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Picchietti S, Buonocore F, Guerra L, Belardinelli MC, De Wolf T, Couto A, Fausto AM, Saraceni PR, Miccoli A, Scapigliati G. Molecular and cellular characterization of European sea bass CD3ε + T lymphocytes and their modulation by microalgal feed supplementation. Cell Tissue Res 2021; 384:149-165. [PMID: 33433686 DOI: 10.1007/s00441-020-03347-x] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2020] [Accepted: 11/10/2020] [Indexed: 11/26/2022]
Abstract
The CD3 coreceptor is a master T cell surface marker, and genes encoding CD3ζ, γδ, and ε chains have been reported in several teleost fish. Here, a complete cDNA sequence of CD3ɛ chain was identified from a sea bass (Dicentrarchus labrax L.) gill transcriptome. Its basal expression was quantified in both lymphoid and non-lymphoid organs of sea bass juveniles with real-time qPCR analysis. After either in vitro stimulation of head kidney leukocytes with the T-cell mitogen phytohaemagglutinin or in vivo stimulation with an orally administered Vibrio anguillarum vaccine, CD3ε expression levels increased in head kidney leukocytes, confirming that CD3ε T cells may play important roles in fish systemic protection against pathogens. Further, three peptides were designed on the CD3ɛ cytoplasmic tail region and employed as immunogens for antibody production in rabbit. One antiserum so obtained, named RACD3/1, immunostained a band of the expected size in a western blot of a sea bass thymocyte lysate. The distribution of CD3ε+ lymphocyte population in the lymphoid organs and mucosal tissues was addressed in healthy fish by IHC. In decreasing percentage order, CD3ε+ lymphocytes were detected by flow cytometry in thymus, peripheral blood leukocytes, gills, head kidney, gut, and spleen. Finally, a significant in vivo enhancement of CD3ε+ T intestinal lymphocytes was found in fish fed on diets in which 100% fish meal was replaced by the microalgae Nannochloropsis sp. biomass. These results indicate that CD3ε+ T cells are involved in nutritional immune responses.
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Affiliation(s)
- Simona Picchietti
- Department for Innovation in Biological, Agro-Food and Forest Systems (DIBAF), University of Tuscia, Viterbo, Italy.
| | - Francesco Buonocore
- Department for Innovation in Biological, Agro-Food and Forest Systems (DIBAF), University of Tuscia, Viterbo, Italy
| | - Laura Guerra
- Department for Innovation in Biological, Agro-Food and Forest Systems (DIBAF), University of Tuscia, Viterbo, Italy
| | - Maria Cristina Belardinelli
- Department for Innovation in Biological, Agro-Food and Forest Systems (DIBAF), University of Tuscia, Viterbo, Italy
| | - Tania De Wolf
- INVE Aquaculture Research Center, Dendermond, Belgium
| | - Ana Couto
- Interdisciplinary Centre of Marine and Environmental Research (CIIMAR), University of Porto, Porto, Portugal
| | - Anna Maria Fausto
- Department for Innovation in Biological, Agro-Food and Forest Systems (DIBAF), University of Tuscia, Viterbo, Italy
| | - Paolo Roberto Saraceni
- Department for Innovation in Biological, Agro-Food and Forest Systems (DIBAF), University of Tuscia, Viterbo, Italy
| | - Andrea Miccoli
- Department for Innovation in Biological, Agro-Food and Forest Systems (DIBAF), University of Tuscia, Viterbo, Italy
| | - Giuseppe Scapigliati
- Department for Innovation in Biological, Agro-Food and Forest Systems (DIBAF), University of Tuscia, Viterbo, Italy
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2
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Buonocore F, Gerdol M, Pallavicini A, Stocchi V, Randelli E, Belardinelli MC, Miccoli A, Saraceni PR, Secombes CJ, Scapigliati G, Wang T. Identification, molecular characterization and functional analysis of interleukin (IL)-2 and IL-2like (IL-2L) cytokines in sea bass (Dicentrarchus labrax L.). Cytokine 2019; 126:154898. [PMID: 31706201 DOI: 10.1016/j.cyto.2019.154898] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2019] [Revised: 10/17/2019] [Accepted: 10/22/2019] [Indexed: 01/18/2023]
Abstract
In mammals, interleukin (IL)-2, initially known as a T-cell grow factor, is an immunomodulatory cytokine involved in the proliferation of T cells upon antigen activation. In bony fish, some IL-2 orthologs have been identified, but, recently, an additional IL-2like (IL-2L) gene has been found. In this paper, we report the presence of these two divergent IL-2 isoforms in sea bass (Dicentrarchus labrax L.). Genomic analyses revealed that they originated from a gene duplication event, as happened in most percomorphs. These two IL-2 paralogs show differences in the amino acid sequence and in the exon 4 size, and these features could be an indication that they bind preferentially to different specific IL-2 receptors. Sea bass IL-2 paralogs are highly expressed in gut and spleen, which are tissues and organs involved in fish T cell immune functions, and the two cytokines could be up-regulated by both PHA stimulation and vaccination with a bacterial vaccine, with IL-2L being more inducible. To investigate the functional activities of sea bass IL-2 and IL-2L we produced the corresponding recombinant molecules in E. coli and used them to in vitro stimulate HK and spleen leukocytes. IL-2L is able to up-regulate the expression of markers related to different T cell subsets (Th1, Th2 and Th17) and to Treg cells in HK, whereas it has little effect in spleen. IL-2 is not active on these markers in HK, but shows an effect on Th1 markers in spleen. Finally, the stimulation with recombinant IL-2 and IL-2L is also able to induce in vitro proliferation of HK- and spleen-derived leukocytes. In conclusion, we have demonstrated that sea bass possess two IL-2 paralogs that likely have an important role in regulating T cell development in this species and that show distinct bioactivities.
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Affiliation(s)
- Francesco Buonocore
- Department for Innovation in Biological, Agro-food and Forest Systems, University of Tuscia, Largo dell'Università snc, 05100 Viterbo, VT, Italy.
| | - Marco Gerdol
- Department of Life Sciences, University of Trieste, Via Giorgieri 5, 34127 Trieste, TS, Italy
| | - Alberto Pallavicini
- Department of Life Sciences, University of Trieste, Via Giorgieri 5, 34127 Trieste, TS, Italy
| | - Valentina Stocchi
- Department for Innovation in Biological, Agro-food and Forest Systems, University of Tuscia, Largo dell'Università snc, 05100 Viterbo, VT, Italy
| | - Elisa Randelli
- Department for Innovation in Biological, Agro-food and Forest Systems, University of Tuscia, Largo dell'Università snc, 05100 Viterbo, VT, Italy
| | - Maria Cristina Belardinelli
- Department for Innovation in Biological, Agro-food and Forest Systems, University of Tuscia, Largo dell'Università snc, 05100 Viterbo, VT, Italy
| | - Andrea Miccoli
- Department for Innovation in Biological, Agro-food and Forest Systems, University of Tuscia, Largo dell'Università snc, 05100 Viterbo, VT, Italy
| | - Paolo Roberto Saraceni
- Department for Innovation in Biological, Agro-food and Forest Systems, University of Tuscia, Largo dell'Università snc, 05100 Viterbo, VT, Italy
| | - Christopher J Secombes
- Scottish Fish Immunology Research Centre, School of Biological Sciences, University of Aberdeen, Aberdeen AB24 2TZ, UK
| | - Giuseppe Scapigliati
- Department for Innovation in Biological, Agro-food and Forest Systems, University of Tuscia, Largo dell'Università snc, 05100 Viterbo, VT, Italy
| | - Tiehui Wang
- Scottish Fish Immunology Research Centre, School of Biological Sciences, University of Aberdeen, Aberdeen AB24 2TZ, UK
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Shen X, Ngoh SY, Thevasagayam NM, Prakki SRS, Bhandare P, Tan AWK, Tan GQ, Singh S, Phua NCH, Vij S, Orbán L. BAC-pool sequencing and analysis confirms growth-associated QTLs in the Asian seabass genome. Sci Rep 2016; 6:36647. [PMID: 27821852 PMCID: PMC5099610 DOI: 10.1038/srep36647] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2015] [Accepted: 10/19/2016] [Indexed: 12/31/2022] Open
Abstract
The Asian seabass is an important marine food fish that has been cultured for several decades in Asia Pacific. However, the lack of a high quality reference genome has hampered efforts to improve its selective breeding. A 3D BAC pool set generated in this study was screened using 22 SSR markers located on linkage group 2 which contains a growth-related QTL region. Seventy-two clones corresponding to 22 FPC contigs were sequenced by Illumina MiSeq technology. We co-assembled the MiSeq-derived scaffolds from each FPC contig with error-corrected PacBio reads, resulting in 187 sequences covering 9.7 Mb. Eleven genes annotated within this region were found to be potentially associated with growth and their tissue-specific expression was investigated. Correlation analysis demonstrated that SNPs in ctsb, skp1 and ppp2ca can be potentially used as markers for selecting fast-growing fingerlings. Conserved syntenies between seabass LG2 and five other teleosts were identified. This study i) provided a 10 Mb targeted genome assembly; ii) demonstrated NGS of BAC pools as a potential approach for mining candidates underlying QTLs of this species; iii) detected eleven genes potentially responsible for growth in the QTL region; and iv) identified useful SNP markers for selective breeding programs of Asian seabass.
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Affiliation(s)
- Xueyan Shen
- Reproductive Genomics Group, Temasek Life Sciences Laboratory, 117604 Singapore
| | - Si Yan Ngoh
- Reproductive Genomics Group, Temasek Life Sciences Laboratory, 117604 Singapore.,Nanyang Technological University, 639798 Singapore
| | | | | | - Pranjali Bhandare
- Reproductive Genomics Group, Temasek Life Sciences Laboratory, 117604 Singapore
| | - Andy Wee Kiat Tan
- Reproductive Genomics Group, Temasek Life Sciences Laboratory, 117604 Singapore
| | - Gui Quan Tan
- Reproductive Genomics Group, Temasek Life Sciences Laboratory, 117604 Singapore
| | | | | | - Shubha Vij
- Reproductive Genomics Group, Temasek Life Sciences Laboratory, 117604 Singapore
| | - László Orbán
- Reproductive Genomics Group, Temasek Life Sciences Laboratory, 117604 Singapore.,Department of Animal Sciences and Animal Husbandry, Georgikon Faculty, University of Pannonia, 8360 Keszthely, Hungary.,Centre for Comparative Genomics, Murdoch University, Murdoch 6150, Australia
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Bertolini F, Geraci C, Schiavo G, Sardina MT, Chiofalo V, Fontanesi L. Whole genome semiconductor based sequencing of farmed European sea bass (Dicentrarchus labrax) Mediterranean genetic stocks using a DNA pooling approach. Mar Genomics 2016; 28:63-70. [DOI: 10.1016/j.margen.2016.03.007] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2016] [Revised: 03/14/2016] [Accepted: 03/14/2016] [Indexed: 12/30/2022]
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Tine M, Kuhl H, Gagnaire PA, Louro B, Desmarais E, Martins RST, Hecht J, Knaust F, Belkhir K, Klages S, Dieterich R, Stueber K, Piferrer F, Guinand B, Bierne N, Volckaert FAM, Bargelloni L, Power DM, Bonhomme F, Canario AVM, Reinhardt R. European sea bass genome and its variation provide insights into adaptation to euryhalinity and speciation. Nat Commun 2014; 5:5770. [PMID: 25534655 PMCID: PMC4284805 DOI: 10.1038/ncomms6770] [Citation(s) in RCA: 268] [Impact Index Per Article: 26.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2014] [Accepted: 11/05/2014] [Indexed: 01/30/2023] Open
Abstract
The European sea bass (Dicentrarchus labrax) is a temperate-zone euryhaline teleost of prime importance for aquaculture and fisheries. This species is subdivided into two naturally hybridizing lineages, one inhabiting the north-eastern Atlantic Ocean and the other the Mediterranean and Black seas. Here we provide a high-quality chromosome-scale assembly of its genome that shows a high degree of synteny with the more highly derived teleosts. We find expansions of gene families specifically associated with ion and water regulation, highlighting adaptation to variation in salinity. We further generate a genome-wide variation map through RAD-sequencing of Atlantic and Mediterranean populations. We show that variation in local recombination rates strongly influences the genomic landscape of diversity within and differentiation between lineages. Comparing predictions of alternative demographic models to the joint allele-frequency spectrum indicates that genomic islands of differentiation between sea bass lineages were generated by varying rates of introgression across the genome following a period of geographical isolation. The European sea bass is an economically important fish species, which is subject to intense selective breeding. Here, the authors sequence the genome of the European sea bass and highlight gene family expansions underlying adaptation to salinity change, as well as the genomic architecture of speciation between two divergent sea bass lineages.
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Affiliation(s)
- Mbaye Tine
- 1] Max Planck Genome-centre Cologne, Carl-von-Linné-Weg 10, D-50829 Köln, Germany [2] Max Planck Institute for Molecular Genetics, Ihnestrasse 63, D-14195 Berlin, Germany [3]
| | - Heiner Kuhl
- 1] Max Planck Institute for Molecular Genetics, Ihnestrasse 63, D-14195 Berlin, Germany [2]
| | - Pierre-Alexandre Gagnaire
- 1] Institut des Sciences de l'Evolution (UMR 5554), CNRS-UM2-IRD, Place Eugène Bataillon, F-34095 Montpellier, France [2] Station Méditerranéenne de l'Environnement Littoral, Université Montpellier 2, 2 Rue des Chantiers, F-34200 Sète, France [3]
| | - Bruno Louro
- CCMAR-Centre of Marine Sciences, University of Algarve, Building 7, Campus de Gambelas, 8005-139 Faro, Portugal
| | - Erick Desmarais
- Institut des Sciences de l'Evolution (UMR 5554), CNRS-UM2-IRD, Place Eugène Bataillon, F-34095 Montpellier, France
| | - Rute S T Martins
- CCMAR-Centre of Marine Sciences, University of Algarve, Building 7, Campus de Gambelas, 8005-139 Faro, Portugal
| | - Jochen Hecht
- 1] Max Planck Institute for Molecular Genetics, Ihnestrasse 63, D-14195 Berlin, Germany [2] BCRT, Charité-Universitätsmedizin Berlin, Augustenburger Platz 1, D-13353 Berlin, Germany
| | - Florian Knaust
- Max Planck Institute for Molecular Genetics, Ihnestrasse 63, D-14195 Berlin, Germany
| | - Khalid Belkhir
- Institut des Sciences de l'Evolution (UMR 5554), CNRS-UM2-IRD, Place Eugène Bataillon, F-34095 Montpellier, France
| | - Sven Klages
- Max Planck Institute for Molecular Genetics, Ihnestrasse 63, D-14195 Berlin, Germany
| | - Roland Dieterich
- Max Planck Genome-centre Cologne, Carl-von-Linné-Weg 10, D-50829 Köln, Germany
| | - Kurt Stueber
- Max Planck Genome-centre Cologne, Carl-von-Linné-Weg 10, D-50829 Köln, Germany
| | - Francesc Piferrer
- Institut de Ciències del Mar, Consejo Superior de Investigaciones Científicas (CSIC), Passeig Marítim, 37-49, 08003 Barcelona, Spain
| | - Bruno Guinand
- Institut des Sciences de l'Evolution (UMR 5554), CNRS-UM2-IRD, Place Eugène Bataillon, F-34095 Montpellier, France
| | - Nicolas Bierne
- 1] Institut des Sciences de l'Evolution (UMR 5554), CNRS-UM2-IRD, Place Eugène Bataillon, F-34095 Montpellier, France [2] Station Méditerranéenne de l'Environnement Littoral, Université Montpellier 2, 2 Rue des Chantiers, F-34200 Sète, France
| | - Filip A M Volckaert
- Laboratory of Biodiversity and Evolutionary Genomics, University of Leuven, Charles Deberiotstraat 32, B-3000 Leuven, Belgium
| | - Luca Bargelloni
- Dipartimento di Biomedicina Comparata e Alimentazione, Università di Padova, I-35124 Padova, Italy
| | - Deborah M Power
- CCMAR-Centre of Marine Sciences, University of Algarve, Building 7, Campus de Gambelas, 8005-139 Faro, Portugal
| | - François Bonhomme
- 1] Institut des Sciences de l'Evolution (UMR 5554), CNRS-UM2-IRD, Place Eugène Bataillon, F-34095 Montpellier, France [2] Station Méditerranéenne de l'Environnement Littoral, Université Montpellier 2, 2 Rue des Chantiers, F-34200 Sète, France
| | - Adelino V M Canario
- CCMAR-Centre of Marine Sciences, University of Algarve, Building 7, Campus de Gambelas, 8005-139 Faro, Portugal
| | - Richard Reinhardt
- 1] Max Planck Genome-centre Cologne, Carl-von-Linné-Weg 10, D-50829 Köln, Germany [2] Max Planck Institute for Molecular Genetics, Ihnestrasse 63, D-14195 Berlin, Germany
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6
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Advances in European sea bass genomics and future perspectives. Mar Genomics 2014; 18 Pt A:71-5. [PMID: 25011579 DOI: 10.1016/j.margen.2014.06.010] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2014] [Revised: 06/24/2014] [Accepted: 06/27/2014] [Indexed: 12/18/2022]
Abstract
Only recently available sequenced and annotated teleost fish genomes were restricted to a few model species, none of which were for aquaculture. The application of marker assisted selection for improved production traits had been largely restricted to the salmon industry and genetic and Quantitative Trait Loci (QTL) maps were available for only a few species. With the advent of next generation sequencing the landscape is rapidly changing and today the genomes of several aquaculture species have been sequenced. The European sea bass, Dicentrarchus labrax, is a good example of a commercially important aquaculture species in Europe for which in the last decade a wealth of genomic resources, including a chromosomal scale genome assembly, physical and linkage maps as well as relevant QTL have been generated. The current challenge is to stimulate the uptake of the resources by the industry so that the full potential of this scientific endeavor can be exploited and produce benefits for producers and the public alike.
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Consolidation of the genetic and cytogenetic maps of turbot (Scophthalmus maximus) using FISH with BAC clones. Chromosoma 2014; 123:281-91. [PMID: 24473579 DOI: 10.1007/s00412-014-0452-2] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2013] [Revised: 01/09/2014] [Accepted: 01/10/2014] [Indexed: 10/25/2022]
Abstract
Bacterial artificial chromosomes (BAC) have been widely used for fluorescence in situ hybridization (FISH) mapping of chromosome landmarks in different organisms, including a few in teleosts. In this study, we used BAC-FISH to consolidate the previous genetic and cytogenetic maps of the turbot (Scophthalmus maximus), a commercially important pleuronectiform. The maps consisted of 24 linkage groups (LGs) but only 22 chromosomes. All turbot LGs were assigned to specific chromosomes using BAC probes obtained from a turbot 5× genomic BAC library. It consisted of 46,080 clones with inserts of at least 100 kb and <5 % empty vectors. These BAC probes contained gene-derived or anonymous markers, most of them linked to quantitative trait loci (QTL) related to productive traits. BAC clones were mapped by FISH to unique marker-specific chromosomal positions, which showed a notable concordance with previous genetic mapping data. The two metacentric pairs were cytogenetically assigned to LG2 and LG16, and the nucleolar organizer region (NOR)-bearing pair was assigned to LG15. Double-color FISH assays enabled the consolidation of the turbot genetic map into 22 linkage groups by merging LG8 with LG18 and LG21 with LG24. In this work, a first-generation probe panel of BAC clones anchored to the turbot linkage and cytogenetical map was developed. It is a useful tool for chromosome traceability in turbot, but also relevant in the context of pleuronectiform karyotypes, which often show small hardly identifiable chromosomes. This panel will also be valuable for further integrative genomics of turbot within Pleuronectiformes and teleosts, especially for fine QTL mapping for aquaculture traits, comparative genomics, and whole-genome assembly.
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8
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Jiang Y, Ninwichian P, Liu S, Zhang J, Kucuktas H, Sun F, Kaltenboeck L, Sun L, Bao L, Liu Z. Generation of physical map contig-specific sequences useful for whole genome sequence scaffolding. PLoS One 2013; 8:e78872. [PMID: 24205335 PMCID: PMC3811975 DOI: 10.1371/journal.pone.0078872] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2013] [Accepted: 09/16/2013] [Indexed: 11/29/2022] Open
Abstract
Along with the rapid advances of the nextgen sequencing technologies, more and more species are added to the list of organisms whose whole genomes are sequenced. However, the assembled draft genome of many organisms consists of numerous small contigs, due to the short length of the reads generated by nextgen sequencing platforms. In order to improve the assembly and bring the genome contigs together, more genome resources are needed. In this study, we developed a strategy to generate a valuable genome resource, physical map contig-specific sequences, which are randomly distributed genome sequences in each physical contig. Two-dimensional tagging method was used to create specific tags for 1,824 physical contigs, in which the cost was dramatically reduced. A total of 94,111,841 100-bp reads and 315,277 assembled contigs are identified containing physical map contig-specific tags. The physical map contig-specific sequences along with the currently available BAC end sequences were then used to anchor the catfish draft genome contigs. A total of 156,457 genome contigs (~79% of whole genome sequencing assembly) were anchored and grouped into 1,824 pools, in which 16,680 unique genes were annotated. The physical map contig-specific sequences are valuable resources to link physical map, genetic linkage map and draft whole genome sequences, consequently have the capability to improve the whole genome sequences assembly and scaffolding, and improve the genome-wide comparative analysis as well. The strategy developed in this study could also be adopted in other species whose whole genome assembly is still facing a challenge.
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Affiliation(s)
- Yanliang Jiang
- The Fish Molecular Genetics and Biotechnology Laboratory, Aquatic Genomics Unit, School of Fisheries, Aquaculture and Aquatic Sciences and Program of Cell and Molecular Biosciences, Auburn University, Auburn, Alabama, United States of America
| | - Parichart Ninwichian
- The Fish Molecular Genetics and Biotechnology Laboratory, Aquatic Genomics Unit, School of Fisheries, Aquaculture and Aquatic Sciences and Program of Cell and Molecular Biosciences, Auburn University, Auburn, Alabama, United States of America
| | - Shikai Liu
- The Fish Molecular Genetics and Biotechnology Laboratory, Aquatic Genomics Unit, School of Fisheries, Aquaculture and Aquatic Sciences and Program of Cell and Molecular Biosciences, Auburn University, Auburn, Alabama, United States of America
| | - Jiaren Zhang
- The Fish Molecular Genetics and Biotechnology Laboratory, Aquatic Genomics Unit, School of Fisheries, Aquaculture and Aquatic Sciences and Program of Cell and Molecular Biosciences, Auburn University, Auburn, Alabama, United States of America
| | - Huseyin Kucuktas
- The Fish Molecular Genetics and Biotechnology Laboratory, Aquatic Genomics Unit, School of Fisheries, Aquaculture and Aquatic Sciences and Program of Cell and Molecular Biosciences, Auburn University, Auburn, Alabama, United States of America
| | - Fanyue Sun
- The Fish Molecular Genetics and Biotechnology Laboratory, Aquatic Genomics Unit, School of Fisheries, Aquaculture and Aquatic Sciences and Program of Cell and Molecular Biosciences, Auburn University, Auburn, Alabama, United States of America
| | - Ludmilla Kaltenboeck
- The Fish Molecular Genetics and Biotechnology Laboratory, Aquatic Genomics Unit, School of Fisheries, Aquaculture and Aquatic Sciences and Program of Cell and Molecular Biosciences, Auburn University, Auburn, Alabama, United States of America
| | - Luyang Sun
- The Fish Molecular Genetics and Biotechnology Laboratory, Aquatic Genomics Unit, School of Fisheries, Aquaculture and Aquatic Sciences and Program of Cell and Molecular Biosciences, Auburn University, Auburn, Alabama, United States of America
| | - Lisui Bao
- The Fish Molecular Genetics and Biotechnology Laboratory, Aquatic Genomics Unit, School of Fisheries, Aquaculture and Aquatic Sciences and Program of Cell and Molecular Biosciences, Auburn University, Auburn, Alabama, United States of America
| | - Zhanjiang Liu
- The Fish Molecular Genetics and Biotechnology Laboratory, Aquatic Genomics Unit, School of Fisheries, Aquaculture and Aquatic Sciences and Program of Cell and Molecular Biosciences, Auburn University, Auburn, Alabama, United States of America
- * E-mail:
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9
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Mehinto AC, Martyniuk CJ, Spade DJ, Denslow ND. Applications for next-generation sequencing in fish ecotoxicogenomics. Front Genet 2012; 3:62. [PMID: 22539934 PMCID: PMC3336092 DOI: 10.3389/fgene.2012.00062] [Citation(s) in RCA: 52] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2012] [Accepted: 03/02/2012] [Indexed: 01/23/2023] Open
Abstract
The new technologies for next-generation sequencing (NGS) and global gene expression analyses that are widely used in molecular medicine are increasingly applied to the field of fish biology. This has facilitated new directions to address research areas that could not be previously considered due to the lack of molecular information for ecologically relevant species. Over the past decade, the cost of NGS has decreased significantly, making it possible to use non-model fish species to investigate emerging environmental issues. NGS technologies have permitted researchers to obtain large amounts of raw data in short periods of time. There have also been significant improvements in bioinformatics to assemble the sequences and annotate the genes, thus facilitating the management of these large datasets.The combination of DNA sequencing and bioinformatics has improved our abilities to design custom microarrays and study the genome and transcriptome of a wide variety of organisms. Despite the promising results obtained using these techniques in fish studies, NGS technologies are currently underused in ecotoxicogenomics and few studies have employed these methods. These issues should be addressed in order to exploit the full potential of NGS in ecotoxicological studies and expand our understanding of the biology of non-model organisms.
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Affiliation(s)
- Alvine C Mehinto
- Center for Environmental and Human Toxicology, Department of Physiological Sciences, University of Florida, Gainesville, FL, USA
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10
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Navarro-Martín L, Viñas J, Ribas L, Díaz N, Gutiérrez A, Di Croce L, Piferrer F. DNA methylation of the gonadal aromatase (cyp19a) promoter is involved in temperature-dependent sex ratio shifts in the European sea bass. PLoS Genet 2011; 7:e1002447. [PMID: 22242011 PMCID: PMC3248465 DOI: 10.1371/journal.pgen.1002447] [Citation(s) in RCA: 308] [Impact Index Per Article: 23.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2011] [Accepted: 11/16/2011] [Indexed: 11/18/2022] Open
Abstract
Sex ratio shifts in response to temperature are common in fish and reptiles. However, the mechanism linking temperature during early development and sex ratios has remained elusive. We show in the European sea bass (sb), a fish in which temperature effects on sex ratios are maximal before the gonads form, that juvenile males have double the DNA methylation levels of females in the promoter of gonadal aromatase (cyp19a), the enzyme that converts androgens into estrogens. Exposure to high temperature increased the cyp19a promoter methylation levels of females, indicating that induced-masculinization involves DNA methylation-mediated control of aromatase gene expression, with an observed inverse relationship between methylation levels and expression. Although different CpGs within the sb cyp19a promoter exhibited different sensitivity to temperature, we show that the increased methylation of the sb cyp19a promoter, which occurs in the gonads but not in the brain, is not a generalized effect of temperature. Importantly, these effects were also observed in sexually undifferentiated fish and were not altered by estrogen treatment. Thus, methylation of the sb cyp19a promoter is the cause of the lower expression of cyp19a in temperature-masculinized fish. In vitro, induced methylation of the sb cyp19a promoter suppressed the ability of SF-1 and Foxl2 to stimulate transcription. Finally, a CpG differentially methylated by temperature and adjacent to a Sox transcription factor binding site is conserved across species. Thus, DNA methylation of the aromatase promoter may be an essential component of the long-sought-after mechanism connecting environmental temperature and sex ratios in vertebrate species with temperature-dependent sex determination.
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Affiliation(s)
- Laia Navarro-Martín
- Institut de Ciències del Mar, Consejo Superior de Investigaciones Científicas (CSIC), Barcelona, Spain
| | - Jordi Viñas
- Institut de Ciències del Mar, Consejo Superior de Investigaciones Científicas (CSIC), Barcelona, Spain
| | - Laia Ribas
- Institut de Ciències del Mar, Consejo Superior de Investigaciones Científicas (CSIC), Barcelona, Spain
| | - Noelia Díaz
- Institut de Ciències del Mar, Consejo Superior de Investigaciones Científicas (CSIC), Barcelona, Spain
| | - Arantxa Gutiérrez
- Centre de Regulació Genòmica (CRG)/ICREA and Univeristat Pompeu Fabra (UPF), Barcelona, Spain
| | - Luciano Di Croce
- Centre de Regulació Genòmica (CRG)/ICREA and Univeristat Pompeu Fabra (UPF), Barcelona, Spain
| | - Francesc Piferrer
- Institut de Ciències del Mar, Consejo Superior de Investigaciones Científicas (CSIC), Barcelona, Spain
- * E-mail:
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Jiang Y, Lu J, Peatman E, Kucuktas H, Liu S, Wang S, Sun F, Liu Z. A pilot study for channel catfish whole genome sequencing and de novo assembly. BMC Genomics 2011; 12:629. [PMID: 22192763 PMCID: PMC3266365 DOI: 10.1186/1471-2164-12-629] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2011] [Accepted: 12/22/2011] [Indexed: 12/11/2022] Open
Abstract
Background Recent advances in next-generation sequencing technologies have drastically increased throughput and significantly reduced sequencing costs. However, the average read lengths in next-generation sequencing technologies are short as compared with that of traditional Sanger sequencing. The short sequence reads pose great challenges for de novo sequence assembly. As a pilot project for whole genome sequencing of the catfish genome, here we attempt to determine the proper sequence coverage, the proper software for assembly, and various parameters used for the assembly of a BAC physical map contig spanning approximately a million of base pairs. Results A combination of low sequence coverage of 454 and Illumina sequencing appeared to provide effective assembly as reflected by a high N50 value. Using 454 sequencing alone, a sequencing depth of 18 X was sufficient to obtain the good quality assembly, whereas a 70 X Illumina appeared to be sufficient for a good quality assembly. Additional sequencing coverage after 18 X of 454 or after 70 X of Illumina sequencing does not provide significant improvement of the assembly. Considering the cost of sequencing, a 2 X 454 sequencing, when coupled to 70 X Illumina sequencing, provided an assembly of reasonably good quality. With several software tested, Newbler with a seed length of 16 and ABySS with a K-value of 60 appear to be appropriate for the assembly of 454 reads alone and Illumina paired-end reads alone, respectively. Using both 454 and Illumina paired-end reads, a hybrid assembly strategy using Newbler for initial 454 sequence assembly, Velvet for initial Illumina sequence assembly, followed by a second step assembly using MIRA provided the best assembly of the physical map contig, resulting in 193 contigs with a N50 value of 13,123 bp. Conclusions A hybrid sequencing strategy using low sequencing depth of 454 and high sequencing depth of Illumina provided the good quality assembly with high N50 value and relatively low cost. A combination of Newbler, Velvet, and MIRA can be used to assemble the 454 sequence reads and the Illumina reads effectively. The assembled sequence can serve as a resource for comparative genome analysis. Additional long reads using the third generation sequencing platforms are needed to sequence through repetitive genome regions that should further enhance the sequence assembly.
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Affiliation(s)
- Yanliang Jiang
- The Fish Molecular Genetics and Biotechnology Laboratory, Department of Fisheries and Allied Aquacultures, Program of Cell and Molecular Biosciences, Aquatic Genomics Unit, 203 Swingle Hall, Auburn University, Auburn, AL 36849, USA
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