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Crider J, Quiniou SMA, Felch KL, Showmaker K, Bengtén E, Wilson M. A Comprehensive Annotation of the Channel Catfish ( Ictalurus punctatus) T Cell Receptor Alpha/Delta, Beta, and Gamma Loci. Front Immunol 2021; 12:786402. [PMID: 34899754 PMCID: PMC8656973 DOI: 10.3389/fimmu.2021.786402] [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: 09/30/2021] [Accepted: 11/05/2021] [Indexed: 12/28/2022] Open
Abstract
The complete germline repertoires of the channel catfish, Ictalurus punctatus, T cell receptor (TR) loci, TRAD, TRB, and TRG were obtained by analyzing genomic data from PacBio sequencing. The catfish TRB locus spans 214 kb, and contains 112 TRBV genes, a single TRBD gene, 31 TRBJ genes and two TRBC genes. In contrast, the TRAD locus is very large, at 1,285 kb. It consists of four TRDD genes, one TRDJ gene followed by the exons for TRDC, 125 TRAJ genes and the exons encoding the TRAC. Downstream of the TRAC, are 140 TRADV genes, and all of them are in the opposite transcriptional orientation. The catfish TRGC locus spans 151 kb and consists of four diverse V-J-C cassettes. Altogether, this locus contains 15 TRGV genes and 10 TRGJ genes. To place our data into context, we also analyzed the zebrafish TR germline gene repertoires. Overall, our findings demonstrated that catfish possesses a more restricted repertoire compared to the zebrafish. For example, the 140 TRADV genes in catfish form eight subgroups based on members sharing 75% nucleotide identity. However, the 149 TRAD genes in zebrafish form 53 subgroups. This difference in subgroup numbers between catfish and zebrafish is best explained by expansions of catfish TRADV subgroups, which likely occurred through multiple, relatively recent gene duplications. Similarly, 112 catfish TRBV genes form 30 subgroups, while the 51 zebrafish TRBV genes are placed into 36 subgroups. Notably, several catfish and zebrafish TRB subgroups share ancestor nodes. In addition, the complete catfish TR gene annotation was used to compile a TR gene segment database, which was applied in clonotype analysis of an available gynogenetic channel catfish transcriptome. Combined, the TR annotation and clonotype analysis suggested that the expressed TRA, TRB, and TRD repertoires were generated by different mechanisms. The diversity of the TRB repertoire depends on the number of TRBV subgroups and TRBJ genes, while TRA diversity relies on the many different TRAJ genes, which appear to be only minimally trimmed. In contrast, TRD diversity relies on nucleotide additions and the utilization of up to four TRDD segments.
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Affiliation(s)
- Jonathan Crider
- Department of Microbiology and Immunology, University of Mississippi Medical Center, Jackson, MS, United States
| | - Sylvie M A Quiniou
- Warmwater Aquaculture Research Unit, United States Department of Agriculture - Agricultural Research Service (USDA-ARS), Stoneville, MS, United States
| | - Kristianna L Felch
- Department of Microbiology and Immunology, University of Mississippi Medical Center, Jackson, MS, United States
| | - Kurt Showmaker
- Department of Pharmacology and Toxicology, University of Mississippi Medical Center, Jackson, MS, United States.,Department of Data Science, John D. Bower School of Population Health, University of Mississippi Medical Center, Jackson, MS, United States
| | - Eva Bengtén
- Department of Microbiology and Immunology, University of Mississippi Medical Center, Jackson, MS, United States
| | - Melanie Wilson
- Department of Microbiology and Immunology, University of Mississippi Medical Center, Jackson, MS, United States
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Edholm ES, Fenton CG, Mondot S, Paulssen RH, Lefranc MP, Boudinot P, Magadan S. Profiling the T Cell Receptor Alpha/Delta Locus in Salmonids. Front Immunol 2021; 12:753960. [PMID: 34733285 PMCID: PMC8559430 DOI: 10.3389/fimmu.2021.753960] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2021] [Accepted: 09/28/2021] [Indexed: 12/17/2022] Open
Abstract
In jawed vertebrates, two major T cell populations have been characterized. They are defined as α/β or γ/δ T cells, based on the expressed T cell receptor. Salmonids (family Salmonidae) include two key teleost species for aquaculture, rainbow trout (Oncorhynchus mykiss) and Atlantic salmon (Salmo salar) which constitute important models for fish immunology and important targets for vaccine development. The growing interest to decipher the dynamics of adaptive immune responses against pathogens or vaccines has resulted in recent efforts to sequence the immunoglobulin (IG) or antibodies and T cell receptor (TR) repertoire in these species. In this context, establishing a comprehensive and coherent locus annotation is the fundamental basis for the analysis of high-throughput repertoire sequencing data. We therefore decided to revisit the description and annotation of TRA/TRD locus in Atlantic salmon and two strains of rainbow trout (Swanson and Arlee) using the now available high-quality genome assemblies. Phylogenetic analysis of functional TRA/TRD V genes from these three genomes led to the definition of 25 subgroups shared by both species, some with particular feature. A total of 128 TRAJ genes were identified in Salmo, the majority with a close counterpart in Oncorhynchus. Analysis of expressed TRA repertoire indicates that most TRAV gene subgroups are expressed at mucosal and systemic level. The present work on TRA/TRD locus annotation along with the analysis of TRA repertoire sequencing data show the feasibility and advantages of a common salmonid TRA/TRD nomenclature that allows an accurate annotation and analysis of high-throughput sequencing results, across salmonid T cell subsets.
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Affiliation(s)
- Eva-Stina Edholm
- Faculty of Biosciences, Fisheries & Economics, Norwegian College of Fishery Science, University of Tromsø-The Arctic University of Norway, Tromsø, Norway
| | - Christopher Graham Fenton
- Clinical Bioinformatics Research Group, Genomics Support Centre Tromsø (GSCT), Department of Clinical Medicine, Faculty of Health Sciences, University of Tromsø - The Arctic University of Norway, Tromsø, Norway
| | - Stanislas Mondot
- Université Paris-Saclay, INRAE, AgroParisTech, Micalis Institute, Jouy-en-Josas, France.,GABI, INRA, AgroParisTech, Université Paris-Saclay, Jouy-en-Josas, France
| | - Ruth H Paulssen
- Clinical Bioinformatics Research Group, Genomics Support Centre Tromsø (GSCT), Department of Clinical Medicine, Faculty of Health Sciences, University of Tromsø - The Arctic University of Norway, Tromsø, Norway
| | - Marie-Paule Lefranc
- IMGT®, The International ImMunoGeneTics Information System (IMGT), Laboratoire d´ImmunoGénétique Moléculaire (LIGM), Institut de Génétique Humaine (IGH), CNRS, University of Montpellier, Montpellier Cedex, France
| | - Pierre Boudinot
- Université Paris Saclay, INRAE, UVSQ, Virologie et Immunologie Moléculaires, Jouy-en-Josas, France
| | - Susana Magadan
- Immunology Laboratory, Biomedical Research Center (CINBIO), University of Vigo, Vigo, Spain.,Galicia Sur Health Research Institute (IIS-GS), Hospital Alvaro Cunqueiro, Vigo, Spain
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Miccoli A, Guerra L, Pianese V, Saraceni PR, Buonocore F, Taddei AR, Couto A, De Wolf T, Fausto AM, Scapigliati G, Picchietti S. Molecular, Cellular and Functional Analysis of TRγ Chain along the European Sea Bass Dicentrarchus labrax Development. Int J Mol Sci 2021; 22:ijms22073376. [PMID: 33806063 PMCID: PMC8036326 DOI: 10.3390/ijms22073376] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2021] [Revised: 03/22/2021] [Accepted: 03/23/2021] [Indexed: 11/16/2022] Open
Abstract
In jawed vertebrates, adaptive immune responses are enabled by T cells. Two lineages were characterized based on their T cell receptor (TcR) heterodimers, namely αβ or γδ peptide chains, which display an Ig domain-type sequence that is somatically rearranged. γδ T cells have been less extensively characterized than αβ and teleost fish, in particular, suffer from a severe scarcity of data. In this paper, we worked on the well-known model, the European sea bass Dicentrarchus labrax, to broaden the understanding of teleost γδ-T cells. The T cell receptor chain (TR) γ transcript was expressed at a later developmental stage than TRβ, suggesting a layered appearance of fish immune cells, and the thymus displayed statistically-significant higher mRNA levels than any other organ or lymphoid tissue investigated. The polyclonal antibody developed against the TRγ allowed the localization of TRγ-expressing cells in lymphoid organs along the ontogeny. Cell positivity was investigated through flow cytometry and the highest percentage was found in peripheral blood leukocytes, followed by thymus, gut, gills, spleen and head kidney. Numerous TRγ-expressing cells were localized in the gut mucosa, and the immunogold labelling revealed ultrastructural features that are typical of T cells. At last, microalgae-based diet formulations significantly modulated the abundance of TRγ+ cells in the posterior intestine, hinting at a putative involvement in nutritional immunity. From a comparative immunological perspective, our results contribute to the comprehension of the diversity and functionalities of γδ T cells during the development of a commercially relevant marine teleost model.
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Affiliation(s)
- Andrea Miccoli
- Department for Innovation in Biological, Agro-Food and Forest Systems, University of Tuscia, Largo dell’Università, 01100 Viterbo, Italy; (A.M.); (L.G.); (V.P.); (P.R.S.); (F.B.); (A.M.F.); (G.S.)
| | - Laura Guerra
- Department for Innovation in Biological, Agro-Food and Forest Systems, University of Tuscia, Largo dell’Università, 01100 Viterbo, Italy; (A.M.); (L.G.); (V.P.); (P.R.S.); (F.B.); (A.M.F.); (G.S.)
| | - Valeria Pianese
- Department for Innovation in Biological, Agro-Food and Forest Systems, University of Tuscia, Largo dell’Università, 01100 Viterbo, Italy; (A.M.); (L.G.); (V.P.); (P.R.S.); (F.B.); (A.M.F.); (G.S.)
| | - Paolo Roberto Saraceni
- Department for Innovation in Biological, Agro-Food and Forest Systems, University of Tuscia, Largo dell’Università, 01100 Viterbo, Italy; (A.M.); (L.G.); (V.P.); (P.R.S.); (F.B.); (A.M.F.); (G.S.)
| | - Francesco Buonocore
- Department for Innovation in Biological, Agro-Food and Forest Systems, University of Tuscia, Largo dell’Università, 01100 Viterbo, Italy; (A.M.); (L.G.); (V.P.); (P.R.S.); (F.B.); (A.M.F.); (G.S.)
| | - Anna Rita Taddei
- Section of Electron Microscopy, Great Equipment Center, University of Tuscia, 01100 Viterbo, Italy;
| | - Ana Couto
- Interdisciplinary Centre of Marine and Environmental Research (CIIMAR), University of Porto, Av. General Norton de Matos, 4450-208 Matosinhos, Portugal;
| | - Tania De Wolf
- INVE Aquaculture Research Center, 57016 Rosignano Solvay, Italy;
| | - Anna Maria Fausto
- Department for Innovation in Biological, Agro-Food and Forest Systems, University of Tuscia, Largo dell’Università, 01100 Viterbo, Italy; (A.M.); (L.G.); (V.P.); (P.R.S.); (F.B.); (A.M.F.); (G.S.)
| | - Giuseppe Scapigliati
- Department for Innovation in Biological, Agro-Food and Forest Systems, University of Tuscia, Largo dell’Università, 01100 Viterbo, Italy; (A.M.); (L.G.); (V.P.); (P.R.S.); (F.B.); (A.M.F.); (G.S.)
| | - Simona Picchietti
- Department for Innovation in Biological, Agro-Food and Forest Systems, University of Tuscia, Largo dell’Università, 01100 Viterbo, Italy; (A.M.); (L.G.); (V.P.); (P.R.S.); (F.B.); (A.M.F.); (G.S.)
- Correspondence: ; Tel.: +39-0761-357-135
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Yamaguchi T, Takizawa F, Furihata M, Soto-Lampe V, Dijkstra JM, Fischer U. Teleost cytotoxic T cells. FISH & SHELLFISH IMMUNOLOGY 2019; 95:422-439. [PMID: 31669897 DOI: 10.1016/j.fsi.2019.10.041] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/19/2019] [Revised: 10/21/2019] [Accepted: 10/22/2019] [Indexed: 06/10/2023]
Abstract
Cell-mediated cytotoxicity is one of the major mechanisms by which vertebrates control intracellular pathogens. Two cell types are the main players in this immune response, natural killer (NK) cells and cytotoxic T lymphocytes (CTL). While NK cells recognize altered target cells in a relatively unspecific manner CTLs use their T cell receptor to identify pathogen-specific peptides that are presented by major histocompatibility (MHC) class I molecules on the surface of infected cells. However, several other signals are needed to regulate cell-mediated cytotoxicity involving a complex network of cytokine- and ligand-receptor interactions. Since the first description of MHC class I molecules in teleosts during the early 90s of the last century a remarkable amount of information on teleost immune responses has been published. The corresponding studies describe teleost cells and molecules that are involved in CTL responses of higher vertebrates. These studies are backed by functional investigations on the killing activity of CTLs in a few teleost species. The present knowledge on teleost CTLs still leaves considerable room for further investigations on the mechanisms by which CTLs act. Nevertheless the information on teleost CTLs and their regulation might already be useful for the control of fish diseases by designing efficient vaccines against such diseases where CTL responses are known to be decisive for the elimination of the corresponding pathogen. This review summarizes the present knowledge on CTL regulation and functions in teleosts. In a special chapter, the role of CTLs in vaccination is discussed.
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Affiliation(s)
- Takuya Yamaguchi
- Federal Research Institute for Animal Health, Friedrich-Loeffler-Institut, 17493, Greifswald-Insel Riems, Germany
| | - Fumio Takizawa
- Laboratory of Marine Biotechnology, Faculty of Marine Science and Technology, Fukui Prefectural University, Obama, Fukui, 917-0003, Japan
| | - Mitsuru Furihata
- Nagano Prefectural Fisheries Experimental Station, 2871 Akashina-nakagawate, Azumino-shi, Nagano-ken, 399-7102, Japan
| | - Veronica Soto-Lampe
- Federal Research Institute for Animal Health, Friedrich-Loeffler-Institut, 17493, Greifswald-Insel Riems, Germany
| | - Johannes M Dijkstra
- Institute for Comprehensive Medical Science, Fujita Health University, Toyoake, Aichi, 470-1192, Japan
| | - Uwe Fischer
- Federal Research Institute for Animal Health, Friedrich-Loeffler-Institut, 17493, Greifswald-Insel Riems, Germany.
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Taylor EB, Chinchar VG, Quiniou SMA, Wilson M, Bengtén E. Cloning and characterization of antiviral cytotoxic T lymphocytes in channel catfish, Ictalurus punctatus. Virology 2019; 540:184-194. [PMID: 31929000 DOI: 10.1016/j.virol.2019.11.014] [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: 08/15/2019] [Revised: 11/10/2019] [Accepted: 11/25/2019] [Indexed: 01/05/2023]
Abstract
To determine the role of piscine anti-viral cytotoxic cells, we analyzed the response of channel catfish to Ictalurid herpesvirus 1, commonly designated channel catfish virus (CCV). Peripheral blood leukocytes (PBL) from catfish immunized with MHC-matched, CCV-infected G14D cells (G14D-CCV) showed marked lysis of G14D-CCV but little to no lysis of uninfected allogenic (3B11) or syngeneic (G14D) cells. Expansion of effectors by in vitro culture in the presence of irradiated G14D-CCV cells generated cultures with enhanced cytotoxicity and often broader target range. Cytotoxic effectors expressed rearranged TCR genes, perforin, granzyme, and IFN-γ. Four clonal cytotoxic lines were developed and unique TCR gene rearrangements including γδ were detected. Furthermore, catfish CTL clones were either CD4+/CD8- or CD4-/CD8-. Two CTL lines showed markedly enhanced killing of G14D-CCV targets, while the other two lines displayed a broader target range. Collectively, catfish virus-specific CTL display unique features that illustrate the diversity of the ectothermic vertebrate immune response.
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Affiliation(s)
- Erin B Taylor
- Department of Microbiology and Immunology, University of Mississippi Medical Center, Jackson, MS, 39216, USA
| | - V Gregory Chinchar
- Department of Microbiology and Immunology, University of Mississippi Medical Center, Jackson, MS, 39216, USA
| | - Sylvie M A Quiniou
- Warmwater Aquaculture Research Unit, U.S. Department of Agriculture, Agricultural Research Service, Stoneville, MS, 38776, USA
| | - Melanie Wilson
- Department of Microbiology and Immunology, University of Mississippi Medical Center, Jackson, MS, 39216, USA
| | - Eva Bengtén
- Department of Microbiology and Immunology, University of Mississippi Medical Center, Jackson, MS, 39216, USA.
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Tafalla C, Leal E, Yamaguchi T, Fischer U. T cell immunity in the teleost digestive tract. DEVELOPMENTAL AND COMPARATIVE IMMUNOLOGY 2016; 64:167-177. [PMID: 26905634 DOI: 10.1016/j.dci.2016.02.019] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/01/2015] [Revised: 02/10/2016] [Accepted: 02/16/2016] [Indexed: 06/05/2023]
Abstract
Fish (along with cyclostomes) constitute the most ancient animal group in which an acquired immune system is present. As in higher vertebrates, both B and T lymphocytes cooperate in implementing an adequate response. Although there is still a debate on whether fish possess a true gut associated lymphoid tissue (GALT), the presence of diffuse B and T lymphocytes throughout all mucosal surfaces has been demonstrated in a wide variety of fish species. The lack of antibodies against T lymphocyte markers has hampered the performance of functional assays in both systemic and mucosal compartments. However, most components associated with T lymphocyte function have been identified in fish through extensive genomic research, suggesting similar functionalities for fish and mammalian T lymphocytes. Thus, the aim of this review is to briefly summarize what is known in teleost concerning the characteristics and functionalities of the different T cell subsets, to then focus on what is known to date regarding their presence and role in the gastrointestinal tract, through either direct functional assays or indirectly by conclusions drawn from transcriptomic analysis.
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Affiliation(s)
- Carolina Tafalla
- Centro de Investigación en Sanidad Animal (CISA-INIA), Valdeolmos, Madrid, Spain.
| | - Esther Leal
- Centro de Investigación en Sanidad Animal (CISA-INIA), Valdeolmos, Madrid, Spain
| | - Takuya Yamaguchi
- Friedrich-Loeffler-Institut, Federal Research Institute for Animal Health, Greifswald-Insel Riems, Germany
| | - Uwe Fischer
- Friedrich-Loeffler-Institut, Federal Research Institute for Animal Health, Greifswald-Insel Riems, Germany
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Genomic organization of the zebrafish (Danio rerio) T cell receptor alpha/delta locus and analysis of expressed products. Immunogenetics 2016; 68:365-79. [PMID: 26809968 DOI: 10.1007/s00251-016-0904-3] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2015] [Accepted: 01/18/2016] [Indexed: 12/27/2022]
Abstract
In testing the hypothesis that all jawed vertebrate classes employ immunoglobulin heavy chain V (IgHV) gene segments in their T cell receptor (TCR)δ encoding loci, we found that some basic characterization was required of zebrafish TCRδ. We began by annotating and characterizing the TCRα/δ locus of Danio rerio based on the most recent genome assembly, GRCz10. We identified a total of 141 theoretically functional V segments which we grouped into 41 families based upon 70 % nucleotide identity. This number represents the second greatest count of apparently functional V genes thus far described in an antigen receptor locus with the exception of cattle TCRα/δ. Cloning, relative quantitative PCR, and deep sequencing results corroborate that zebrafish do express TCRδ, but these data suggest only at extremely low levels and in limited diversity in the spleens of the adult fish. While we found no evidence for IgH-TCRδ rearrangements in this fish, by determining the locus organization we were able to suggest how the evolution of the teleost α/δ locus could have lost IgHVs that exist in sharks and frogs. We also found evidence of surprisingly low TCRδ expression and repertoire diversity in this species.
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Peatman E, Lange M, Zhao H, Beck BH. Physiology and immunology of mucosal barriers in catfish (Ictalurus spp.). Tissue Barriers 2015; 3:e1068907. [PMID: 26716071 DOI: 10.1080/21688370.2015.1068907] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2015] [Revised: 06/23/2015] [Accepted: 06/27/2015] [Indexed: 10/23/2022] Open
Abstract
The mucosal barriers of catfish (Ictalurus spp) constitute the first line of defense against pathogen invasion while simultaneously carrying out a diverse array of other critical physiological processes, including nutrient adsorption, osmoregulation, waste excretion, and environmental sensing. Catfish depend more heavily on mucosal barriers than their terrestrial counterparts as they are continuously interacting with the aquatic microbiota. Our understanding of these barriers, while growing, is still limited relative to that of mammalian model systems. Nevertheless, a combination of molecular and cellular studies in catfish over the last few decades, and particularly within the last few years, has helped to elucidate many of the primary actors and pathways critical to their mucosal health. Here we describe aspects of innate and adaptive immune responses in the primary mucosal tissues (skin, gill, and intestine) of catfish, focusing on mucus-driven responses, pathogen recognition, soluble mediators, and immunoglobulin and T-cell derived immunity. Modulation of mucosal barriers will be critical moving forward for crafting better diets, improving vaccine delivery, enhancing water quality, and ensuring sustainable production practices in catfish.
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Affiliation(s)
- Eric Peatman
- School of Fisheries, Aquaculture, and Aquatic Sciences; Auburn University ; Auburn, AL USA
| | - Miles Lange
- United States Department of Agriculture; Agricultural Research Service; Stuttgart National Aquaculture Research Center ; Stuttgart, AR USA
| | - Honggang Zhao
- School of Fisheries, Aquaculture, and Aquatic Sciences; Auburn University ; Auburn, AL USA
| | - Benjamin H Beck
- United States Department of Agriculture; Agricultural Research Service; Stuttgart National Aquaculture Research Center ; Stuttgart, AR USA
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