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Wang X, Qu M, Liu Y, Schneider RF, Song Y, Chen Z, Zhang H, Zhang Y, Yu H, Zhang S, Li D, Qin G, Ma S, Zhong J, Yin J, Liu S, Fan G, Meyer A, Wang D, Lin Q. Genomic basis of evolutionary adaptation in a warm-blooded fish. Innovation (N Y) 2022; 3:100185. [PMID: 34984407 PMCID: PMC8693259 DOI: 10.1016/j.xinn.2021.100185] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2021] [Accepted: 11/07/2021] [Indexed: 11/16/2022] Open
Abstract
Few fishes have evolved elevated body temperatures compared with ambient temperatures, and only in opah (Lampris spp) is the entire body affected. To understand the molecular basis of endothermy, we analyzed the opah genome and identified 23 genes with convergent amino acid substitutions across fish, birds, and mammals, including slc8b1, which encodes the mitochondrial Na+/Ca2+ exchanger and is essential for heart function and metabolic heat production. Among endothermic fishes, 44 convergent genes with suggestive metabolic functions were identified, such as glrx3, encoding a crucial protein for hemoglobin maturation. Numerous genes involved in the production and retention of metabolic heat were also found to be under positive selection. Analyses of opah's unique inner-heat-producing pectoral muscle layer (PMI), an evolutionary key innovation, revealed that many proteins were co-opted from dorsal swimming muscles for thermogenesis and oxidative phosphorylation. Thus, the opah genome provides valuable resources and opportunities to uncover the genetic basis of thermal adaptations in fish.
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Affiliation(s)
- Xin Wang
- CAS Key Laboratory of Tropical Marine Bio-resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou 510301, China.,Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou 511458, China
| | - Meng Qu
- CAS Key Laboratory of Tropical Marine Bio-resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou 510301, China.,Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou 511458, China
| | - Yali Liu
- CAS Key Laboratory of Tropical Marine Bio-resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou 510301, China.,Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou 511458, China
| | - Ralf F Schneider
- Marine Evolutionary Ecology, GEOMAR Helmholtz Centre for Ocean Research Kiel, 24105 Kiel, Germany
| | - Yue Song
- BGI-Qingdao, Qingdao 266555, China
| | - Zelin Chen
- CAS Key Laboratory of Tropical Marine Bio-resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou 510301, China.,Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou 511458, China
| | - Hao Zhang
- CAS Key Laboratory of Tropical Marine Bio-resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou 510301, China.,Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou 511458, China.,State Key Laboratory of Marine Environmental Science/College of the Environment and Ecology, Xiamen University, Xiamen 361102, China
| | - Yanhong Zhang
- CAS Key Laboratory of Tropical Marine Bio-resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou 510301, China.,Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou 511458, China
| | - Haiyan Yu
- CAS Key Laboratory of Tropical Marine Bio-resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou 510301, China
| | | | - Dongxu Li
- State Key Laboratory of Marine Environmental Science/College of the Environment and Ecology, Xiamen University, Xiamen 361102, China
| | - Geng Qin
- CAS Key Laboratory of Tropical Marine Bio-resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou 510301, China.,Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou 511458, China
| | - Shaobo Ma
- CAS Key Laboratory of Tropical Marine Bio-resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou 510301, China.,Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou 511458, China
| | - Jia Zhong
- CAS Key Laboratory of Tropical Marine Bio-resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou 510301, China.,Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou 511458, China
| | - Jianping Yin
- CAS Key Laboratory of Tropical Marine Bio-resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou 510301, China.,Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou 511458, China
| | - Shuaishuai Liu
- CAS Key Laboratory of Tropical Marine Bio-resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou 510301, China.,Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou 511458, China
| | - Guangyi Fan
- BGI-Qingdao, Qingdao 266555, China.,BGI-Shenzhen, Shenzhen 518083, China
| | - Axel Meyer
- Department of Biology, University of Konstanz, Konstanz 78464, Germany
| | - Dazhi Wang
- State Key Laboratory of Marine Environmental Science/College of the Environment and Ecology, Xiamen University, Xiamen 361102, China
| | - Qiang Lin
- CAS Key Laboratory of Tropical Marine Bio-resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou 510301, China.,Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou 511458, China.,University of the Chinese Academy of Sciences, Beijing 100101, China.,Laboratory for Marine Fisheries Science and Food Production Processes, Pilot National Laboratory for Marine Science and Technology (Qingdao), Qingdao 266237, China
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Marisaldi L, Basili D, Gioacchini G, Canapa A, Carnevali O. De novo transcriptome assembly, functional annotation and characterization of the Atlantic bluefin tuna (Thunnus thynnus) larval stage. Mar Genomics 2020; 58:100834. [PMID: 33371994 DOI: 10.1016/j.margen.2020.100834] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2020] [Revised: 12/10/2020] [Accepted: 12/11/2020] [Indexed: 10/22/2022]
Abstract
In the present work, we assembled and characterized a de novo larval transcriptome of the Atlantic bluefin tuna Thunnus thynnus by taking advantage of publicly available databases with the goal of better understanding its larval development. The assembled transcriptome comprised 37,117 protein-coding transcripts, of which 13,633 full-length (>80% coverage), with an Ex90N50 of 3061 bp and 76% of complete and single-copy core vertebrate genes orthologues. Of these transcripts, 34,980 had a hit against the EggNOG database and 14,983 with the KEGG database. Codon usage bias was identified in processes such as translation and muscle development. By comparing our data with a set of representative fish species, 87.1% of tuna transcripts were included in orthogroups with other species and 5.1% in assembly-specific orthogroups, which were enriched in terms related to muscle and bone development, visual system and ion transport. Following this comparative approach, protein families related to myosin, extracellular matrix and immune system resulted significantly expanded in the Atlantic bluefin tuna. Altogether, these results provide a glimpse of how the Atlantic bluefin tuna might have achieved early physical advantages over competing species in the pelagic environment. The information generated lays the foundation for future research on the more detailed exploration of physiological responses at the molecular level in different larval stages and paves the way to evolutionary studies on the Atlantic bluefin tuna.
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Affiliation(s)
- Luca Marisaldi
- Department of Life and Environmental Sciences, Università Politecnica delle Marche, Ancona 60131, Italy
| | - Danilo Basili
- Department of Life and Environmental Sciences, Università Politecnica delle Marche, Ancona 60131, Italy; Centre for Molecular Informatics, Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, UK
| | - Giorgia Gioacchini
- Department of Life and Environmental Sciences, Università Politecnica delle Marche, Ancona 60131, Italy
| | - Adriana Canapa
- Department of Life and Environmental Sciences, Università Politecnica delle Marche, Ancona 60131, Italy
| | - Oliana Carnevali
- Department of Life and Environmental Sciences, Università Politecnica delle Marche, Ancona 60131, Italy.
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Ciezarek A, Gardner L, Savolainen V, Block B. Skeletal muscle and cardiac transcriptomics of a regionally endothermic fish, the Pacific bluefin tuna, Thunnus orientalis. BMC Genomics 2020; 21:642. [PMID: 32942994 PMCID: PMC7499911 DOI: 10.1186/s12864-020-07058-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2019] [Accepted: 09/08/2020] [Indexed: 11/29/2022] Open
Abstract
Background The Pacific bluefin tuna (Thunnus orientalis) is a regionally endothermic fish that maintains temperatures in their swimming musculature, eyes, brain and viscera above that of the ambient water. Within their skeletal muscle, a thermal gradient exists, with deep muscles, close to the backbone, operating at elevated temperatures compared to superficial muscles near the skin. Their heart, by contrast, operates at ambient temperature, which in bluefin tunas can range widely. Cardiac function in tunas reduces in cold waters, yet the heart must continue to supply blood for metabolically demanding endothermic tissues. Physiological studies indicate Pacific bluefin tuna have an elevated cardiac capacity and increased cold-tolerance compared to warm-water tuna species, primarily enabled by increased capacity for sarcoplasmic reticulum calcium cycling within the cardiac muscles. Results Here, we compare tissue-specific gene-expression profiles of different cardiac and skeletal muscle tissues in Pacific bluefin tuna. There was little difference in the overall expression of calcium-cycling and cardiac contraction pathways between atrium and ventricle. However, expression of a key sarcoplasmic reticulum calcium-cycling gene, SERCA2b, which plays a key role maintaining intracellular calcium stores, was higher in atrium than ventricle. Expression of genes involved in aerobic metabolism and cardiac contraction were higher in the ventricle than atrium. The two morphologically distinct tissues that derive the ventricle, spongy and compact myocardium, had near-identical levels of gene expression. More genes had higher expression in the cool, superficial muscle than in the warm, deep muscle in both the aerobic red muscle (slow-twitch) and anaerobic white muscle (fast-twitch), suggesting thermal compensation. Conclusions We find evidence of widespread transcriptomic differences between the Pacific tuna ventricle and atrium, with potentially higher rates of calcium cycling in the atrium associated with the higher expression of SERCA2b compared to the ventricle. We find no evidence that genes associated with thermogenesis are upregulated in the deep, warm muscle compared to superficial, cool muscle. Heat generation may be enabled by by the high aerobic capacity of bluefin tuna red muscle.
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Affiliation(s)
- Adam Ciezarek
- Department of Life Sciences, Silwood Park Campus, Imperial College London, Ascot, UK. .,Earlham Institute, Norwich Research Park, Norwich, UK.
| | - Luke Gardner
- Department of Biology, Hopkins Marine Station, Stanford University, Pacific Grove, CA, USA
| | - Vincent Savolainen
- Department of Life Sciences, Silwood Park Campus, Imperial College London, Ascot, UK
| | - Barbara Block
- Department of Biology, Hopkins Marine Station, Stanford University, Pacific Grove, CA, USA
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Machado AM, Muñoz-Merida A, Fonseca E, Veríssimo A, Pinto R, Felício M, da Fonseca RR, Froufe E, Castro LFC. Liver transcriptome resources of four commercially exploited teleost species. Sci Data 2020; 7:214. [PMID: 32636445 PMCID: PMC7340784 DOI: 10.1038/s41597-020-0565-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2019] [Accepted: 06/09/2020] [Indexed: 01/10/2023] Open
Abstract
The generation of omic resources is central to develop adequate management strategies for species with economic value. Here, we provide high-coverage RNA-seq datasets of liver tissue (containing between 80,2 and 88,4 million of paired-end reads) from four wildtype teleost species with high commercial value: Trachurus trachurus (TTR; Atlantic horse mackerel), Scomber scombrus (SSC; Atlantic mackerel), Trisopterus luscus (TLU; pout), and Micromesistius poutassou (MPO; blue whiting). A comprehensive assembly pipeline, using de novo single and multi-kmer assembly approaches, produced 64 single high-quality liver transcriptomes - 16 per species. The final assemblies, with N50 values ranging from 2,543-3,700 bp and BUSCO (Benchmarking Universal Single-Copy Orthologs) completeness values between 81.8-86.5% of the Actinopterygii gene set, were subjected to open reading frame (ORF) prediction and functional annotation. Our study provides the first transcriptomic resources for these species and offers valuable tools to evaluate both neutral and selected genetic variation among populations, and to identify candidate genes for environmental adaptation assisting in the investigation of the effects of global changes in fisheries.
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Affiliation(s)
- André M Machado
- CIIMAR - Interdisciplinary Centre of Marine and Environmental Research, U. Porto - University of Porto, Porto, Portugal.
| | - Antonio Muñoz-Merida
- CIBIO-InBIO, Research Network in Biodiversity and Evolutionary Biology, Universidade do Porto, Campus Agrário de Vairão, 4485-661, Vairão, Portugal
| | - Elza Fonseca
- CIIMAR - Interdisciplinary Centre of Marine and Environmental Research, U. Porto - University of Porto, Porto, Portugal
- Department of Biology, Faculty of Sciences, U. Porto - University of Porto, Porto, Portugal
| | - Ana Veríssimo
- CIBIO-InBIO, Research Network in Biodiversity and Evolutionary Biology, Universidade do Porto, Campus Agrário de Vairão, 4485-661, Vairão, Portugal
- Department of Biology, Faculty of Sciences, U. Porto - University of Porto, Porto, Portugal
| | - Rui Pinto
- CIIMAR - Interdisciplinary Centre of Marine and Environmental Research, U. Porto - University of Porto, Porto, Portugal
| | - Mónica Felício
- Portuguese Institute for the Sea and Atmosphere, I.P. (IPMA), Lisbon, Portugal
| | - Rute R da Fonseca
- Center for Macroecology, Evolution and Climate, Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark
| | - Elsa Froufe
- CIIMAR - Interdisciplinary Centre of Marine and Environmental Research, U. Porto - University of Porto, Porto, Portugal
| | - L Filipe C Castro
- CIIMAR - Interdisciplinary Centre of Marine and Environmental Research, U. Porto - University of Porto, Porto, Portugal.
- Department of Biology, Faculty of Sciences, U. Porto - University of Porto, Porto, Portugal.
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Bernard AM, Richards VP, Stanhope MJ, Shivji MS. Transcriptome-Derived Microsatellites Demonstrate Strong Genetic Differentiation in Pacific White Sharks. J Hered 2019; 109:771-779. [PMID: 30204894 DOI: 10.1093/jhered/esy045] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2018] [Accepted: 09/08/2018] [Indexed: 01/25/2023] Open
Abstract
Recent advances in genome-scale sequencing technology have allowed the development of high resolution genetic markers for the study of nonmodel taxa. In particular, transcriptome sequencing has proven to be highly useful in generating genomic markers for use in population genetic studies, allowing for insight into species connectivity, as well as local adaptive processes as many transcriptome-derived markers are found within or associated with functional genes. Herein, we developed a set of 30 microsatellite markers from a heart transcriptome for the white shark (Carcharodon carcharias), a widely distributed and globally vulnerable marine predator. Using these markers as well as 10 published anonymous genomic microsatellite loci, we provide 1) the first nuclear genetic assessment of the cross-Pacific connectivity of white sharks, and 2) a comparison of the levels of inferred differentiation across microsatellite marker sets (i.e., transcriptome vs. anonymous) to assess their respective utility to elucidate the population genetic dynamics of white sharks. Significant (FST = 0.083, P = 0.05; G″ST = 0.200; P = 0.001) genetic differentiation was found between Southwestern Pacific (n = 19) and Northeastern Pacific (n = 20) white sharks, indicating restricted, cross Pacific gene flow in this species. Transcriptome-derived microsatellite marker sets identified much higher (up to 2×) levels of genetic differentiation than anonymous genomic markers, underscoring potential utility of transcriptome markers in identifying subtle population genetic differences within highly vagile, globally distributed marine species.Subject areas: Population structure and phylogeography; Conservation genetics and biodiversity.
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Affiliation(s)
- Andrea M Bernard
- Save Our Seas Shark Research Center & Guy Harvey Research Institute, Nova Southeastern University, Halmos College of Natural Sciences and Oceanography, North Ocean Drive, Dania Beach, FL
| | - Vincent P Richards
- Department of Biological Sciences, College of Science, Clemson University, Clemson, SC
| | - Michael J Stanhope
- Department of Population Medicine and Diagnostic Sciences, College of Veterinary Medicine, Cornell University, Ithaca, NY
| | - Mahmood S Shivji
- Save Our Seas Shark Research Center & Guy Harvey Research Institute, Nova Southeastern University, Halmos College of Natural Sciences and Oceanography, North Ocean Drive, Dania Beach, FL
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Larson SE, Daly-Engel TS, Phillips NM. Review of Current Conservation Genetic Analyses of Northeast Pacific Sharks. ADVANCES IN MARINE BIOLOGY 2017; 77:79-110. [PMID: 28882215 DOI: 10.1016/bs.amb.2017.06.005] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Conservation genetics is an applied science that utilizes molecular tools to help solve problems in species conservation and management. It is an interdisciplinary specialty in which scientists apply the study of genetics in conjunction with traditional ecological fieldwork and other techniques to explore molecular variation, population boundaries, and evolutionary relationships with the goal of enabling resource managers to better protect biodiversity and identify unique populations. Several shark species in the northeast Pacific (NEP) have been studied using conservation genetics techniques, which are discussed here. The primary methods employed to study population genetics of sharks have historically been nuclear microsatellites and mitochondrial (mt) DNA. These markers have been used to assess genetic diversity, mating systems, parentage, relatedness, and genetically distinct populations to inform management decisions. Novel approaches in conservation genetics, including next-generation DNA and RNA sequencing, environmental DNA (eDNA), and epigenetics are just beginning to be applied to elasmobranch evolution, physiology, and ecology. Here, we review the methods and results of past studies, explore future directions for shark conservation genetics, and discuss the implications of molecular research and techniques for the long-term management of shark populations in the NEP.
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Affiliation(s)
| | | | - Nicole M Phillips
- The University of Southern Mississippi, Hattiesburg, MS, United States
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