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Li N, Bao L, Zhou T, Yuan Z, Liu S, Dunham R, Li Y, Wang K, Xu X, Jin Y, Zeng Q, Gao S, Fu Q, Liu Y, Yang Y, Li Q, Meyer A, Gao D, Liu Z. Genome sequence of walking catfish (Clarias batrachus) provides insights into terrestrial adaptation. BMC Genomics 2018; 19:952. [PMID: 30572844 PMCID: PMC6302426 DOI: 10.1186/s12864-018-5355-9] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2018] [Accepted: 12/09/2018] [Indexed: 11/22/2022] Open
Abstract
Background Walking catfish (Clarias batrachus) is a freshwater fish capable of air-breathing and locomotion on land. It usually inhabits various low-oxygen habitats, burrows inside the mudflat, and sometimes “walks” to search for suitable environments during summer. It has evolved accessory air-breathing organs for respiring air and corresponding mechanisms to survive in such challenging environments. Thereby, it serves as a great model for understanding adaptations to terrestrial life. Results Comparative genomics with channel catfish (Ictalurus punctatus) revealed specific adaptations of C. batrachus in DNA repair, enzyme activator activity, and small GTPase regulator activity. Comparative analysis with 11 non-air-breathing fish species suggested adaptive evolution in gene expression and nitrogenous waste metabolic processes. Further, myoglobin, olfactory receptor related to class A G protein-coupled receptor 1, and sulfotransferase 6b1 genes were found to be expanded in the air-breathing walking catfish genome, with 15, 15, and 12 copies, respectively, compared to non-air-breathing fishes that possess only 1–2 copies of these genes. Additionally, we sequenced and compared the transcriptomes of the gill and the air-breathing organ to characterize the mechanism of aerial respiration involved in elastic fiber formation, oxygen binding and transport, angiogenesis, ion homeostasis and acid-base balance. The hemoglobin genes were expressed dramatically higher in the air-breathing organ than in the gill of walking catfish. Conclusions This study provides an important genomic resource for understanding the adaptive mechanisms of walking catfish to terrestrial environments. It is possible that the coupling of enhanced abilities for oxygen storage and oxygen transport through genomic expansion of myoglobin genes and transcriptomic up-regulation of hemoglobin and angiogenesis-related genes are important components of the molecular basis for adaptation of this aquatic species to terrestrial life. Electronic supplementary material The online version of this article (10.1186/s12864-018-5355-9) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Ning Li
- Fish Molecular Genetics and Biotechnology Laboratory, School of Fisheries, Aquaculture and Aquatic Sciences, Auburn University, Auburn, AL, 36849, USA
| | - Lisui Bao
- Fish Molecular Genetics and Biotechnology Laboratory, School of Fisheries, Aquaculture and Aquatic Sciences, Auburn University, Auburn, AL, 36849, USA
| | - Tao Zhou
- Fish Molecular Genetics and Biotechnology Laboratory, School of Fisheries, Aquaculture and Aquatic Sciences, Auburn University, Auburn, AL, 36849, USA
| | - Zihao Yuan
- Fish Molecular Genetics and Biotechnology Laboratory, School of Fisheries, Aquaculture and Aquatic Sciences, Auburn University, Auburn, AL, 36849, USA
| | - Shikai Liu
- Fish Molecular Genetics and Biotechnology Laboratory, School of Fisheries, Aquaculture and Aquatic Sciences, Auburn University, Auburn, AL, 36849, USA
| | - Rex Dunham
- School of Fisheries, Aquaculture and Aquatic Sciences, Auburn University, Auburn, AL, 36849, USA
| | - Yuanning Li
- Department of Biological Sciences & Molette Biology Laboratory for Environmental and Climate Change Studies, Auburn University, Auburn, AL, 36849, USA
| | - Kun Wang
- Center for Ecological and Environmental Sciences, Northwestern Polytechnical University, Xi'an, 710072, China
| | - Xiaoyan Xu
- Fish Molecular Genetics and Biotechnology Laboratory, School of Fisheries, Aquaculture and Aquatic Sciences, Auburn University, Auburn, AL, 36849, USA
| | - Yulin Jin
- Fish Molecular Genetics and Biotechnology Laboratory, School of Fisheries, Aquaculture and Aquatic Sciences, Auburn University, Auburn, AL, 36849, USA
| | - Qifan Zeng
- Fish Molecular Genetics and Biotechnology Laboratory, School of Fisheries, Aquaculture and Aquatic Sciences, Auburn University, Auburn, AL, 36849, USA
| | - Sen Gao
- Fish Molecular Genetics and Biotechnology Laboratory, School of Fisheries, Aquaculture and Aquatic Sciences, Auburn University, Auburn, AL, 36849, USA
| | - Qiang Fu
- Fish Molecular Genetics and Biotechnology Laboratory, School of Fisheries, Aquaculture and Aquatic Sciences, Auburn University, Auburn, AL, 36849, USA
| | - Yang Liu
- Fish Molecular Genetics and Biotechnology Laboratory, School of Fisheries, Aquaculture and Aquatic Sciences, Auburn University, Auburn, AL, 36849, USA
| | - Yujia Yang
- Fish Molecular Genetics and Biotechnology Laboratory, School of Fisheries, Aquaculture and Aquatic Sciences, Auburn University, Auburn, AL, 36849, USA
| | - Qi Li
- Shellfish Genetics and Breeding Laboratory, Fisheries College, Ocean University of China, Qingdao, 266003, Shandong, China
| | - Axel Meyer
- Department of Biology, University of Konstanz, 78464, Konstanz, Germany
| | - Dongya Gao
- Fish Molecular Genetics and Biotechnology Laboratory, School of Fisheries, Aquaculture and Aquatic Sciences, Auburn University, Auburn, AL, 36849, USA
| | - Zhanjiang Liu
- Department of Biology, College of Arts and Sciences, Syracuse University, Syracuse, NY, 13244, USA.
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Anttila K, Dhillon RS, Boulding EG, Farrell AP, Glebe BD, Elliott JAK, Wolters WR, Schulte PM. Variation in temperature tolerance among families of Atlantic salmon (Salmo salar) is associated with hypoxia tolerance, ventricle size and myoglobin level. J Exp Biol 2013; 216:1183-90. [DOI: 10.1242/jeb.080556] [Citation(s) in RCA: 126] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
SUMMARY
In fishes, performance failure at high temperature is thought to be due to a limitation on oxygen delivery (the theory of oxygen and capacity limited thermal tolerance, OCLTT), which suggests that thermal tolerance and hypoxia tolerance might be functionally associated. Here we examined variation in temperature and hypoxia tolerance among 41 families of Atlantic salmon (Salmo salar), which allowed us to evaluate the association between these two traits. Both temperature and hypoxia tolerance varied significantly among families and there was a significant positive correlation between critical maximum temperature (CTmax) and hypoxia tolerance, supporting the OCLTT concept. At the organ and cellular levels, we also discovered support for the OCLTT concept as relative ventricle mass (RVM) and cardiac myoglobin (Mb) levels both correlated positively with CTmax (R2=0.21, P<0.001 and R2=0.17, P=0.003, respectively). A large RVM has previously been shown to be associated with high cardiac output, which might facilitate tissue oxygen supply during elevated oxygen demand at high temperatures, while Mb facilitates the oxygen transfer from the blood to tissues, especially during hypoxia. The data presented here demonstrate for the first time that RVM and Mb are correlated with increased upper temperature tolerance in fish. High phenotypic variation between families and greater similarity among full- and half-siblings suggests that there is substantial standing genetic variation in thermal and hypoxia tolerance, which could respond to selection either in aquaculture or in response to anthropogenic stressors such as global climate change.
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Affiliation(s)
- Katja Anttila
- Department of Zoology, 6270 University Boulevard, University of British Columbia, Vancouver, BC, Canada, V6T 1Z4
| | - Rashpal S. Dhillon
- Department of Zoology, 6270 University Boulevard, University of British Columbia, Vancouver, BC, Canada, V6T 1Z4
| | - Elizabeth G. Boulding
- Department of Integrative Biology, University of Guelph, Guelph, ON, Canada, N1G 2W1
| | - Anthony P. Farrell
- Department of Zoology, 6270 University Boulevard, University of British Columbia, Vancouver, BC, Canada, V6T 1Z4
- Faculty of Land and Food Systems, 2357 Main Mall, University of British Columbia, Vancouver, BC, Canada, V6T 1Z4
| | - Brian D. Glebe
- Fisheries and Oceans Canada, Aquaculture Division, St Andrews Biological Station, 531 Brandy Cove Rd, St Andrews, NB, Canada, E5B 2L9
| | - Jake A. K. Elliott
- Kelly Cove Salmon (KCS), Division Cooke Aquaculture, 874 Main Street, Blacks Harbour, NB, Canada, E5H 1E6
| | - William R. Wolters
- National Cold Water Marine Aquaculture Center, 25 Salmon Farm Road, Franklin, ME 04634, USA
| | - Patricia M. Schulte
- Department of Zoology, 6270 University Boulevard, University of British Columbia, Vancouver, BC, Canada, V6T 1Z4
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Helbo S, Weber RE, Fago A. Expression patterns and adaptive functional diversity of vertebrate myoglobins. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2013; 1834:1832-9. [PMID: 23388387 DOI: 10.1016/j.bbapap.2013.01.037] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/03/2012] [Revised: 01/23/2013] [Accepted: 01/26/2013] [Indexed: 02/06/2023]
Abstract
Recent years have witnessed a new round of research on one of the most studied proteins - myoglobin (Mb), the oxygen (O2) carrier of skeletal and heart muscle. Two major discoveries have stimulated research in this field: 1) that Mb has additional protecting functions, such as the regulation of in vivo levels of the signaling molecule nitric oxide (NO) by scavenging and generating NO during normoxia and hypoxia, respectively; and 2) that Mb in vertebrates (particularly fish) is expressed as tissue-specific isoforms in other tissues than heart and skeletal muscle, such as vessel endothelium, liver and brain, as found in cyprinid fish. Furthermore, Mb has also been found to protect against oxidative stress after hypoxia and reoxygenation and to undergo allosteric, O2-linked S-nitrosation, as in rainbow trout. Overall, the emerging evidence, particularly from fish species, indicates that Mb fulfills a broader array of physiological functions in a wider range of different tissues than hitherto appreciated. This new knowledge helps to better understand how variations in Mb structure and function may correlate with differences in animals' lifestyles and hypoxia-tolerance. This review integrates old and new results on Mb expression patterns and functional properties amongst vertebrates and discusses how these may relate to adaptive variations in different species. This article is part of a special issue entitled: Oxygen Binding and Sensing Proteins.
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Affiliation(s)
- Signe Helbo
- Department of Bioscience, Aarhus University, Denmark.
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Faust HA, Gamperl AK, Rodnick KJ. All rainbow trout (Oncorhynchus mykiss) are not created equal:intra-specific variation in cardiac hypoxia tolerance. J Exp Biol 2004; 207:1005-15. [PMID: 14766959 DOI: 10.1242/jeb.00824] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
SUMMARYAll of our previous work, and that of other investigators, shows that the trout heart only partially recovers following brief exposure to severe hypoxia or anoxia (i.e. it is hypoxia-sensitive). However, in preliminary studies, we found evidence to suggest that rainbow trout reared at a farm in Oregon (USA)have a significant degree of inherent myocardial hypoxia tolerance. To evaluate whether hearts from these trout are indeed hypoxia-tolerant, and thus to determine whether intra-specific variation in rainbow trout myocardial hypoxia tolerance exists, we measured in situ cardiac function and monitored myoglobin and lactate dehydrogenase (LDH) release (both indices of myocardial damage) in hearts that were exposed to varying durations(10–30 min) of severe hypoxia (PO =5–10 mmHg). There was a strong positive relationship between the duration of severe hypoxia and the degree of post-hypoxic myocardial dysfunction. However, the resulting dysfunction was modest, with hearts exposed to 30 min of severe hypoxia recovering 77% of their initial maximum cardiac output. Furthermore,myoglobin was not detected in the perfusate, and ventricular LDH activity did not vary in response to the duration of severe hypoxia. These data (1)indicate that trout from this farm have extremely hypoxia-tolerant hearts; (2)suggest that considerable intra-specific variation exists in trout myocardial hypoxia tolerance; and (3) provide preliminary evidence that trout hearts are not irreversibly damaged, but are merely `stunned', following brief periods(10–30 min) of severe hypoxia.
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Affiliation(s)
- Heather A Faust
- Department of Biology, Portland State University, PO Box 0751, Portland, OR 97207-0751, USA
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Johnston IA, Harrison P. Morphometrics and ultrastructure of myocardial tissue in Notothenioid fishes. FISH PHYSIOLOGY AND BIOCHEMISTRY 1987; 3:1-6. [PMID: 24233247 DOI: 10.1007/bf02183988] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
Abstract
Antarctic fish of the family Channichthyidae (Icefishes) lack the respiratory pigments haemoglobin and myoglobin. The morphometrics and ultrastructure of the ventricular myocardium of a benthic icefish,Chaenocephalus aceratus has been compared with that of a red-blooded Notothenioid fish,Notothenia neglecta, of similar habit.The mass of ventricular muscle as a percentage of bodyweight is 3 times greater in adultC. aceratus (0.32%) thanN. neglecta (0.11%). Myoglobin concentration in the ventricle ofN. neglecta, 20 nmoles/g, is comparable to that of temperate teleosts with similar activity patterns. The volume and surface densities of mitochondria are 41.5% and 0.32 μm(-1) for Icefish and 25% and 0.15 μm(-1) forN. neglecta, Cytochrome oxidase activities are similar in the two tissues whilst the volume density of myofibrils is higher forN. neglecta (47%) thanC. aceratus (29.9%).The proliferation of mitochondria in the myocardium of Icefish will reduce the diffusion path-length for oxygen between ventricular lumen and the outer mitochondrial membrane and may compensate for the absence of myoglobin.
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Affiliation(s)
- I A Johnston
- British Antarctic Survey, Natural Environment Research Council, Madingley Road, High Cross, Cambridge, CB3 OET, England
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