L Zippay
- Sonoma State University, Department of Biology, Rohnert Park, CA 94928, United States of America
| | - Sean P Place
- Sonoma State University, Department of Biology, Rohnert Park, CA 94928, United States of America.
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Divergence, evolution and adaptation in ray-finned fish genomes. SCIENCE CHINA-LIFE SCIENCES 2019; 62:1003-1018. [PMID: 31098893 DOI: 10.1007/s11427-018-9499-5] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/04/2019] [Accepted: 02/12/2019] [Indexed: 02/06/2023]
Abstract
With the rapid development of next-generation sequencing technologies and bioinformatics, over 50 ray-finned fish genomes by far have been sequenced with high quality. The genomic work provides abundant genetic resources for deep understanding of divergence, evolution and adaptation in the fish genomes. They are also instructive for identification of candidate genes for functional verification, molecular breeding, and development of novel marine drugs. As an example of other omics data, the Fish-T1K project generated a big database of fish transcriptomes to integrate with these published fish genomes for potential applications. In this review, we highlight the above-mentioned recent investigations and core topics on the ray-finned fish genome research, with a main goal to obtain a deeper understanding of fish biology for theoretical and practical applications.
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Kim BM, Ahn DH, Kang S, Jeong J, Jo E, Kim BK, Kim JH, Park H. Skin transcriptome profiling reveals the distinctive molecular effects of temperature changes on Antarctic bullhead notothen. Mol Cell Toxicol 2019. [DOI: 10.1007/s13273-019-0020-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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11
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Bilyk KT, Zhuang X, Murphy KR, Cheng CHC. A tale of two genes: divergent evolutionary fate of haptoglobin and hemopexin in hemoglobinless antarctic icefishes. J Exp Biol 2019; 222:jeb.188573. [DOI: 10.1242/jeb.188573] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2018] [Accepted: 02/06/2019] [Indexed: 12/31/2022]
Abstract
Evolution of Antarctic notothenioid fishes in the isolated freezing Southern Ocean have led to remarkable trait gains and losses. One of the most extraordinary was the loss of the major oxygen carrier hemoglobin (Hb) in the icefishes (family Channichthyidae). While the mechanisms of this loss and the resulting compensatory changes have been well studied, the impact of Hb loss on the network of genes that once supported its recycling and disposal has remained unexplored. Here we report the functional fate and underlying molecular changes of two such key Hb-supporting proteins across the icefish family - haptoglobin (Hp) and hemopexin (Hx), crucial in removing cytotoxic free Hb and heme respectively. Hp plays a critical role in binding free Hb for intracellular recycling and absent its primary client, icefish Hp transcription is now vanishingly little and translation into a functional protein is nearly silenced. Hp genotype degeneration has manifested in separate lineages of the icefish phylogeny with three distinct nonsense mutations and a deletion-frameshift, as well as mutated polyadenylation signal sequences. Thus, Hb loss appears to have diminished selective constraint on Hp maintenance, resulting in its stochastic, co-evolutionary drift towards extinction. Hx binds free heme for iron recycling in hepatocytes. In contrast to Hp, Hx genotype integrity is preserved in the icefishes and transcription occurs at comparable levels to the red-blooded notothenioids. The persistence of Hx likely owes to continued selective pressure for its function from mitochondrial and non-Hb cellular hemoproteins.
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Affiliation(s)
- Kevin T. Bilyk
- Department of Biology, Western Kentucky University, USA
- Department of Animal Biology, University of Illinois, Urbana Champaign, USA
| | - Xuan Zhuang
- Department of Ecology & Evolution, University of Chicago, USA
| | - Katherine R. Murphy
- Department of Animal Biology, University of Illinois, Urbana Champaign, USA
- Laboratories of Analytical Biology, National Museum of Natural History, Smithsonian Institution, USA
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12
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Berthelot C, Clarke J, Desvignes T, William Detrich H, Flicek P, Peck LS, Peters M, Postlethwait JH, Clark MS. Adaptation of Proteins to the Cold in Antarctic Fish: A Role for Methionine? Genome Biol Evol 2019; 11:220-231. [PMID: 30496401 PMCID: PMC6336007 DOI: 10.1093/gbe/evy262] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/26/2018] [Indexed: 12/25/2022] Open
Abstract
The evolution of antifreeze glycoproteins has enabled notothenioid fish to flourish in the freezing waters of the Southern Ocean. Whereas successful at the biodiversity level to life in the cold, paradoxically at the cellular level these stenothermal animals have problems producing, folding, and degrading proteins at their ambient temperatures of -1.86 °C. In this first multi-species transcriptome comparison of the amino acid composition of notothenioid proteins with temperate teleost proteins, we show that, unlike psychrophilic bacteria, Antarctic fish provide little evidence for the mass alteration of protein amino acid composition to enhance protein folding and reduce protein denaturation in the cold. The exception was the significant overrepresentation of positions where leucine in temperate fish proteins was replaced by methionine in the notothenioid orthologues. We hypothesize that these extra methionines have been preferentially assimilated into the genome to act as redox sensors in the highly oxygenated waters of the Southern Ocean. This redox hypothesis is supported by analyses of notothenioids showing enrichment of genes associated with responses to environmental stress, particularly reactive oxygen species. So overall, although notothenioid fish show cold-associated problems with protein homeostasis, they may have modified only a selected number of biochemical pathways to work efficiently below 0 °C. Even a slight warming of the Southern Ocean might disrupt the critical functions of this handful of key pathways with considerable impacts for the functioning of this ecosystem in the future.
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Affiliation(s)
- Camille Berthelot
- Laboratoire Dynamique et Organisation des Génomes (Dyogen), Institut de Biologie de l'Ecole Normale Supérieure – UMR 8197, INSERM U1024, Paris Cedex 05, France
- European Molecular Biology Laboratory, European Bioinformatics Institute, Cambridge, United Kingdom
| | - Jane Clarke
- Department of Chemistry, University of Cambridge, United Kingdom
| | | | - H William Detrich
- Department of Marine and Environmental Sciences, Marine Science Center, Northeastern University
| | - Paul Flicek
- European Molecular Biology Laboratory, European Bioinformatics Institute, Cambridge, United Kingdom
| | - Lloyd S Peck
- British Antarctic Survey, Natural Environment Research Council, Cambridge, United Kingdom
| | - Michael Peters
- Department of Marine and Environmental Sciences, Marine Science Center, Northeastern University
| | | | - Melody S Clark
- British Antarctic Survey, Natural Environment Research Council, Cambridge, United Kingdom
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13
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Head Kidney Transcriptome Analysis and Characterization for the Sub-Antarctic Notothenioid Fish Eleginops maclovinus. FISHES 2018. [DOI: 10.3390/fishes3010008] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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14
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Harrisson KA, Amish SJ, Pavlova A, Narum SR, Telonis‐Scott M, Rourke ML, Lyon J, Tonkin Z, Gilligan DM, Ingram BA, Lintermans M, Gan HM, Austin CM, Luikart G, Sunnucks P. Signatures of polygenic adaptation associated with climate across the range of a threatened fish species with high genetic connectivity. Mol Ecol 2017; 26:6253-6269. [DOI: 10.1111/mec.14368] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2017] [Revised: 09/22/2017] [Accepted: 09/25/2017] [Indexed: 12/25/2022]
Affiliation(s)
- Katherine A. Harrisson
- School of Biological Sciences Monash University Clayton Vic. Australia
- Department of Ecology Environment and Evolution School of Life Sciences La Trobe University Bundoora Vic. Australia
- Arthur Rylah Institute for Environmental Research Heidelberg Vic. Australia
| | - Stephen J. Amish
- Conservation Genomics Group Division of Biological Sciences University of Montana Missoula MT USA
- Flathead Lake Biological Station University of Montana Polson MT USA
| | - Alexandra Pavlova
- School of Biological Sciences Monash University Clayton Vic. Australia
| | - Shawn R. Narum
- Columbia River Inter‐Tribal Fish Commission Hagerman Fish Culture Experiment Station Hagerman IDUSA
| | | | - Meaghan L. Rourke
- Department of Primary Industries DPI Fisheries Narrandera NSW Australia
| | - Jarod Lyon
- Arthur Rylah Institute for Environmental Research Heidelberg Vic. Australia
| | - Zeb Tonkin
- Arthur Rylah Institute for Environmental Research Heidelberg Vic. Australia
| | - Dean M. Gilligan
- Department of Primary Industries DPI Fisheries, Batemans Bay Fisheries Office Batemans Bay NSW Australia
| | | | - Mark Lintermans
- Institute for Applied Ecology University of Canberra Canberra ACT Australia
| | - Han Ming Gan
- Centre for Integrative Ecology School of Life and Environmental Sciences Deakin University Geelong Vic. Australia
- School of Science Monash University Malaysia Petaling Jaya Selangor Malaysia
- Genomics Facility, Tropical Medicine and Biology Platform Monash University Malaysia Petaling Jaya Selangor Malaysia
| | - Christopher M. Austin
- Centre for Integrative Ecology School of Life and Environmental Sciences Deakin University Geelong Vic. Australia
- School of Science Monash University Malaysia Petaling Jaya Selangor Malaysia
- Genomics Facility, Tropical Medicine and Biology Platform Monash University Malaysia Petaling Jaya Selangor Malaysia
| | - Gordon Luikart
- Conservation Genomics Group Division of Biological Sciences University of Montana Missoula MT USA
- Flathead Lake Biological Station University of Montana Polson MT USA
| | - Paul Sunnucks
- School of Biological Sciences Monash University Clayton Vic. Australia
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15
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Chatchaiphan S, Srisapoome P, Kim JH, Devlin RH, Na-Nakorn U. De Novo Transcriptome Characterization and Growth-Related Gene Expression Profiling of Diploid and Triploid Bighead Catfish (Clarias macrocephalus Günther, 1864). MARINE BIOTECHNOLOGY (NEW YORK, N.Y.) 2017; 19:36-48. [PMID: 28181037 DOI: 10.1007/s10126-017-9730-3] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/18/2016] [Accepted: 12/31/2016] [Indexed: 06/06/2023]
Abstract
To enhance understanding of triploid gene expression, the transcriptome information from bighead catfish (Clarias macrocephalus Günther, 1864) was studied using the paired-end Illumina HiSeq™ 2000 sequencing platform. In total, 68,227,832 raw reads were generated from liver tissues and 53,149 unigenes were assembled, with an average length of 765 bp and N50 length of 1283 bp. Of these unigenes, 33,428 (62.89%) could be annotated according to their homology with matches in the NCBI non-redundant (Nr), NCBI nucleotide (Nt), Swiss-Prot, Clusters of Orthologous Groups (COG), gene ontology (GO), or Kyoto Encyclopedia of Genes and Genomes (KEGG) databases. Relative expression of liver genes between diploid and triploid bighead catfish revealed more than 90% of the annotated unigenes similarly expressed, regardless of ploidy, whereas 362 upregulated and 83 downregulated with at least a twofold change in triploid relative to diploid. Quantitative real-time PCR of 15 differentially expressed growth-related genes showed consistency between the expression profiles of those genes with the results from RNA-seq analysis. Our results showed that genes in C. macrocephalus liver responded independently to triploidy with the majority showing similar expression levels between diploid and triploid (a dosage compensation phenomenon). The underlying mechanism of the varying gene expression patterns was discussed. Notably, 5 of the top 20 upregulated genes associated with stress response and thus may reflect stress caused by triploidy. The present study adds a substantial contribution to the sequence data available for C. macrocephalus and hence provides valuable resources for further studies. Furthermore, it gives information that may enhance understanding of triploid physiology.
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Affiliation(s)
- Satid Chatchaiphan
- Graduate Program in Aquaculture, The Graduate School, Kasetsart University, Chatuchak, Bangkok, 10900, Thailand
| | - Prapansak Srisapoome
- Department of Aquaculture, Faculty of Fisheries, Kasetsart University, Chatuchak, Bangkok, 10900, Thailand
| | - Jin-Hyoung Kim
- Division of Life Sciences, Korea Polar Research Institute, Incheon, 21990, South Korea
| | - Robert H Devlin
- Fisheries and Oceans Canada, Centre for Aquaculture and Environmental Research, West Vancouver, BC, V7V1N6, Canada
| | - Uthairat Na-Nakorn
- Department of Aquaculture, Faculty of Fisheries, Kasetsart University, Chatuchak, Bangkok, 10900, Thailand.
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16
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Lindgren AR, Buckley BA, Eppley SM, Reysenbach AL, Stedman KM, Wagner JT. Life on the Edge-the Biology of Organisms Inhabiting Extreme Environments: An Introduction to the Symposium. Integr Comp Biol 2016; 56:493-9. [PMID: 27471225 DOI: 10.1093/icb/icw094] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Life persists, even under extremely harsh conditions. While the existence of extremophiles is well known, the mechanisms by which these organisms evolve, perform basic metabolic functions, reproduce, and survive under extreme physical stress are often entirely unknown. Recent technological advances in terms of both sampling and studying extremophiles have yielded new insight into their evolution, physiology and behavior, from microbes and viruses to plants to eukaryotes. The goal of the "Life on the Edge-the Biology of Organisms Inhabiting Extreme Environments" symposium was to unite researchers from taxonomically and methodologically diverse backgrounds to highlight new advances in extremophile biology. Common themes and new insight that emerged from the symposium included the important role of symbiotic associations, the continued challenges associated with sampling and studying extremophiles and the important role these organisms play in terms of studying climate change. As we continue to explore our planet, especially in difficult to reach areas from the poles to the deep sea, we expect to continue to discover new and extreme circumstances under which life can persist.
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Affiliation(s)
- Annie R Lindgren
- The Center for Life in Extreme Environments, Portland State University, Portland, OR 97201, USA
| | - Bradley A Buckley
- The Center for Life in Extreme Environments, Portland State University, Portland, OR 97201, USA
| | - Sarah M Eppley
- The Center for Life in Extreme Environments, Portland State University, Portland, OR 97201, USA
| | - Anna-Louise Reysenbach
- The Center for Life in Extreme Environments, Portland State University, Portland, OR 97201, USA
| | - Kenneth M Stedman
- The Center for Life in Extreme Environments, Portland State University, Portland, OR 97201, USA
| | - Josiah T Wagner
- The Center for Life in Extreme Environments, Portland State University, Portland, OR 97201, USA
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17
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Hu P, Liu M, Liu Y, Wang J, Zhang D, Niu H, Jiang S, Wang J, Zhang D, Han B, Xu Q, Chen L. Transcriptome comparison reveals a genetic network regulating the lower temperature limit in fish. Sci Rep 2016; 6:28952. [PMID: 27356472 PMCID: PMC4928090 DOI: 10.1038/srep28952] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2016] [Accepted: 06/13/2016] [Indexed: 12/13/2022] Open
Abstract
Transcriptional plasticity is a major driver of phenotypic differences between species. The lower temperature limit (LTL), namely the lower end of survival temperature, is an important trait delimiting the geographical distribution of a species, however, the genetic mechanisms are poorly understood. We investigated the inter-species transcriptional diversification in cold responses between zebrafish Danio rerio and tilapia Oreochromis niloticus, which were reared at a common temperature (28 °C) but have distinct LTLs. We identified significant expressional divergence between the two species in the orthologous genes from gills when the temperature cooled to the LTL of tilapia (8 °C). Five KEGG pathways were found sequentially over-represented in the zebrafish/tilapia divergently expressed genes in the duration (12 hour) of 8 °C exposure, forming a signaling cascade from metabolic regulation to apoptosis via FoxO signaling. Consistently, we found differential progression of apoptosis in the gills of the two species in which zebrafish manifested a delayed and milder apoptotic phenotype than tilapia, corresponding with a lower LTL of zebrafish. We identified diverged expression in 25 apoptosis-related transcription factors between the two species which forms an interacting network with diverged factors involving the FoxO signaling and metabolic regulation. We propose a genetic network which regulates LTL in fishes.
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Affiliation(s)
- Peng Hu
- Key Laboratory of Aquacultural Resources and Utilization, Ministry of Education, College of Fisheries and Life Sciences, Shanghai Ocean University, Shanghai, 201306, China
| | - Mingli Liu
- Key Laboratory of Aquacultural Resources and Utilization, Ministry of Education, College of Fisheries and Life Sciences, Shanghai Ocean University, Shanghai, 201306, China
| | - Yimeng Liu
- Key Laboratory of Aquacultural Resources and Utilization, Ministry of Education, College of Fisheries and Life Sciences, Shanghai Ocean University, Shanghai, 201306, China
| | - Jinfeng Wang
- Key Laboratory of Aquacultural Resources and Utilization, Ministry of Education, College of Fisheries and Life Sciences, Shanghai Ocean University, Shanghai, 201306, China
| | - Dong Zhang
- Key Laboratory of Aquacultural Resources and Utilization, Ministry of Education, College of Fisheries and Life Sciences, Shanghai Ocean University, Shanghai, 201306, China
| | - Hongbo Niu
- Key Laboratory of Aquacultural Resources and Utilization, Ministry of Education, College of Fisheries and Life Sciences, Shanghai Ocean University, Shanghai, 201306, China
| | - Shouwen Jiang
- Key Laboratory of Aquacultural Resources and Utilization, Ministry of Education, College of Fisheries and Life Sciences, Shanghai Ocean University, Shanghai, 201306, China
| | - Jian Wang
- Key Laboratory of Aquacultural Resources and Utilization, Ministry of Education, College of Fisheries and Life Sciences, Shanghai Ocean University, Shanghai, 201306, China
| | - Dongsheng Zhang
- Key Laboratory of Aquacultural Resources and Utilization, Ministry of Education, College of Fisheries and Life Sciences, Shanghai Ocean University, Shanghai, 201306, China
| | - Bingshe Han
- Key Laboratory of Aquacultural Resources and Utilization, Ministry of Education, College of Fisheries and Life Sciences, Shanghai Ocean University, Shanghai, 201306, China
| | - Qianghua Xu
- Key Laboratory of Sustainable Exploitation of Oceanic Fisheries Resources, Ministry of Education, College of Marine Sciences, Shanghai Ocean University, Shanghai, 201306, China
| | - Liangbiao Chen
- Key Laboratory of Aquacultural Resources and Utilization, Ministry of Education, College of Fisheries and Life Sciences, Shanghai Ocean University, Shanghai, 201306, China
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18
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Papetti C, Lucassen M, Pörtner HO. Integrated studies of organismal plasticity through physiological and transcriptomic approaches: examples from marine polar regions. Brief Funct Genomics 2016; 15:365-72. [PMID: 27345433 DOI: 10.1093/bfgp/elw024] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Transcriptomic methods are now widely used in functional genomic research. The vast amount of information received from these studies comes along with the challenge of developing a precise picture of the functional consequences and the characteristic regulatory mechanisms. Here we assess recent studies in marine species and their adaptation to polar (and seasonal) cold and explore how they have been able to draw reliable conclusions from transcriptomic patterns on functional consequences in the organisms. Our analysis indicates that the interpretation of transcriptomic data suffers from insufficient understanding of the consequences for whole organism performance and fitness and comes with the risk of supporting only preliminary and superficial statements.We propose that the functional understanding of transcriptomic data may be improved by their tighter integration into overarching physiological concepts that support the more specific interpretation of the 'omics' data and, at the same time, can be developed further through embedding the transcriptomic phenomena observed. Such possibilities have not been fully exploited.In the context of thermal adaptation and limitation, we explore preliminary evidence that the concept of oxygen and capacity limited thermal tolerance (OCLTT) may provide sufficient complexity to guide the integration of such data and the development of associated functional hypotheses. At the same time, we identify a lack of methodological approaches linking genes and function to higher levels of integration, in terms of organism and ecosystem functioning, at temporal and geographical scales, to support more reliable conclusions and be predictive with respect to the effects of global changes.
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19
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Beers JM, Jayasundara N. Antarctic notothenioid fish: what are the future consequences of 'losses' and 'gains' acquired during long-term evolution at cold and stable temperatures? ACTA ACUST UNITED AC 2016; 218:1834-45. [PMID: 26085661 DOI: 10.1242/jeb.116129] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Antarctic notothenioids dominate the fish fauna of the Southern Ocean. Evolution for millions of years at cold and stable temperatures has led to the acquisition of numerous biochemical traits that allow these fishes to thrive in sub-zero waters. The gain of antifreeze glycoproteins has afforded notothenioids the ability to avert freezing and survive at temperatures often hovering near the freezing point of seawater. Additionally, possession of cold-adapted proteins and membranes permits them to sustain appropriate metabolic rates at exceptionally low body temperatures. The notothenioid genome is also distinguished by the disappearance of traits in some species, losses that might prove costly in a warmer environment. Perhaps the best-illustrated example is the lack of expression of hemoglobin in white-blooded icefishes from the family Channichthyidae. Loss of key elements of the cellular stress response, notably the heat shock response, has also been observed. Along with their attainment of cold tolerance, notothenioids have developed an extreme stenothermy and many species perish at temperatures only a few degrees above their habitat temperatures. Thus, in light of today's rapidly changing climate, it is critical to evaluate how these extreme stenotherms will respond to rising ocean temperatures. It is conceivable that the remarkable cold specialization of notothenioids may ultimately leave them vulnerable to future thermal increases and threaten their fitness and survival. Within this context, our review provides a current summary of the biochemical losses and gains that are known for notothenioids and examines these cold-adapted traits with a focus on processes underlying thermal tolerance and acclimation capacity.
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Affiliation(s)
- Jody M Beers
- Hopkins Marine Station, Stanford University, 120 Ocean View Boulevard, Pacific Grove, CA 93950, USA
| | - Nishad Jayasundara
- Nicholas School of the Environment, Duke University, 450 Research Drive, Durham, NC 27708, USA
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20
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Logan CA, Buckley BA. Transcriptomic responses to environmental temperature in eurythermal and stenothermal fishes. ACTA ACUST UNITED AC 2016; 218:1915-24. [PMID: 26085668 DOI: 10.1242/jeb.114397] [Citation(s) in RCA: 91] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
Ectothermic species like fishes differ greatly in the thermal ranges they tolerate; some eurythermal species may encounter temperature ranges in excess of 25°C, whereas stenothermal species in polar and tropical waters live at essentially constant temperatures. Thermal specialization comes with fitness trade-offs and as temperature increases due to global warming, the physiological basis of specialization and thermal plasticity has become of great interest. Over the past 50 years, comparative physiologists have studied the physiological and molecular differences between stenothermal and eurythermal fishes. It is now well known that many stenothermal fishes have lost an inducible heat shock response (HSR). Recent advances in transcriptomics have now made it possible to examine genome-wide changes in gene expression (GE) in non-model ecologically important fish, broadening our view beyond the HSR to regulation of genes involved in hundreds of other cellular processes. Here, we review the major findings from transcriptomic studies of extreme eurythermal and stenothermal fishes in response to acute and long-term exposure to temperature, both time scales being critically important for predicting climate change responses. We consider possible molecular adaptations that underlie eurythermy and stenothermy in teleosts. Furthermore, we highlight the challenges that still face the field of comparative environmental genomics and suggest fruitful paths of future investigation.
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Affiliation(s)
- Cheryl A Logan
- Division of Science and Environmental Policy, California State University, Monterey Bay, Seaside, CA 93955, USA
| | - Bradley A Buckley
- Center for Life in Extreme Environments, Portland State University, Portland, OR 97207, USA
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21
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Huth TJ, Place SP. RNA-seq reveals a diminished acclimation response to the combined effects of ocean acidification and elevated seawater temperature in Pagothenia borchgrevinki. Mar Genomics 2016; 28:87-97. [PMID: 26969095 DOI: 10.1016/j.margen.2016.02.004] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2015] [Revised: 02/11/2016] [Accepted: 02/11/2016] [Indexed: 02/02/2023]
Abstract
PURPOSE The IPCC has reasserted the strong influence of anthropogenic CO2 contributions on global climate change and highlighted the polar-regions as highly vulnerable. With these predictions the cold adapted fauna endemic to the Southern Ocean, which is dominated by fishes of the sub-order Notothenioidei, will face considerable challenges in the near future. Recent physiological studies have demonstrated that the synergistic stressors of elevated temperature and ocean acidification have a considerable, although variable, impact on notothenioid fishes. The present study explored the transcriptomic response of Pagothenia borchgrevinki to increased temperatures and pCO2 after 7, 28 and 56days of acclimation. We compared this response to short term studies assessing heat stress alone and foretell the potential impacts of these stressors on P. borchgrevinki's ability to survive a changing Southern Ocean. RESULTS P. borchgrevinki did demonstrate a coordinated stress response to the dual-stressor condition, and even indicated that some level of inducible heat shock response may be conserved in this notothenioid species. However, the stress response of P. borchgrevinki was considerably less robust than that observed previously in the closely related notothenioid, Trematomus bernacchii, and varied considerably when compared across different acclimation time-points. Furthermore, the molecular response of these fish under multiple stressors displayed distinct differences compared to their response to short term heat stress alone. CONCLUSIONS When exposed to increased sea surface temperatures, combined with ocean acidification, P. borchgrevinki demonstrated a coordinated stress response that has already peaked by 7days of acclimation and quickly diminished over time. However, this response is less dramatic than other closely related notothenioids under identical conditions, supporting previous research suggesting that this notothenioid species is less sensitive to environmental variation.
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Affiliation(s)
- Troy J Huth
- University of South Carolina, Department of Biological Sciences, Columbia, SC 29208, USA.
| | - Sean P Place
- Sonoma State University, Department of Biology, Rohnert Park, CA 94928, USA.
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22
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Huth TJ, Place SP. Transcriptome wide analyses reveal a sustained cellular stress response in the gill tissue of Trematomus bernacchii after acclimation to multiple stressors. BMC Genomics 2016; 17:127. [PMID: 26897172 PMCID: PMC4761167 DOI: 10.1186/s12864-016-2454-3] [Citation(s) in RCA: 68] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2015] [Accepted: 02/09/2016] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND As global climate change progresses, the Southern Ocean surrounding Antarctica is poised to undergo potentially rapid and substantial changes in temperature and pCO2. To survive in this challenging environment, the highly cold adapted endemic fauna of these waters must demonstrate sufficient plasticity to accommodate these changing conditions or face inexorable decline. Previous studies of notothenioids have focused upon the short-term response to heat stress; and more recently the longer-term physiological response to the combined stress of increasing temperatures and pCO2. This inquiry explores the transcriptomic response of Trematomus bernacchii to increased temperatures and pCO2 at 7, 28 and 56 days, in an attempt to discern the innate plasticity of T. bernacchii available to cope with a changing Southern Ocean. RESULTS Differential gene expression analysis supported previous research in that T. bernacchii exhibits no inducible heat shock response to stress conditions. However, T. bernacchii did demonstrate a strong stress response to the multi-stressor condition in the form of metabolic shifts, DNA damage repair, immune system processes, and activation of apoptotic pathways combined with negative regulation of cell proliferation. This response declined in magnitude over time, but aspects of this response remained detectable throughout the acclimation period. CONCLUSIONS When exposed to the multi-stressor condition, T. bernacchii demonstrates a cellular stress response that persists for a minimum of 7 days before returning to near basal levels of expression at longer acclimation times. However, subtle changes in expression persist in fish acclimated for 56 days that may significantly affect the fitness T. bernacchii over time.
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Affiliation(s)
- Troy J Huth
- Department of Biological Sciences, University of South Carolina, Columbia, SC, 29208, USA.
| | - Sean P Place
- Department of Biology, Sonoma State University, Rohnert Park, CA, 94928, USA.
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23
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Liu S, Luo J, Chai J, Ren L, Zhou Y, Huang F, Liu X, Chen Y, Zhang C, Tao M, Lu B, Zhou W, Lin G, Mai C, Yuan S, Wang J, Li T, Qin Q, Feng H, Luo K, Xiao J, Zhong H, Zhao R, Duan W, Song Z, Wang Y, Wang J, Zhong L, Wang L, Ding Z, Du Z, Lu X, Gao Y, Murphy RW, Liu Y, Meyer A, Zhang YP. Genomic incompatibilities in the diploid and tetraploid offspring of the goldfish × common carp cross. Proc Natl Acad Sci U S A 2016; 113:1327-32. [PMID: 26768847 PMCID: PMC4747765 DOI: 10.1073/pnas.1512955113] [Citation(s) in RCA: 74] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
Polyploidy is much rarer in animals than in plants but it is not known why. The outcome of combining two genomes in vertebrates remains unpredictable, especially because polyploidization seldom shows positive effects and more often results in lethal consequences because viable gametes fail to form during meiosis. Fortunately, the goldfish (maternal) × common carp (paternal) hybrids have reproduced successfully up to generation 22, and this hybrid lineage permits an investigation into the genomics of hybridization and tetraploidization. The first two generations of these hybrids are diploids, and subsequent generations are tetraploids. Liver transcriptomes from four generations and their progenitors reveal chimeric genes (>9%) and mutations of orthologous genes. Characterizations of 18 randomly chosen genes from genomic DNA and cDNA confirm the chimera. Some of the chimeric and differentially expressed genes relate to mutagenesis, repair, and cancer-related pathways in 2nF1. Erroneous DNA excision between homologous parental genes may drive the high percentage of chimeric genes, or even more potential mechanisms may result in this phenomenon. Meanwhile, diploid offspring show paternal-biased expression, yet tetraploids show maternal-biased expression. These discoveries reveal that fast and unstable changes are mainly deleterious at the level of transcriptomes although some offspring still survive their genomic abnormalities. In addition, the synthetic effect of genome shock might have resulted in greatly reduced viability of 2nF2 hybrid offspring. The goldfish × common carp hybrids constitute an ideal system for unveiling the consequences of intergenomic interactions in hybrid vertebrate genomes and their fertility.
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Affiliation(s)
- Shaojun Liu
- Key Laboratory of Protein Chemistry and Fish Developmental Biology of Education Ministry of China, College of Life Sciences, Hunan Normal University, Changsha, 410081, Hunan, China;
| | - Jing Luo
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan University, Kunming, 650091, Yunnan, China; Key Laboratory for Animal Genetic Diversity and Evolution of High Education in Yunnan Province, School of Life Sciences, Yunnan University, Kunming, 650091, Yunnan, China
| | - Jing Chai
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan University, Kunming, 650091, Yunnan, China; Key Laboratory for Animal Genetic Diversity and Evolution of High Education in Yunnan Province, School of Life Sciences, Yunnan University, Kunming, 650091, Yunnan, China; State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650223, Yunnan, China; Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, 650204, China
| | - Li Ren
- Key Laboratory of Protein Chemistry and Fish Developmental Biology of Education Ministry of China, College of Life Sciences, Hunan Normal University, Changsha, 410081, Hunan, China
| | - Yi Zhou
- Key Laboratory of Protein Chemistry and Fish Developmental Biology of Education Ministry of China, College of Life Sciences, Hunan Normal University, Changsha, 410081, Hunan, China
| | - Feng Huang
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan University, Kunming, 650091, Yunnan, China; Key Laboratory for Animal Genetic Diversity and Evolution of High Education in Yunnan Province, School of Life Sciences, Yunnan University, Kunming, 650091, Yunnan, China
| | - Xiaochuan Liu
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan University, Kunming, 650091, Yunnan, China; Key Laboratory for Animal Genetic Diversity and Evolution of High Education in Yunnan Province, School of Life Sciences, Yunnan University, Kunming, 650091, Yunnan, China
| | - Yubao Chen
- Key Laboratory of Protein Chemistry and Fish Developmental Biology of Education Ministry of China, College of Life Sciences, Hunan Normal University, Changsha, 410081, Hunan, China
| | - Chun Zhang
- Key Laboratory of Protein Chemistry and Fish Developmental Biology of Education Ministry of China, College of Life Sciences, Hunan Normal University, Changsha, 410081, Hunan, China
| | - Min Tao
- Key Laboratory of Protein Chemistry and Fish Developmental Biology of Education Ministry of China, College of Life Sciences, Hunan Normal University, Changsha, 410081, Hunan, China
| | - Bin Lu
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan University, Kunming, 650091, Yunnan, China; Key Laboratory for Animal Genetic Diversity and Evolution of High Education in Yunnan Province, School of Life Sciences, Yunnan University, Kunming, 650091, Yunnan, China
| | - Wei Zhou
- School of Software, Yunnan University, Kunming, 650091, Yunnan, China
| | - Guoliang Lin
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan University, Kunming, 650091, Yunnan, China; Key Laboratory for Animal Genetic Diversity and Evolution of High Education in Yunnan Province, School of Life Sciences, Yunnan University, Kunming, 650091, Yunnan, China
| | - Chao Mai
- School of Software, Yunnan University, Kunming, 650091, Yunnan, China
| | - Shuo Yuan
- School of Software, Yunnan University, Kunming, 650091, Yunnan, China
| | - Jun Wang
- Key Laboratory of Protein Chemistry and Fish Developmental Biology of Education Ministry of China, College of Life Sciences, Hunan Normal University, Changsha, 410081, Hunan, China
| | - Tao Li
- Key Laboratory of Protein Chemistry and Fish Developmental Biology of Education Ministry of China, College of Life Sciences, Hunan Normal University, Changsha, 410081, Hunan, China
| | - Qinbo Qin
- Key Laboratory of Protein Chemistry and Fish Developmental Biology of Education Ministry of China, College of Life Sciences, Hunan Normal University, Changsha, 410081, Hunan, China
| | - Hao Feng
- Key Laboratory of Protein Chemistry and Fish Developmental Biology of Education Ministry of China, College of Life Sciences, Hunan Normal University, Changsha, 410081, Hunan, China
| | - Kaikun Luo
- Key Laboratory of Protein Chemistry and Fish Developmental Biology of Education Ministry of China, College of Life Sciences, Hunan Normal University, Changsha, 410081, Hunan, China
| | - Jun Xiao
- Key Laboratory of Protein Chemistry and Fish Developmental Biology of Education Ministry of China, College of Life Sciences, Hunan Normal University, Changsha, 410081, Hunan, China
| | - Huan Zhong
- Key Laboratory of Protein Chemistry and Fish Developmental Biology of Education Ministry of China, College of Life Sciences, Hunan Normal University, Changsha, 410081, Hunan, China
| | - Rurong Zhao
- Key Laboratory of Protein Chemistry and Fish Developmental Biology of Education Ministry of China, College of Life Sciences, Hunan Normal University, Changsha, 410081, Hunan, China
| | - Wei Duan
- Key Laboratory of Protein Chemistry and Fish Developmental Biology of Education Ministry of China, College of Life Sciences, Hunan Normal University, Changsha, 410081, Hunan, China
| | - Zhenyan Song
- Key Laboratory of Protein Chemistry and Fish Developmental Biology of Education Ministry of China, College of Life Sciences, Hunan Normal University, Changsha, 410081, Hunan, China
| | - Yanqin Wang
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan University, Kunming, 650091, Yunnan, China; Key Laboratory for Animal Genetic Diversity and Evolution of High Education in Yunnan Province, School of Life Sciences, Yunnan University, Kunming, 650091, Yunnan, China
| | - Jing Wang
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan University, Kunming, 650091, Yunnan, China; Key Laboratory for Animal Genetic Diversity and Evolution of High Education in Yunnan Province, School of Life Sciences, Yunnan University, Kunming, 650091, Yunnan, China
| | - Li Zhong
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan University, Kunming, 650091, Yunnan, China; Key Laboratory for Animal Genetic Diversity and Evolution of High Education in Yunnan Province, School of Life Sciences, Yunnan University, Kunming, 650091, Yunnan, China
| | - Lu Wang
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan University, Kunming, 650091, Yunnan, China; Key Laboratory for Animal Genetic Diversity and Evolution of High Education in Yunnan Province, School of Life Sciences, Yunnan University, Kunming, 650091, Yunnan, China
| | - Zhaoli Ding
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650223, Yunnan, China
| | - Zhenglin Du
- Core Genomic Facility, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, 100029, China
| | - Xuemei Lu
- Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, 100101, China
| | - Yun Gao
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650223, Yunnan, China
| | - Robert W Murphy
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650223, Yunnan, China; Centre for Biodiversity and Conservation Biology, Royal Ontario Museum, Toronto, ON, Canada M5S 2C6
| | - Yun Liu
- Key Laboratory of Protein Chemistry and Fish Developmental Biology of Education Ministry of China, College of Life Sciences, Hunan Normal University, Changsha, 410081, Hunan, China
| | - Axel Meyer
- Department of Biology, University of Konstanz, 78457 Konstanz, Germany
| | - Ya-Ping Zhang
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan University, Kunming, 650091, Yunnan, China; Key Laboratory for Animal Genetic Diversity and Evolution of High Education in Yunnan Province, School of Life Sciences, Yunnan University, Kunming, 650091, Yunnan, China; State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650223, Yunnan, China;
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24
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Papetti C, Windisch HS, La Mesa M, Lucassen M, Marshall C, Lamare MD. Non-Antarctic notothenioids: Past phylogenetic history and contemporary phylogeographic implications in the face of environmental changes. Mar Genomics 2015; 25:1-9. [PMID: 26610933 DOI: 10.1016/j.margen.2015.11.007] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2015] [Revised: 11/12/2015] [Accepted: 11/12/2015] [Indexed: 12/31/2022]
Abstract
The non-Antarctic Notothenioidei families, Bovichtidae, Pseudaphritidae and Eleginopsidae, diverged early from the main notothenioid lineage. They are important in clarifying the early evolutionary processes that triggered notothenioid evolution in the Antarctic. The early-diverged group represents 8% of all notothenioid species and never established themselves on the Antarctic shelf. Most attention has been paid to the Antarctic notothenioids and their limited physiological tolerance to climate change and increased temperatures. In this review, we discuss key life history traits that are characteristic of the non-Antarctic early-diverged notothenioid taxa as well as the genetic resources and population differentiation information available for this group. We emphasise the population fitness and dynamics of these species and indicate how resource management and conservation of the group can be strengthened through an integrative approach. Both Antarctic waters and the non-Antarctic regions face rapid temperature rises combined with strong anthropogenic exploitation. While it is expected that early-diverged notothenioid species may have physiological advantages over high Antarctic species, it is difficult to predict how climate changes might alter the geographic range, behaviour, phenology and ultimately genetic variability of these species. It is possible, however, that their high degree of endemism and dependence on local environmental specificities to complete their life cycles might enhance their vulnerability.
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Affiliation(s)
- Chiara Papetti
- Section of Integrative Ecophysiology, Alfred-Wegener-Institute for Polar and Marine Research, Am Handelshafen 12, Bremerhaven 27570, Germany.
| | - Heidrun S Windisch
- Institute for Cell Biology and Zoology, Heinrich-Heine-University, Universitätsstrasse 1, Düsseldorf 40225, Germany.
| | - Mario La Mesa
- ISMAR-CNR, Istituto di Scienze Marine, Sede di Ancona, Largo Fiera della Pesca, 60125 Ancona, Italy.
| | - Magnus Lucassen
- Section of Integrative Ecophysiology, Alfred-Wegener-Institute for Polar and Marine Research, Am Handelshafen 12, Bremerhaven 27570, Germany.
| | - Craig Marshall
- Department of Biochemistry and Genetics, University of Otago, PO Box 56, Dunedin 9054, New Zealand.
| | - Miles D Lamare
- Department of Marine Sciences, University of Otago, PO Box 56, Dunedin 9054, New Zealand.
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25
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Hu YC, Kang CK, Tang CH, Lee TH. Transcriptomic Analysis of Metabolic Pathways in Milkfish That Respond to Salinity and Temperature Changes. PLoS One 2015; 10:e0134959. [PMID: 26263550 PMCID: PMC4532362 DOI: 10.1371/journal.pone.0134959] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2015] [Accepted: 07/16/2015] [Indexed: 12/20/2022] Open
Abstract
Milkfish (Chanos chanos), an important marine aquaculture species in southern Taiwan, show considerable euryhalinity but have low tolerance to sudden drops in water temperatures in winter. Here, we used high throughput next-generation sequencing (NGS) to identify molecular and biological processes involved in the responses to environmental changes. Preliminary tests revealed that seawater (SW)-acclimated milkfish tolerated lower temperatures than the fresh water (FW)-acclimated group. Although FW- and SW-acclimated milkfish have different levels of tolerance for hypothermal stress, to date, the molecular physiological basis of this difference has not been elucidated. Here, we performed a next-generation sequence analysis of mRNAs from four groups of milkfish. We obtained 29669 unigenes with an average length of approximately 1936 base pairs. Gene ontology (GO) analysis was performed after gene annotation. A large number of genes for molecular regulation were identified through a transcriptomic comparison in a KEGG analysis. Basal metabolic pathways involved in hypothermal tolerance, such as glycolysis, fatty acid metabolism, amino acid catabolism and oxidative phosphorylation, were analyzed using PathVisio and Cytoscape software. Our results indicate that in response to hypothermal stress, genes for oxidative phosphorylation, e.g., succinate dehydrogenase, were more highly up-regulated in SW than FW fish. Moreover, SW and FW milkfish used different strategies when exposed to hypothermal stress: SW milkfish up-regulated oxidative phosphorylation and catabolism genes to produce more energy budget, whereas FW milkfish down-regulated genes related to basal metabolism to reduce energy loss.
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Affiliation(s)
- Yau-Chung Hu
- Ph.D. Program in Microbial Genomics, National Chung Hsing University, Taichung, and Academia Sinica, Taipei, Taiwan
| | - Chao-Kai Kang
- Tainan Hydraulics Laboratory, National Cheng Kung University, Tainan, Taiwan
| | - Cheng-Hao Tang
- Graduate Institute of Marine Biology, National Dong Hwa University, Pingtung, Taiwan
- National Museum of Marine Biology and Aquarium, Pingtung, Taiwan
- * E-mail: (C-HT); (T-HL)
| | - Tsung-Han Lee
- Department of Life Sciences, National Chung Hsing University, Taichung, Taiwan
- Department of Biological Science and Technology, China Medical University, Taichung, Taiwan
- * E-mail: (C-HT); (T-HL)
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26
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Simmons DBD, Benskin JP, Cosgrove JR, Duncker BP, Ekman DR, Martyniuk CJ, Sherry JP. Omics for aquatic ecotoxicology: control of extraneous variability to enhance the analysis of environmental effects. ENVIRONMENTAL TOXICOLOGY AND CHEMISTRY 2015; 34:1693-1704. [PMID: 25827364 DOI: 10.1002/etc.3002] [Citation(s) in RCA: 48] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/08/2014] [Revised: 01/09/2015] [Accepted: 03/30/2015] [Indexed: 06/04/2023]
Abstract
There are multiple sources of biological and technical variation in a typical ecotoxicology study that may not be revealed by traditional endpoints but that become apparent in an omics dataset. As researchers increasingly apply omics technologies to environmental studies, it will be necessary to understand and control the main source(s) of variability to facilitate meaningful interpretation of such data. For instance, can variability in omics studies be addressed by changing the approach to study design and data analysis? Are there statistical methods that can be employed to correctly interpret omics data and make use of unattributed, inherent variability? The present study presents a review of experimental design and statistical considerations applicable to the use of omics methods in systems toxicology studies. In addition to highlighting potential sources that contribute to experimental variability, this review suggests strategies with which to reduce and/or control such variability so as to improve reliability, reproducibility, and ultimately the application of omics data for systems toxicology.
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Affiliation(s)
- Denina B D Simmons
- Emerging Methods Section, Aquatic Contaminants Research Division, Water Science & Technology Directorate, Environment Canada, Ontario, Canada
| | | | | | | | - Drew R Ekman
- Ecosystems Research Division, National Exposure Research Laboratory, Office of Research and Development, US Environmental Protection Agency, Athens, Georgia, USA
| | - Christopher J Martyniuk
- Center for Environmental and Human Toxicology & Department of Physiological Sciences, University of Florida, Gainesville, Florida, USA
| | - James P Sherry
- Emerging Methods Section, Aquatic Contaminants Research Division, Water Science & Technology Directorate, Environment Canada, Ontario, Canada
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27
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Hu P, Liu M, Zhang D, Wang J, Niu H, Liu Y, Wu Z, Han B, Zhai W, Shen Y, Chen L. Global identification of the genetic networks and cis-regulatory elements of the cold response in zebrafish. Nucleic Acids Res 2015; 43:9198-213. [PMID: 26227973 PMCID: PMC4627065 DOI: 10.1093/nar/gkv780] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/25/2014] [Accepted: 07/20/2015] [Indexed: 12/17/2022] Open
Abstract
The transcriptional programs of ectothermic teleosts are directly influenced by water temperature. However, the cis- and trans-factors governing cold responses are not well characterized. We profiled transcriptional changes in eight zebrafish tissues exposed to mildly and severely cold temperatures using RNA-Seq. A total of 1943 differentially expressed genes (DEGs) were identified, from which 34 clusters representing distinct tissue and temperature response expression patterns were derived using the k-means fuzzy clustering algorithm. The promoter regions of the clustered DEGs that demonstrated strong co-regulation were analysed for enriched cis-regulatory elements with a motif discovery program, DREME. Seventeen motifs, ten known and seven novel, were identified, which covered 23% of the DEGs. Two motifs predicted to be the binding sites for the transcription factors Bcl6 and Jun, respectively, were chosen for experimental verification, and they demonstrated the expected cold-induced and cold-repressed patterns of gene regulation. Protein interaction modeling of the network components followed by experimental validation suggested that Jun physically interacts with Bcl6 and might be a hub factor that orchestrates the cold response in zebrafish. Thus, the methodology used and the regulatory networks uncovered in this study provide a foundation for exploring the mechanisms of cold adaptation in teleosts.
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Affiliation(s)
- Peng Hu
- Key Laboratory of Aquacultural Resources and Utilization, Ministry of Education, College of Fisheries and Life Sciences, Shanghai Ocean University, Shanghai 201306, China Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
| | - Mingli Liu
- Key Laboratory of Aquacultural Resources and Utilization, Ministry of Education, College of Fisheries and Life Sciences, Shanghai Ocean University, Shanghai 201306, China
| | - Dong Zhang
- Key Laboratory of Aquacultural Resources and Utilization, Ministry of Education, College of Fisheries and Life Sciences, Shanghai Ocean University, Shanghai 201306, China
| | - Jinfeng Wang
- Key Laboratory of Aquacultural Resources and Utilization, Ministry of Education, College of Fisheries and Life Sciences, Shanghai Ocean University, Shanghai 201306, China
| | - Hongbo Niu
- Key Laboratory of Aquacultural Resources and Utilization, Ministry of Education, College of Fisheries and Life Sciences, Shanghai Ocean University, Shanghai 201306, China
| | - Yimeng Liu
- Key Laboratory of Aquacultural Resources and Utilization, Ministry of Education, College of Fisheries and Life Sciences, Shanghai Ocean University, Shanghai 201306, China
| | - Zhichao Wu
- Key Laboratory of Aquacultural Resources and Utilization, Ministry of Education, College of Fisheries and Life Sciences, Shanghai Ocean University, Shanghai 201306, China
| | - Bingshe Han
- Key Laboratory of Aquacultural Resources and Utilization, Ministry of Education, College of Fisheries and Life Sciences, Shanghai Ocean University, Shanghai 201306, China
| | - Wanying Zhai
- Key Laboratory of Aquacultural Resources and Utilization, Ministry of Education, College of Fisheries and Life Sciences, Shanghai Ocean University, Shanghai 201306, China
| | - Yu Shen
- Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
| | - Liangbiao Chen
- Key Laboratory of Aquacultural Resources and Utilization, Ministry of Education, College of Fisheries and Life Sciences, Shanghai Ocean University, Shanghai 201306, China
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28
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Evans TG. Considerations for the use of transcriptomics in identifying the ‘genes that matter’ for environmental adaptation. J Exp Biol 2015; 218:1925-35. [DOI: 10.1242/jeb.114306] [Citation(s) in RCA: 87] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
ABSTRACT
Transcriptomics has emerged as a powerful approach for exploring physiological responses to the environment. However, like any other experimental approach, transcriptomics has its limitations. Transcriptomics has been criticized as an inappropriate method to identify genes with large impacts on adaptive responses to the environment because: (1) genes with large impacts on fitness are rare; (2) a large change in gene expression does not necessarily equate to a large effect on fitness; and (3) protein activity is most relevant to fitness, and mRNA abundance is an unreliable indicator of protein activity. In this review, these criticisms are re-evaluated in the context of recent systems-level experiments that provide new insight into the relationship between gene expression and fitness during environmental stress. In general, these criticisms remain valid today, and indicate that exclusively using transcriptomics to screen for genes that underlie environmental adaptation will overlook constitutively expressed regulatory genes that play major roles in setting tolerance limits. Standard practices in transcriptomic data analysis pipelines may also be limiting insight by prioritizing highly differentially expressed and conserved genes over those genes that undergo moderate fold-changes and cannot be annotated. While these data certainly do not undermine the continued and widespread use of transcriptomics within environmental physiology, they do highlight the types of research questions for which transcriptomics is best suited and the need for more gene functional analyses. Such information is pertinent at a time when transcriptomics has become increasingly tractable and many researchers may be contemplating integrating transcriptomics into their research programs.
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29
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Thanh NM, Jung H, Lyons RE, Njaci I, Yoon BH, Chand V, Tuan NV, Thu VTM, Mather P. Optimizing de novo transcriptome assembly and extending genomic resources for striped catfish (Pangasianodon hypophthalmus). Mar Genomics 2015; 23:87-97. [PMID: 25979246 DOI: 10.1016/j.margen.2015.05.001] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2014] [Revised: 05/03/2015] [Accepted: 05/03/2015] [Indexed: 12/17/2022]
Abstract
Striped catfish (Pangasianodon hypophthalmus) is a commercially important freshwater fish used in inland aquaculture in the Mekong Delta, Vietnam. The culture industry is facing a significant challenge however from saltwater intrusion into many low topographical coastal provinces across the Mekong Delta as a result of predicted climate change impacts. Developing genomic resources for this species can facilitate the production of improved culture lines that can withstand raised salinity conditions, and so we have applied high-throughput Ion Torrent sequencing of transcriptome libraries from six target osmoregulatory organs from striped catfish as a genomic resource for use in future selection strategies. We obtained 12,177,770 reads after trimming and processing with an average length of 97bp. De novo assemblies were generated using CLC Genomic Workbench, Trinity and Velvet/Oases with the best overall contig performance resulting from the CLC assembly. De novo assembly using CLC yielded 66,451 contigs with an average length of 478bp and N50 length of 506bp. A total of 37,969 contigs (57%) possessed significant similarity with proteins in the non-redundant database. Comparative analyses revealed that a significant number of contigs matched sequences reported in other teleost fishes, ranging in similarity from 45.2% with Atlantic cod to 52% with zebrafish. In addition, 28,879 simple sequence repeats (SSRs) and 55,721 single nucleotide polymorphisms (SNPs) were detected in the striped catfish transcriptome. The sequence collection generated in the current study represents the most comprehensive genomic resource for P. hypophthalmus available to date. Our results illustrate the utility of next-generation sequencing as an efficient tool for constructing a large genomic database for marker development in non-model species.
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Affiliation(s)
- Nguyen Minh Thanh
- International University - VNU HCMC, Quarter 6, Linh Trung Ward, Thu Duc District, Ho Chi Minh City, Viet Nam.
| | - Hyungtaek Jung
- Centre for Tropical Crops and Biocommodities, Queensland University of Technology, GPO Box 2434, Brisbane, QLD 4001, Australia; Science and Engineering Faculty, Queensland University of Technology, GPO Box 2434, Brisbane, QLD 4001, Australia.
| | - Russell E Lyons
- Animal Genetics Laboratory, School of Veterinary Science, University of Queensland, Gatton, QLD 4343, Australia.
| | - Isaac Njaci
- Centre for Tropical Crops and Biocommodities, Queensland University of Technology, GPO Box 2434, Brisbane, QLD 4001, Australia.
| | - Byoung-Ha Yoon
- Medical Genomics Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon 305-806, Republic of Korea; Department of Functional Genomics, Korea University of Science and Technology, Daejoen 305-333, Republic of Korea.
| | - Vincent Chand
- Science and Engineering Faculty, Queensland University of Technology, GPO Box 2434, Brisbane, QLD 4001, Australia.
| | - Nguyen Viet Tuan
- Science and Engineering Faculty, Queensland University of Technology, GPO Box 2434, Brisbane, QLD 4001, Australia.
| | - Vo Thi Minh Thu
- International University - VNU HCMC, Quarter 6, Linh Trung Ward, Thu Duc District, Ho Chi Minh City, Viet Nam.
| | - Peter Mather
- Science and Engineering Faculty, Queensland University of Technology, GPO Box 2434, Brisbane, QLD 4001, Australia.
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30
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Porcelli D, Butlin RK, Gaston KJ, Joly D, Snook RR. The environmental genomics of metazoan thermal adaptation. Heredity (Edinb) 2015; 114:502-14. [PMID: 25735594 PMCID: PMC4815515 DOI: 10.1038/hdy.2014.119] [Citation(s) in RCA: 55] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2014] [Revised: 11/06/2014] [Accepted: 11/11/2014] [Indexed: 01/07/2023] Open
Abstract
Continued and accelerating change in the thermal environment places an ever-greater priority on understanding how organisms are going to respond. The paradigm of ‘move, adapt or die', regarding ways in which organisms can respond to environmental stressors, stimulates intense efforts to predict the future of biodiversity. Assuming that extinction is an unpalatable outcome, researchers have focussed attention on how organisms can shift in their distribution to stay in the same thermal conditions or can stay in the same place by adapting to a changing thermal environment. How likely these respective outcomes might be depends on the answer to a fundamental evolutionary question, namely what genetic changes underpin adaptation to the thermal environment. The increasing access to and decreasing costs of next-generation sequencing (NGS) technologies, which can be applied to both model and non-model systems, provide a much-needed tool for understanding thermal adaptation. Here we consider broadly what is already known from non-NGS studies about thermal adaptation, then discuss the benefits and challenges of different NGS methodologies to add to this knowledge base. We then review published NGS genomics and transcriptomics studies of thermal adaptation to heat stress in metazoans and compare these results with previous non-NGS patterns. We conclude by summarising emerging patterns of genetic response and discussing future directions using these increasingly common techniques.
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Affiliation(s)
- D Porcelli
- Department of Animal and Plant Sciences, University of Sheffield, Sheffield, UK
| | - R K Butlin
- 1] Department of Animal and Plant Sciences, University of Sheffield, Sheffield, UK [2] Sven Lovén Centre-Tjärnö, University of Gothenburg, Strömstad, Sweden
| | - K J Gaston
- Environment and Sustainability Institute, University of Exeter, Penryn, UK
| | - D Joly
- 1] Laboratoire Evolution, Génomes et Spéciation, CNRS-UPR 9034, Gif sur Yvette, France [2] Université Paris-Sud, Orsay, France
| | - R R Snook
- Department of Animal and Plant Sciences, University of Sheffield, Sheffield, UK
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31
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Gerdol M, Buonocore F, Scapigliati G, Pallavicini A. Analysis and characterization of the head kidney transcriptome from the Antarctic fish Trematomus bernacchii (Teleostea, Notothenioidea): a source for immune relevant genes. Mar Genomics 2014; 20:13-5. [PMID: 25557849 DOI: 10.1016/j.margen.2014.12.005] [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] [Received: 10/31/2014] [Revised: 12/01/2014] [Accepted: 12/19/2014] [Indexed: 11/24/2022]
Abstract
In this study we describe the de novo assembled head kidney transcriptome of the Antarctic notothenioid fish Trematomus bernacchii, an important model species for biochemical, environmental and immunological studies. RNA-seq data was generated using Illumina paired-end sequencing, obtaining ~7 Gbp of sequence data, which were assembled into 96,641 contigs and annotated with the Trinotate pipeline. Since this sequence collection is expected to contain a relevant number of immunity-related transcripts, it will be used as a reference for future immunological studies in this species.
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Affiliation(s)
- Marco Gerdol
- Department of Life Sciences, University of Trieste, Via Giorgieri 5, 34127 Trieste, TS, Italy.
| | - Francesco Buonocore
- Department for Innovation in Biological, Agro-food and Forest Systems, University of Tuscia, Largo dell'Università snc, Viterbo, VT, Italy.
| | - Giuseppe Scapigliati
- Department for Innovation in Biological, Agro-food and Forest Systems, University of Tuscia, Largo dell'Università snc, Viterbo, VT, Italy.
| | - Alberto Pallavicini
- Department of Life Sciences, University of Trieste, Via Giorgieri 5, 34127 Trieste, TS, Italy.
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32
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Poelchau MF, Huang X, Goff A, Reynolds J, Armbruster P. An experimental and bioinformatics protocol for RNA-Seq analyses of photoperiodic diapause in the Asian tiger mosquito, Aedes albopictus. J Vis Exp 2014:e51961. [PMID: 25490084 DOI: 10.3791/51961] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/31/2022] Open
Abstract
Photoperiodic diapause is an important adaptation that allows individuals to escape harsh seasonal environments via a series of physiological changes, most notably developmental arrest and reduced metabolism. Global gene expression profiling via RNA-Seq can provide important insights into the transcriptional mechanisms of photoperiodic diapause. The Asian tiger mosquito, Aedes albopictus, is an outstanding organism for studying the transcriptional bases of diapause due to its ease of rearing, easily induced diapause, and the genomic resources available. This manuscript presents a general experimental workflow for identifying diapause-induced transcriptional differences in A. albopictus. Rearing techniques, conditions necessary to induce diapause and non-diapause development, methods to estimate percent diapause in a population, and RNA extraction and integrity assessment for mosquitoes are documented. A workflow to process RNA-Seq data from Illumina sequencers culminates in a list of differentially expressed genes. The representative results demonstrate that this protocol can be used to effectively identify genes differentially regulated at the transcriptional level in A. albopictus due to photoperiodic differences. With modest adjustments, this workflow can be readily adapted to study the transcriptional bases of diapause or other important life history traits in other mosquitoes.
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Affiliation(s)
| | - Xin Huang
- Department of Biology, Georgetown University
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Sex determination in Antarctic notothenioid fish: chromosomal clues and evolutionary hypotheses. Polar Biol 2014. [DOI: 10.1007/s00300-014-1601-z] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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Braasch I, Peterson SM, Desvignes T, McCluskey BM, Batzel P, Postlethwait JH. A new model army: Emerging fish models to study the genomics of vertebrate Evo-Devo. JOURNAL OF EXPERIMENTAL ZOOLOGY PART B-MOLECULAR AND DEVELOPMENTAL EVOLUTION 2014; 324:316-41. [PMID: 25111899 DOI: 10.1002/jez.b.22589] [Citation(s) in RCA: 84] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/16/2014] [Revised: 06/19/2014] [Accepted: 06/25/2014] [Indexed: 01/08/2023]
Abstract
Many fields of biology--including vertebrate Evo-Devo research--are facing an explosion of genomic and transcriptomic sequence information and a multitude of fish species are now swimming in this "genomic tsunami." Here, we first give an overview of recent developments in sequencing fish genomes and transcriptomes that identify properties of fish genomes requiring particular attention and propose strategies to overcome common challenges in fish genomics. We suggest that the generation of chromosome-level genome assemblies--for which we introduce the term "chromonome"--should be a key component of genomic investigations in fish because they enable large-scale conserved synteny analyses that inform orthology detection, a process critical for connectivity of genomes. Orthology calls in vertebrates, especially in teleost fish, are complicated by divergent evolution of gene repertoires and functions following two rounds of genome duplication in the ancestor of vertebrates and a third round at the base of teleost fish. Second, using examples of spotted gar, basal teleosts, zebrafish-related cyprinids, cavefish, livebearers, icefish, and lobefin fish, we illustrate how next generation sequencing technologies liberate emerging fish systems from genomic ignorance and transform them into a new model army to answer longstanding questions on the genomic and developmental basis of their biodiversity. Finally, we discuss recent progress in the genetic toolbox for the major fish models for functional analysis, zebrafish, and medaka, that can be transferred to many other fish species to study in vivo the functional effect of evolutionary genomic change as Evo-Devo research enters the postgenomic era.
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Affiliation(s)
- Ingo Braasch
- Institute of Neuroscience, University of Oregon, Eugene, Oregon
| | | | | | | | - Peter Batzel
- Institute of Neuroscience, University of Oregon, Eugene, Oregon
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Windisch HS, Frickenhaus S, John U, Knust R, Pörtner HO, Lucassen M. Stress response or beneficial temperature acclimation: transcriptomic signatures in Antarctic fish (Pachycara brachycephalum). Mol Ecol 2014; 23:3469-82. [DOI: 10.1111/mec.12822] [Citation(s) in RCA: 66] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2014] [Revised: 05/13/2014] [Accepted: 05/26/2014] [Indexed: 01/07/2023]
Affiliation(s)
- H. S. Windisch
- Alfred Wegener Institute; Helmholtz Center for Polar and Marine Research; Am Handelshafen 12 27570 Bremerhaven Germany
| | - S. Frickenhaus
- Alfred Wegener Institute; Helmholtz Center for Polar and Marine Research; Am Handelshafen 12 27570 Bremerhaven Germany
- Hochschule Bremerhaven; Biotechnology; An der Karlstadt 8 27568 Bremerhaven Germany
| | - U. John
- Alfred Wegener Institute; Helmholtz Center for Polar and Marine Research; Am Handelshafen 12 27570 Bremerhaven Germany
| | - R. Knust
- Alfred Wegener Institute; Helmholtz Center for Polar and Marine Research; Am Handelshafen 12 27570 Bremerhaven Germany
| | - H.-O. Pörtner
- Alfred Wegener Institute; Helmholtz Center for Polar and Marine Research; Am Handelshafen 12 27570 Bremerhaven Germany
| | - M. Lucassen
- Alfred Wegener Institute; Helmholtz Center for Polar and Marine Research; Am Handelshafen 12 27570 Bremerhaven Germany
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Shi M, Huang R, Du F, Pei Y, Liao L, Zhu Z, Wang Y. RNA-seq profiles from grass carp tissues after reovirus (GCRV) infection based on singular and modular enrichment analyses. Mol Immunol 2014; 61:44-53. [PMID: 24865419 DOI: 10.1016/j.molimm.2014.05.004] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2013] [Revised: 04/09/2014] [Accepted: 05/07/2014] [Indexed: 11/29/2022]
Abstract
Hemorrhagic disease of the grass carp, Ctenopharyngodon idella, is a fatal disease in fingerlings and yearlings caused by a reovirus, GCRV. RNA-seq data from four diseased grass carp tissues (gill, intestine, liver and spleen) were obtained at 2h before and six times after (2h, 24h, 48h, 72h, 96h and 120h) GCRV challenge. A total of 7.25±0.18 million (M) clean reads and 3.53±0.37M unique reads were obtained per RNA-seq analysis. Compared with controls, there were 9060 unique differentially expressed genes (DEGs) in the four tissues at the six time points post-GCRV challenge. Hierarchical clustering analysis of the DEGs showed that the data from the six time points fell into three branches: 2h, 24h/48h, and 72h/96h/120h. Singular (SEA) and modular enrichment analyses of DEGs per RNA-seq dataset were performed based on gene ontology. The results showed that immune responses occurred in all four tissues, indicating that GCRV probably does not target any tissue specifically. Moreover, during the course of disease, disturbances were observed in lipid and carbohydrate metabolism in each of the organs. SEA of DEGs based on the Kyoto Encyclopedia of Genes and Genomes database was also performed, and this indicated that the complement system and cellular immunity played an important role during the course of hemorrhagic disease. The qPCR of pooled samples of duplicate challenge experiment were used to confirm our RNA-seq approach.
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Affiliation(s)
- Mijuan Shi
- 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 100039, China
| | - Rong Huang
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China
| | - Fukuan Du
- 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
| | - Lanjie Liao
- 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 100039, 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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