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Mendizábal-Castillero M, Merlo MA, Cross I, Rodríguez ME, Rebordinos L. Genomic Characterization of hox Genes in Senegalese Sole ( Solea senegalensis, Kaup 1858): Clues to Evolutionary Path in Pleuronectiformes. Animals (Basel) 2022; 12:ani12243586. [PMID: 36552509 PMCID: PMC9774920 DOI: 10.3390/ani12243586] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2022] [Revised: 12/12/2022] [Accepted: 12/15/2022] [Indexed: 12/23/2022] Open
Abstract
The Senegalese sole (Solea senegalensis, Kaup 1858), a marine flatfish, belongs to the Pleuronectiformes order. It is a commercially important species for fisheries and aquaculture. However, in aquaculture, several production bottlenecks have still to be resolved, including skeletal deformities and high mortality during the larval and juvenile phase. The study aims to characterize the hox gene clusters in S. senegalensis to understand better the developmental and metamorphosis process in this species. Using a BAC library, the clones that contain hox genes were isolated, sequenced by NGS and used as BAC-FISH probes. Subsequently the hox clusters were studied by sequence analysis, comparative genomics, and cytogenetic and phylogenetic analysis. Cytogenetic analysis demonstrated the localization of four BAC clones on chromosome pairs 4, 12, 13, and 16 of the Senegalese sole cytogenomic map. Comparative and phylogenetic analysis showed a highly conserved organization in each cluster and different phylogenetic clustering in each hox cluster. Analysis of structural and repetitive sequences revealed accumulations of polymorphisms mediated by repetitive elements in the hoxba cluster, mainly retroelements. Therefore, a possible loss of the hoxb7a gene can be established in the Pleuronectiformes lineage. This work allows the organization and regulation of hox clusters to be understood, and is a good base for further studies of expression patterns.
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Sousa C, Fernandes SA, Cardoso JCR, Wang Y, Zhai W, Guerreiro PM, Chen L, Canário AVM, Power DM. Toll-Like Receptor Evolution: Does Temperature Matter? Front Immunol 2022; 13:812890. [PMID: 35237266 PMCID: PMC8882821 DOI: 10.3389/fimmu.2022.812890] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2021] [Accepted: 01/03/2022] [Indexed: 11/13/2022] Open
Abstract
Toll-like receptors (TLRs) recognize conserved pathogen-associated molecular patterns (PAMPs) and are an ancient and well-conserved group of pattern recognition receptors (PRRs). The isolation of the Antarctic continent and its unique teleost fish and microbiota prompted the present investigation into Tlr evolution. Gene homologues of tlr members in teleosts from temperate regions were present in the genome of Antarctic Nototheniidae and the non-Antarctic sister lineage Bovichtidae. Overall, in Nototheniidae apart from D. mawsoni, no major tlr gene family expansion or contraction occurred. Instead, lineage and species-specific changes in the ectodomain and LRR of Tlrs occurred, particularly in the Tlr11 superfamily that is well represented in fish. Positive selective pressure and associated sequence modifications in the TLR ectodomain and within the leucine-rich repeats (LRR), important for pathogen recognition, occurred in Tlr5, Tlr8, Tlr13, Tlr21, Tlr22, and Tlr23 presumably associated with the unique Antarctic microbiota. Exposure to lipopolysaccharide (Escherichia coli O111:B4) Gram negative bacteria did not modify tlr gene expression in N. rossii head–kidney or anterior intestine, although increased water temperature (+4°C) had a significant effect.
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Affiliation(s)
- Cármen Sousa
- Centro de Ciências do Mar (CCMAR), Universidade do Algarve, Faro, Portugal
| | | | - João C. R. Cardoso
- Centro de Ciências do Mar (CCMAR), Universidade do Algarve, Faro, Portugal
| | - Ying Wang
- International Research Center for Marine Biosciences, Ministry of Science and Technology, Shanghai Ocean University (SHOU), Shanghai, China
| | - Wanying Zhai
- International Research Center for Marine Biosciences, Ministry of Science and Technology, Shanghai Ocean University (SHOU), Shanghai, China
| | - Pedro M. Guerreiro
- Centro de Ciências do Mar (CCMAR), Universidade do Algarve, Faro, Portugal
| | - Liangbiao Chen
- International Research Center for Marine Biosciences, Ministry of Science and Technology, Shanghai Ocean University (SHOU), Shanghai, China
| | - Adelino V. M. Canário
- Centro de Ciências do Mar (CCMAR), Universidade do Algarve, Faro, Portugal
- International Research Center for Marine Biosciences, Ministry of Science and Technology, Shanghai Ocean University (SHOU), Shanghai, China
| | - Deborah M. Power
- Centro de Ciências do Mar (CCMAR), Universidade do Algarve, Faro, Portugal
- International Research Center for Marine Biosciences, Ministry of Science and Technology, Shanghai Ocean University (SHOU), Shanghai, China
- *Correspondence: Deborah M. Power,
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Salis P, Lee S, Roux N, Lecchini D, Laudet V. The real Nemo movie: Description of embryonic development in Amphiprion ocellaris from first division to hatching. Dev Dyn 2021; 250:1651-1667. [PMID: 33899313 PMCID: PMC8597122 DOI: 10.1002/dvdy.354] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2021] [Revised: 04/13/2021] [Accepted: 04/19/2021] [Indexed: 11/25/2022] Open
Abstract
BACKGROUND Amphiprion ocellaris is one of the rare reef fish species that can be reared in aquaria. It is increasingly used as a model species for Eco-Evo-Devo. Therefore, it is important to have an embryonic development table based on high quality images that will allow for standardized sampling by the scientific community. RESULTS Here we provide high-resolution time-lapse videos to accompany a detailed description of embryonic development in A ocellaris. We describe a series of developmental stages and we define six broad periods of embryogenesis: zygote, cleavage, blastula, gastrula, segmentation, and organogenesis that we further subdivide into 32 stages. These periods highlight the changing spectrum of major developmental processes that occur during embryonic development. CONCLUSIONS We provide an easy system for the determination of embryonic stages, enabling the development of A ocellaris as a coral reef fish model species. This work will facilitate evolutionary development studies, in particular studies of the relationship between climate change and developmental trajectories in the context of coral reefs. Thanks to its lifestyle, complex behavior, and ecology, A ocellaris will undoubtedly become a very attractive model in a wide range of biological fields.
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Affiliation(s)
- Pauline Salis
- Observatoire Océanologique de Banyuls‐sur‐Mer, UMR CNRS 7232 BIOMSorbonne Université ParisBanyuls‐sur‐MerFrance
- EPHE‐UPVD‐CNRS, USR 3278 CRIOBEPSL UniversityMooreaFrench Polynesia
| | - Shu‐hua Lee
- Lab of Marine Eco‐Evo‐Devo, Marine Research StationInstitute of Cellular and Organismic Biology, Academia SinicaTaipeiTaiwan
| | - Natacha Roux
- Observatoire Océanologique de Banyuls‐sur‐Mer, UMR CNRS 7232 BIOMSorbonne Université ParisBanyuls‐sur‐MerFrance
| | - David Lecchini
- EPHE‐UPVD‐CNRS, USR 3278 CRIOBEPSL UniversityMooreaFrench Polynesia
| | - Vincent Laudet
- Lab of Marine Eco‐Evo‐Devo, Marine Research StationInstitute of Cellular and Organismic Biology, Academia SinicaTaipeiTaiwan
- Marine Eco‐Evo‐Devo UnitOkinawa Institute of Science and TechnologyOnna sonOkinawaJapan
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Development of whole-genome multiplex assays and construction of an integrated genetic map using SSR markers in Senegalese sole. Sci Rep 2020; 10:21905. [PMID: 33318526 PMCID: PMC7736592 DOI: 10.1038/s41598-020-78397-w] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2020] [Accepted: 11/20/2020] [Indexed: 11/08/2022] Open
Abstract
The Senegalese sole (Solea senegalensis) is an economically important flatfish species. In this study, a genome draft was analyzed to identify microsatellite (SSR) markers for whole-genome genotyping. A subset of 224 contigs containing SSRs were preselected and validated by using a de novo female hybrid assembly. Overall, the SSR density in the genome was 886.7 markers per megabase of genomic sequences and the dinucleotide motif was the most abundant (52.4%). In silico comparison identified a set of 108 SSRs (with di-, tetra- or pentanucleotide motifs) widely distributed in the genome and suitable for primer design. A total of 106 markers were structured in thirteen multiplex PCR assays (with up to 10-plex) and the amplification conditions were optimized with a high-quality score. Main genetic diversity statistics and genotyping reliability were assessed. A subset of 40 high polymorphic markers were selected to optimize four supermultiplex PCRs (with up to 11-plex) for pedigree analysis. Theoretical exclusion probabilities and real parentage allocation tests using parent–offspring information confirmed their robustness and effectiveness for parental assignment. These new SSR markers were combined with previously published SSRs (in total 229 makers) to construct a new and improved integrated genetic map containing 21 linkage groups that matched with the expected number of chromosomes. Synteny analysis with respect to C. semilaevis provided new clues on chromosome evolution in flatfish and the formation of metacentric and submetacentric chromosomes in Senegalese sole.
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Carballo C, Chronopoulou EG, Letsiou S, Spanidi E, Gardikis K, Labrou NE, Manchado M. Genomic and phylogenetic analysis of choriolysins, and biological activity of hatching liquid in the flatfish Senegalese sole. PLoS One 2019; 14:e0225666. [PMID: 31805094 PMCID: PMC6894847 DOI: 10.1371/journal.pone.0225666] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2019] [Accepted: 11/08/2019] [Indexed: 11/18/2022] Open
Abstract
The hatching enzymes or choriolysins are key proteases in fish life cycle controlling the release of larvae to surrounding environment that have been suggested as target for novel biotechnological uses. Due to the large amounts of eggs released by the flatfish Solea senegalensis, during the spawning season, the hatching liquid properties and choriolysin-encoding genes were investigated in this species. A genomic analysis identified four putative genes referred to as SseHCEa, SseHCEb, SseLCE and SseHE. The phylogenetic analysis classified these paralogs into two clades, the clade I containing SseHCE paralogs and the clade II containing two well-supported subclades named as HE and LCE. The two SseHCE paralogs were intron-less and both genes were tandemly arrayed very close in the genome. The synteny and gene rearrangement identified in the flatfish lineage indicated that the duplication of these two paralogs occurred recently and they are under divergent evolution. The genes SseHE and SseLCE were structured in 8 exons and 7 introns and the synteny was conserved in teleosts. Expression studies confirmed that the four genes were expressed in the hatching gland cells and they migrate co-ordinately from the head to around the yolk sac close to the hatch with specific temporal and intensity expression profiles. Although the mRNA levels of the four genes peaked in the hours previous to larval hatching, the SseHCE and SseLCE paralogs kept a longer expression than SseHE after hatching. These expression patterns were consistent even when larvae were incubated at different temperatures that modified hatching times. The analysis of hatching-liquid using SDS-PAGE and zymography analyses of hatching liquid identified a major band of expected choriolysin size. The optimal pH for protease activity was 8.5 and inhibition assays using EDTA demonstrated that most of the activity in the hatching liquid was due to metalloproteases with Ca2+ ions acting as the most effective metal to restore the activity. All these data provide new clues about the choriolysin evolution and function in flatfish with impact in the aquaculture and the blue cosmetic industry.
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Affiliation(s)
- Carlos Carballo
- IFAPA Centro El Toruño, Junta de Andalucía, El Puerto de Santa María, Spain
| | - Evangelia G. Chronopoulou
- Laboratory of Enzyme Technology, Department of Biotechnology, School of Applied Biology and Biotechnology, Agricultural University of Athens, Athens, Greece
| | - Sophia Letsiou
- Research and Development Department, APIVITA S.A., Athens, Greece
| | - Eleni Spanidi
- Research and Development Department, APIVITA S.A., Athens, Greece
| | | | - Nikolaos E. Labrou
- Laboratory of Enzyme Technology, Department of Biotechnology, School of Applied Biology and Biotechnology, Agricultural University of Athens, Athens, Greece
| | - Manuel Manchado
- IFAPA Centro El Toruño, Junta de Andalucía, El Puerto de Santa María, Spain
- * E-mail:
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Rise ML, Martyniuk CJ, Chen M. Comparative physiology and aquaculture: Toward Omics-enabled improvement of aquatic animal health and sustainable production. COMPARATIVE BIOCHEMISTRY AND PHYSIOLOGY D-GENOMICS & PROTEOMICS 2019; 31:100603. [PMID: 31260856 DOI: 10.1016/j.cbd.2019.100603] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Abstract
Omics-technologies have revolutionized biomedical research over the past two decades, and are now poised to play a transformative role in aquaculture. This article serves as an introduction to a Virtual Special Issue of Comparative Biochemistry and Physiology - Part D: Genomics and Proteomics (CBPD), with the objective to showcase the state-of-the-science for Omics in aquaculture. In this editorial, we describe the role that Omics can play in aquaculture, and provide a synopsis for each of the Special Issue articles that use these technologies to improve aquaculture practices. Current genomic resources available for some aquaculture species are also described. The number of datasets is impressive for species such as Atlantic salmon and rainbow trout, totaling in the thousands (NCBI Gene Expression Omnibus and Sequence Read Archive). We present a conceptual framework that describes how Omics can be leveraged to understand complex responses of aquatic animals in culture for relevant physiological outcomes, such as fecundity, growth, and immunity. Lastly, knowledge gaps and new directions are identified to address current obstacles in aquaculture. Articles in this Special Issue on aquaculture in CBPD highlight the diversity and scope of Omics in aquaculture. As the technology becomes more cost-effective, it is anticipated that genomics, transcriptomics, proteomics, metabolomics and lipidomics will play increasingly important roles in stock diagnostics (e.g. genetics, health, performance). The timing is right, as global concerns are reaching critical levels over food availability/security and water restrictions for humankind.
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Affiliation(s)
- Matthew L Rise
- Department of Ocean Sciences, Memorial University of Newfoundland, 1 Marine Lab Road, St. John's, NL A1C 5S7, Canada
| | - Christopher J Martyniuk
- Department of Physiological Sciences and Center for Environmental and Human Toxicology, University of Florida Genetics Institute, Interdisciplinary Program in Biomedical Sciences Neuroscience, College of Veterinary Medicine, University of Florida, Gainesville, FL 32611, USA.
| | - Muyan Chen
- College of Fisheries, Ocean University of China, Qingdao 266003, China
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García-Angulo A, Merlo MA, Rodríguez ME, Portela-Bens S, Liehr T, Rebordinos L. Genome and Phylogenetic Analysis of Genes Involved in the Immune System of Solea senegalensis - Potential Applications in Aquaculture. Front Genet 2019; 10:529. [PMID: 31244883 PMCID: PMC6579814 DOI: 10.3389/fgene.2019.00529] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2019] [Accepted: 05/14/2019] [Indexed: 01/04/2023] Open
Abstract
Global aquaculture production continues to increase rapidly. One of the most important species of marine fish currently cultivated in Southern Europe is Solea senegalensis, reaching more than 300 Tn in 2017. In the present work, 14 Bacterial Artificial Chromosome (BAC) clones containing candidate genes involved in the immune system (b2m, il10, tlr3, tap1, tnfα, tlr8, trim25, lysg, irf5, hmgb2, calr, trim16, and mx), were examined and compared with other species using multicolor Fluorescence in situ Hybridization (mFISH), massive sequencing and bioinformatic analysis to determine the genomic surroundings and syntenic chromosomal conservation of the genomic region contained in each BAC clone. The mFISH showed that the groups of genes hmgb2-trim25-irf5-b2m; tlr3-lysg; tnfα-tap1, and il10-mx-trim16 were co-localized on the same chromosomes. Synteny results suggested that the studied BACs are placed in a smaller number of chromosomes in S. senegalensis that in other species. Phylogenetic analyses suggested that the evolutionary rate of immune system genes studied is similar among the taxa studied, given that the clustering obtained was in accordance with the accepted phylogenetic relationships among these species. This study contributes to a better understanding of the structure and function of the immune system of the Senegalese sole, which is essential for the development of new technologies and products to improve fish health and productivity.
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Affiliation(s)
- Aglaya García-Angulo
- Área de Genética, Facultad de Ciencias del Mar y Ambientales, Universidad de Cádiz, Cádiz, Spain
| | - Manuel A. Merlo
- Área de Genética, Facultad de Ciencias del Mar y Ambientales, Universidad de Cádiz, Cádiz, Spain
| | - María E. Rodríguez
- Área de Genética, Facultad de Ciencias del Mar y Ambientales, Universidad de Cádiz, Cádiz, Spain
| | - Silvia Portela-Bens
- Área de Genética, Facultad de Ciencias del Mar y Ambientales, Universidad de Cádiz, Cádiz, Spain
| | - Thomas Liehr
- Institute of Human Genetics, Jena University Hospital, Friedrich Schiller University Jena, Jena, Germany
| | - Laureana Rebordinos
- Área de Genética, Facultad de Ciencias del Mar y Ambientales, Universidad de Cádiz, Cádiz, Spain
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8
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Ronza P, Robledo D, Bermúdez R, Losada AP, Pardo BG, Martínez P, Quiroga MI. Integrating Genomic and Morphological Approaches in Fish Pathology Research: The Case of Turbot ( Scophthalmus maximus) Enteromyxosis. Front Genet 2019; 10:26. [PMID: 30766546 PMCID: PMC6365611 DOI: 10.3389/fgene.2019.00026] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2018] [Accepted: 01/16/2019] [Indexed: 01/04/2023] Open
Abstract
Enteromyxosis, caused by Enteromyxum scophthalmi, is one of the most devastating diseases stemming from myxozoan parasites in turbot (Scophthalmus maximus L.), being a limiting factor for its production. The disease develops as a cachectic syndrome, associated to catarrhal enteritis and leukocytic depletion, with morbidity and mortality rates usually reaching 100%. To date, no effective treatment exists and there are different unknown issues concerning its pathogenesis. The gross and microscopic lesions associated to enteromyxosis have been thoroughly described, and several morphopathological studies have been carried out to elucidate the mechanisms of this host-parasite interaction. More recently, efforts have been focused on a multidisciplinary approach, combining histopathology and transcriptome analysis, which has provided significant advances in the understanding of the pathogenesis of this parasitosis. RNA-Seq technology was applied at early and advanced stages of the disease on fishes histologically evaluated and classified based on their lesional degree. In the same way, the transcriptomic data were analyzed in relation to the morphopathological picture and the course of the disease. In this paper, a comprehensive review of turbot enteromyxosis is presented, starting from the disease description up to the most novel information extracted by an integrated approach on the infection mechanisms and host response. Further, we discuss ongoing strategies toward a full understanding of host-pathogen interaction and the identification of suitable biomarkers for early diagnosis and disease management strategies.
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Affiliation(s)
- Paolo Ronza
- Departamento de Anatomía, Producción Animal y Ciencias Clínicas Veterinarias, Universidade de Santiago de Compostela, Lugo, Spain
| | - Diego Robledo
- Royal (Dick) School of Veterinary Studies, The Roslin Institute, The University of Edinburgh, Midlothian, United Kingdom
| | - Roberto Bermúdez
- Departamento de Anatomía, Producción Animal y Ciencias Clínicas Veterinarias, Universidade de Santiago de Compostela, Lugo, Spain
| | - Ana Paula Losada
- Departamento de Anatomía, Producción Animal y Ciencias Clínicas Veterinarias, Universidade de Santiago de Compostela, Lugo, Spain
| | - Belén G Pardo
- Departamento de Zoología, Genética y Antropología Física, Universidade de Santiago de Compostela, Lugo, Spain
| | - Paulino Martínez
- Departamento de Zoología, Genética y Antropología Física, Universidade de Santiago de Compostela, Lugo, Spain
| | - María Isabel Quiroga
- Departamento de Anatomía, Producción Animal y Ciencias Clínicas Veterinarias, Universidade de Santiago de Compostela, Lugo, Spain
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Herkenhoff ME, Oliveira AC, Nachtigall PG, Costa JM, Campos VF, Hilsdorf AWS, Pinhal D. Fishing Into the MicroRNA Transcriptome. Front Genet 2018; 9:88. [PMID: 29616080 PMCID: PMC5868305 DOI: 10.3389/fgene.2018.00088] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2017] [Accepted: 03/02/2018] [Indexed: 01/18/2023] Open
Abstract
In the last decade, several studies have been focused on revealing the microRNA (miRNA) repertoire and determining their functions in farm animals such as poultry, pigs, cattle, and fish. These small non-protein coding RNA molecules (18-25 nucleotides) are capable of controlling gene expression by binding to messenger RNA (mRNA) targets, thus interfering in the final protein output. MiRNAs have been recognized as the main regulators of biological features of economic interest, including body growth, muscle development, fat deposition, and immunology, among other highly valuable traits, in aquatic livestock. Currently, the miRNA repertoire of some farmed fish species has been identified and characterized, bringing insights about miRNA functions, and novel perspectives for improving health and productivity. In this review, we summarize the current advances in miRNA research by examining available data on Neotropical and other key species exploited by fisheries and in aquaculture worldwide and discuss how future studies on Neotropical fish could benefit from this knowledge. We also make a horizontal comparison of major results and discuss forefront strategies for miRNA manipulation in aquaculture focusing on forward-looking ideas for forthcoming research.
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Affiliation(s)
- Marcos E. Herkenhoff
- Laboratory of Genomics and Molecular Evolution, Department of Genetics, Institute of Biosciences of Botucatu, Sao Paulo State University, Botucatu, Brazil
| | - Arthur C. Oliveira
- Laboratory of Genomics and Molecular Evolution, Department of Genetics, Institute of Biosciences of Botucatu, Sao Paulo State University, Botucatu, Brazil
| | - Pedro G. Nachtigall
- Laboratory of Genomics and Molecular Evolution, Department of Genetics, Institute of Biosciences of Botucatu, Sao Paulo State University, Botucatu, Brazil
| | - Juliana M. Costa
- Laboratory of Genomics and Molecular Evolution, Department of Genetics, Institute of Biosciences of Botucatu, Sao Paulo State University, Botucatu, Brazil
| | - Vinicius F. Campos
- Laboratory of Structural Genomics (GenEstrut), Graduate Program of Biotechnology, Technology Developmental Center, Federal University of Pelotas, Pelotas, Brazil
| | | | - Danillo Pinhal
- Laboratory of Genomics and Molecular Evolution, Department of Genetics, Institute of Biosciences of Botucatu, Sao Paulo State University, Botucatu, Brazil
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O'Leary SJ, Hollenbeck CM, Vega RR, Gold JR, Portnoy DS. Genetic mapping and comparative genomics to inform restoration enhancement and culture of southern flounder, Paralichthys lethostigma. BMC Genomics 2018; 19:163. [PMID: 29471804 PMCID: PMC5824557 DOI: 10.1186/s12864-018-4541-0] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2017] [Accepted: 02/13/2018] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Southern flounder, Paralichthys lethostigma, historically support a substantial fishery along the Atlantic and Gulf coasts of the southern United States. Low year-class strengths over the past few years in the western Gulf of Mexico have raised concern that spawning stocks may be overfished. Current management of the resource includes releasing hatchery-raised juveniles to restock bays and estuaries; additionally, there is a growing interest in the potential for commercial aquaculture of the species. Currently, genomic resources for southern flounder do not exist. Here, we used two hatchery-reared families and double-digest, restriction-site-associated DNA (ddRAD) sequencing to create a reduced-representation genomic library consisting of several thousand single nucleotide polymorphisms (SNPs) located throughout the genome. RESULTS The relative position of each SNP-containing locus was determined to create a high-density genetic map spanning the 24 linkage groups of the southern flounder genome. The consensus map was used to identify regions of shared synteny between southern flounder and seven other fish species for which genome assemblies are available. Finally, syntenic blocks were used to localize genes identified from transcripts in European flounder as potentially being involved in ecotoxicological and osmoregulatory responses, as well as QTLs associated with growth and disease resistance in Japanese flounder, on the southern flounder linkage map. CONCLUSIONS The information provided by the linkage map will enrich restoration efforts by providing a foundation for interpreting spatial genetic variation within the species, ultimately furthering an understanding of the adaptive potential and resilience of southern flounder to future changes in local environmental conditions. Further, the map will facilitate the use of genetic markers to enhance restoration and commercial aquaculture.
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Affiliation(s)
- Shannon J O'Leary
- Department of Life Sciences, Marine Genomics Laboratory, Texas A&M University Corpus Christi, 6300 Ocean Drive, Unit 5869, Corpus Christi, TX, 78412, USA.
| | - Christopher M Hollenbeck
- Scottish Oceans Institute, University of St. Andrews, East Sands, St. Andrews, Fife, KY16 8LB, UK
| | - Robert R Vega
- Texas Parks and Wildlife Department, CCA Marine Development Center, 4300 Waldron Road, Corpus Christi, TX, 78418, USA
| | - John R Gold
- Department of Life Sciences, Marine Genomics Laboratory, Texas A&M University Corpus Christi, 6300 Ocean Drive, Unit 5869, Corpus Christi, TX, 78412, USA
| | - David S Portnoy
- Department of Life Sciences, Marine Genomics Laboratory, Texas A&M University Corpus Christi, 6300 Ocean Drive, Unit 5869, Corpus Christi, TX, 78412, USA
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11
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Aliaga-Guerrero M, Paullada-Salmerón JA, Piquer V, Mañanós EL, Muñoz-Cueto JA. Gonadotropin-inhibitory hormone in the flatfish,Solea senegalensis: Molecular cloning, brain localization and physiological effects. J Comp Neurol 2017; 526:349-370. [DOI: 10.1002/cne.24339] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2017] [Revised: 10/11/2017] [Accepted: 10/12/2017] [Indexed: 12/14/2022]
Affiliation(s)
- María Aliaga-Guerrero
- Department of Biology, Faculty of Marine and Environmental Sciences; University of Cádiz, Marine Campus of International Excellence (CEIMAR) and Agrifood Campus of International Excellence (ceiA3); Puerto Real Spain
- INMAR-CACYTMAR Research Institutes, Puerto Real University Campus; Puerto Real Spain
| | - José A. Paullada-Salmerón
- Department of Biology, Faculty of Marine and Environmental Sciences; University of Cádiz, Marine Campus of International Excellence (CEIMAR) and Agrifood Campus of International Excellence (ceiA3); Puerto Real Spain
- INMAR-CACYTMAR Research Institutes, Puerto Real University Campus; Puerto Real Spain
| | - Vanesa Piquer
- Institute of Aquaculture of Torre la Sal, CSIC; Castellón Spain
| | | | - José A. Muñoz-Cueto
- Department of Biology, Faculty of Marine and Environmental Sciences; University of Cádiz, Marine Campus of International Excellence (CEIMAR) and Agrifood Campus of International Excellence (ceiA3); Puerto Real Spain
- INMAR-CACYTMAR Research Institutes, Puerto Real University Campus; Puerto Real Spain
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12
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Extending Immunological Profiling in the Gilthead Sea Bream, Sparus aurata, by Enriched cDNA Library Analysis, Microarray Design and Initial Studies upon the Inflammatory Response to PAMPs. Int J Mol Sci 2017; 18:ijms18020317. [PMID: 28165358 PMCID: PMC5343853 DOI: 10.3390/ijms18020317] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2016] [Revised: 08/31/2016] [Accepted: 10/08/2016] [Indexed: 12/19/2022] Open
Abstract
This study describes the development and validation of an enriched oligonucleotide-microarray platform for Sparus aurata (SAQ) to provide a platform for transcriptomic studies in this species. A transcriptome database was constructed by assembly of gilthead sea bream sequences derived from public repositories of mRNA together with reads from a large collection of expressed sequence tags (EST) from two extensive targeted cDNA libraries characterizing mRNA transcripts regulated by both bacterial and viral challenge. The developed microarray was further validated by analysing monocyte/macrophage activation profiles after challenge with two Gram-negative bacterial pathogen-associated molecular patterns (PAMPs; lipopolysaccharide (LPS) and peptidoglycan (PGN)). Of the approximately 10,000 EST sequenced, we obtained a total of 6837 EST longer than 100 nt, with 3778 and 3059 EST obtained from the bacterial-primed and from the viral-primed cDNA libraries, respectively. Functional classification of contigs from the bacterial- and viral-primed cDNA libraries by Gene Ontology (GO) showed that the top five represented categories were equally represented in the two libraries: metabolism (approximately 24% of the total number of contigs), carrier proteins/membrane transport (approximately 15%), effectors/modulators and cell communication (approximately 11%), nucleoside, nucleotide and nucleic acid metabolism (approximately 7.5%) and intracellular transducers/signal transduction (approximately 5%). Transcriptome analyses using this enriched oligonucleotide platform identified differential shifts in the response to PGN and LPS in macrophage-like cells, highlighting responsive gene-cassettes tightly related to PAMP host recognition. As observed in other fish species, PGN is a powerful activator of the inflammatory response in S. aurata macrophage-like cells. We have developed and validated an oligonucleotide microarray (SAQ) that provides a platform enriched for the study of gene expression in S. aurata with an emphasis upon immunity and the immune response.
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Robledo D, Hermida M, Rubiolo JA, Fernández C, Blanco A, Bouza C, Martínez P. Integrating genomic resources of flatfish (Pleuronectiformes) to boost aquaculture production. COMPARATIVE BIOCHEMISTRY AND PHYSIOLOGY D-GENOMICS & PROTEOMICS 2016; 21:41-55. [PMID: 28063346 DOI: 10.1016/j.cbd.2016.12.001] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/28/2016] [Revised: 12/09/2016] [Accepted: 12/13/2016] [Indexed: 12/15/2022]
Abstract
Flatfish have a high market acceptance thus representing a profitable aquaculture production. The main farmed species is the turbot (Scophthalmus maximus) followed by Japanese flounder (Paralichthys olivaceous) and tongue sole (Cynoglossus semilaevis), but other species like Atlantic halibut (Hippoglossus hippoglossus), Senegalese sole (Solea senegalensis) and common sole (Solea solea) also register an important production and are very promising for farming. Important genomic resources are available for most of these species including whole genome sequencing projects, genetic maps and transcriptomes. In this work, we integrate all available genomic information of these species within a common framework, taking as reference the whole assembled genomes of turbot and tongue sole (>210× coverage). New insights related to the genetic basis of productive traits and new data useful to understand the evolutionary origin and diversification of this group were obtained. Despite a general 1:1 chromosome syntenic relationship between species, the comparison of turbot and tongue sole genomes showed huge intrachromosomic reorganizations. The integration of available mapping information supported specific chromosome fusions along flatfish evolution and facilitated the comparison between species of previously reported genetic associations for productive traits. When comparing transcriptomic resources of the six species, a common set of ~2500 othologues and ~150 common miRNAs were identified, and specific sets of putative missing genes were detected in flatfish transcriptomes, likely reflecting their evolutionary diversification.
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Affiliation(s)
- Diego Robledo
- Department of Zoology, Genetics and Physical Anthropology, Faculty of Biology (CIBUS), Universidade de Santiago de Compostela, 15782 Santiago de Compostela, Spain
| | - Miguel Hermida
- Department of Zoology, Genetics and Physical Anthropology, Faculty of Veterinary, Universidade de Santiago de Compostela, 27002 Lugo, Spain
| | - Juan A Rubiolo
- Department of Zoology, Genetics and Physical Anthropology, Faculty of Veterinary, Universidade de Santiago de Compostela, 27002 Lugo, Spain
| | - Carlos Fernández
- Department of Zoology, Genetics and Physical Anthropology, Faculty of Veterinary, Universidade de Santiago de Compostela, 27002 Lugo, Spain
| | - Andrés Blanco
- Department of Zoology, Genetics and Physical Anthropology, Faculty of Veterinary, Universidade de Santiago de Compostela, 27002 Lugo, Spain
| | - Carmen Bouza
- Department of Zoology, Genetics and Physical Anthropology, Faculty of Veterinary, Universidade de Santiago de Compostela, 27002 Lugo, Spain
| | - Paulino Martínez
- Department of Zoology, Genetics and Physical Anthropology, Faculty of Veterinary, Universidade de Santiago de Compostela, 27002 Lugo, Spain.
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Portela-Bens S, Merlo MA, Rodríguez ME, Cross I, Manchado M, Kosyakova N, Liehr T, Rebordinos L. Integrated gene mapping and synteny studies give insights into the evolution of a sex proto-chromosome in Solea senegalensis. Chromosoma 2016; 126:261-277. [PMID: 27080536 DOI: 10.1007/s00412-016-0589-2] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2015] [Revised: 03/31/2016] [Accepted: 04/04/2016] [Indexed: 11/27/2022]
Abstract
The evolution of genes related to sex and reproduction in fish shows high plasticity and, to date, the sex determination system has only been identified in a few species. Solea senegalensis has 42 chromosomes and an XX/XY chromosome system for sex determination, while related species show the ZZ/ZW system. Next-generation sequencing (NGS), multi-color fluorescence in situ hybridization (mFISH) techniques, and bioinformatics analysis have been carried out, with the objective of revealing new information about sex determination and reproduction in S. senegalensis. To that end, several bacterial artificial chromosome (BAC) clones that contain candidate genes involved in such processes (dmrt1, dmrt2, dmrt3, dmrt4, sox3, sox6, sox8, sox9, lh, cyp19a1a, amh, vasa, aqp3, and nanos3) were analyzed and compared with the same region in other related species. Synteny studies showed that the co-localization of dmrt1-dmrt2-drmt3 in the largest metacentric chromosome of S. senegalensis is coincident with that found in the Z chromosome of Cynoglossus semilaevis, which would potentially make this a sex proto-chromosome. Phylogenetic studies show the close proximity of S. senegalensis to Oryzias latipes, a species with an XX/XY system and a sex master gene. Comparative mapping provides evidence of the preferential association of these candidate genes in particular chromosome pairs. By using the NGS and mFISH techniques, it has been possible to obtain an integrated genetic map, which shows that 15 out of 21 chromosome pairs of S. senegalensis have at least one BAC clone. This result is important for distinguishing those chromosome pairs of S. senegalensis that are similar in shape and size. The mFISH analysis shows the following co-localizations in the same chromosomes: dmrt1-dmrt2-dmrt3, dmrt4-sox9-thrb, aqp3-sox8, cyp19a1a-fshb, igsf9b-sox3, and lysg-sox6.
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Affiliation(s)
- Silvia Portela-Bens
- Área de Genética, Facultad de Ciencias del Mar y Ambientales, Universidad de Cádiz, 11510, Cádiz, Spain
| | - Manuel Alejandro Merlo
- Área de Genética, Facultad de Ciencias del Mar y Ambientales, Universidad de Cádiz, 11510, Cádiz, Spain
| | - María Esther Rodríguez
- Área de Genética, Facultad de Ciencias del Mar y Ambientales, Universidad de Cádiz, 11510, Cádiz, Spain
| | - Ismael Cross
- Área de Genética, Facultad de Ciencias del Mar y Ambientales, Universidad de Cádiz, 11510, Cádiz, Spain
| | - Manuel Manchado
- Centro IFAPA "El Toruño", 11500, Puerto de Santa María, Cádiz, Spain
| | - Nadezda Kosyakova
- Institut für Humangenetik, Universitätsklinikum Jena, 07743, Jena, Germany
| | - Thomas Liehr
- Institut für Humangenetik, Universitätsklinikum Jena, 07743, Jena, Germany
| | - Laureana Rebordinos
- Área de Genética, Facultad de Ciencias del Mar y Ambientales, Universidad de Cádiz, 11510, Cádiz, Spain.
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Figueras A, Robledo D, Corvelo A, Hermida M, Pereiro P, Rubiolo JA, Gómez-Garrido J, Carreté L, Bello X, Gut M, Gut IG, Marcet-Houben M, Forn-Cuní G, Galán B, García JL, Abal-Fabeiro JL, Pardo BG, Taboada X, Fernández C, Vlasova A, Hermoso-Pulido A, Guigó R, Álvarez-Dios JA, Gómez-Tato A, Viñas A, Maside X, Gabaldón T, Novoa B, Bouza C, Alioto T, Martínez P. Whole genome sequencing of turbot (Scophthalmus maximus; Pleuronectiformes): a fish adapted to demersal life. DNA Res 2016; 23:181-92. [PMID: 26951068 PMCID: PMC4909306 DOI: 10.1093/dnares/dsw007] [Citation(s) in RCA: 116] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2015] [Accepted: 02/03/2016] [Indexed: 01/25/2023] Open
Abstract
The turbot is a flatfish (Pleuronectiformes) with increasing commercial value, which has prompted active genomic research aimed at more efficient selection. Here we present the sequence and annotation of the turbot genome, which represents a milestone for both boosting breeding programmes and ascertaining the origin and diversification of flatfish. We compare the turbot genome with model fish genomes to investigate teleost chromosome evolution. We observe a conserved macrosyntenic pattern within Percomorpha and identify large syntenic blocks within the turbot genome related to the teleost genome duplication. We identify gene family expansions and positive selection of genes associated with vision and metabolism of membrane lipids, which suggests adaptation to demersal lifestyle and to cold temperatures, respectively. Our data indicate a quick evolution and diversification of flatfish to adapt to benthic life and provide clues for understanding their controversial origin. Moreover, we investigate the genomic architecture of growth, sex determination and disease resistance, key traits for understanding local adaptation and boosting turbot production, by mapping candidate genes and previously reported quantitative trait loci. The genomic architecture of these productive traits has allowed the identification of candidate genes and enriched pathways that may represent useful information for future marker-assisted selection in turbot.
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Affiliation(s)
- Antonio Figueras
- Instituto de Investigaciones Marinas (IIM), Consejo Superior de Investigaciones Científicas (CSIC), Vigo 36208, Spain
| | - Diego Robledo
- Departamento de Xenética, Facultade de Bioloxía (CIBUS), Universidade de Santiago de Compostela, Santiago de Compostela 15782, Spain
| | - André Corvelo
- Centre Nacional d'Anàlisi Genòmica (CNAG-CRG), Centre de Regulació Genómica, Parc Científic de Barcelona, Barcelona 08028, Spain New York Genome Center, 101 Avenue of the Americas, New York, NY 10013, USA
| | - Miguel Hermida
- Departamento de Xenética, Facultade de Veterinaria, Universidade de Santiago de Compostela, Lugo 27002, Spain
| | - Patricia Pereiro
- Instituto de Investigaciones Marinas (IIM), Consejo Superior de Investigaciones Científicas (CSIC), Vigo 36208, Spain
| | - Juan A Rubiolo
- Departamento de Xenética, Facultade de Veterinaria, Universidade de Santiago de Compostela, Lugo 27002, Spain
| | - Jèssica Gómez-Garrido
- Centre Nacional d'Anàlisi Genòmica (CNAG-CRG), Centre de Regulació Genómica, Parc Científic de Barcelona, Barcelona 08028, Spain
| | - Laia Carreté
- Centre Nacional d'Anàlisi Genòmica (CNAG-CRG), Centre de Regulació Genómica, Parc Científic de Barcelona, Barcelona 08028, Spain
| | - Xabier Bello
- Departamento de Anatomía Patolóxica e Ciencias Forenses, Grupo de Medicina Xenómica, CIMUS, Universidade de Santiago de Compostela, Santiago de Compostela 15782, Spain Xenómica Comparada de Parasitos Humanos, Instituto de Investigación Sanitaria de Santiago (IDIS), Santiago de Compostela 15706, Spain
| | - Marta Gut
- Centre Nacional d'Anàlisi Genòmica (CNAG-CRG), Centre de Regulació Genómica, Parc Científic de Barcelona, Barcelona 08028, Spain
| | - Ivo Glynne Gut
- Centre Nacional d'Anàlisi Genòmica (CNAG-CRG), Centre de Regulació Genómica, Parc Científic de Barcelona, Barcelona 08028, Spain
| | - Marina Marcet-Houben
- Centre Nacional d'Anàlisi Genòmica (CNAG-CRG), Centre de Regulació Genómica, Parc Científic de Barcelona, Barcelona 08028, Spain
| | - Gabriel Forn-Cuní
- Instituto de Investigaciones Marinas (IIM), Consejo Superior de Investigaciones Científicas (CSIC), Vigo 36208, Spain
| | - Beatriz Galán
- Centro de Investigaciones Biológicas (CIB), Consejo Superior de Investigaciones Científicas, Madrid 28040, Spain
| | - José Luis García
- Centro de Investigaciones Biológicas (CIB), Consejo Superior de Investigaciones Científicas, Madrid 28040, Spain
| | - José Luis Abal-Fabeiro
- Departamento de Anatomía Patolóxica e Ciencias Forenses, Grupo de Medicina Xenómica, CIMUS, Universidade de Santiago de Compostela, Santiago de Compostela 15782, Spain Xenómica Comparada de Parasitos Humanos, Instituto de Investigación Sanitaria de Santiago (IDIS), Santiago de Compostela 15706, Spain
| | - Belen G Pardo
- Departamento de Xenética, Facultade de Veterinaria, Universidade de Santiago de Compostela, Lugo 27002, Spain
| | - Xoana Taboada
- Departamento de Xenética, Facultade de Bioloxía (CIBUS), Universidade de Santiago de Compostela, Santiago de Compostela 15782, Spain
| | - Carlos Fernández
- Departamento de Xenética, Facultade de Veterinaria, Universidade de Santiago de Compostela, Lugo 27002, Spain
| | - Anna Vlasova
- Centre Nacional d'Anàlisi Genòmica (CNAG-CRG), Centre de Regulació Genómica, Parc Científic de Barcelona, Barcelona 08028, Spain
| | - Antonio Hermoso-Pulido
- Centre Nacional d'Anàlisi Genòmica (CNAG-CRG), Centre de Regulació Genómica, Parc Científic de Barcelona, Barcelona 08028, Spain
| | - Roderic Guigó
- Centre Nacional d'Anàlisi Genòmica (CNAG-CRG), Centre de Regulació Genómica, Parc Científic de Barcelona, Barcelona 08028, Spain
| | - José Antonio Álvarez-Dios
- Departamento de Matemática Aplicada, Facultade de Matemáticas, Universidade de Santiago de Compostela, 15782 Santiago de Compostela, Spain
| | - Antonio Gómez-Tato
- Departamento de Xeometría e Topoloxía, Facultade de Matemáticas, Universidade de Santiago de Compostela, 15782 Santiago de Compostela, Spain
| | - Ana Viñas
- Departamento de Xenética, Facultade de Bioloxía (CIBUS), Universidade de Santiago de Compostela, Santiago de Compostela 15782, Spain
| | - Xulio Maside
- Departamento de Anatomía Patolóxica e Ciencias Forenses, Grupo de Medicina Xenómica, CIMUS, Universidade de Santiago de Compostela, Santiago de Compostela 15782, Spain Xenómica Comparada de Parasitos Humanos, Instituto de Investigación Sanitaria de Santiago (IDIS), Santiago de Compostela 15706, Spain
| | - Toni Gabaldón
- Centre Nacional d'Anàlisi Genòmica (CNAG-CRG), Centre de Regulació Genómica, Parc Científic de Barcelona, Barcelona 08028, Spain Universitat Pompeu Fabra (UPF), 08003 Barcelona, Spain Institució Catalana de Recerca i Estudis Avançats (ICREA), Pg. Lluís Companys 23, 08010 Barcelona, Spain
| | - Beatriz Novoa
- Instituto de Investigaciones Marinas (IIM), Consejo Superior de Investigaciones Científicas (CSIC), Vigo 36208, Spain
| | - Carmen Bouza
- Departamento de Xenética, Facultade de Veterinaria, Universidade de Santiago de Compostela, Lugo 27002, Spain
| | - Tyler Alioto
- Centre Nacional d'Anàlisi Genòmica (CNAG-CRG), Centre de Regulació Genómica, Parc Científic de Barcelona, Barcelona 08028, Spain
| | - Paulino Martínez
- Departamento de Xenética, Facultade de Veterinaria, Universidade de Santiago de Compostela, Lugo 27002, Spain
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Ribas L, Robledo D, Gómez-Tato A, Viñas A, Martínez P, Piferrer F. Comprehensive transcriptomic analysis of the process of gonadal sex differentiation in the turbot (Scophthalmus maximus). Mol Cell Endocrinol 2016; 422:132-149. [PMID: 26586209 DOI: 10.1016/j.mce.2015.11.006] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/09/2015] [Revised: 11/03/2015] [Accepted: 11/03/2015] [Indexed: 10/22/2022]
Abstract
The turbot is a flatfish with a ZW/ZZ sex determination system but with a still unknown sex determining gene(s), and with a marked sexual growth dimorphism in favor of females. To better understand sexual development in turbot we sampled young turbot encompassing the whole process of gonadal differentiation and conducted a comprehensive transcriptomic study on its sex differentiation using a validated custom oligomicroarray. Also, the expression profiles of 18 canonical reproduction-related genes were studied along gonad development. The expression levels of gonadal aromatase cyp19a1a alone at three months of age allowed the accurate and early identification of sex before the first signs of histological differentiation. A total of 56 differentially expressed genes (DEG) that had not previously been related to sex differentiation in fish were identified within the first three months of age, of which 44 were associated with ovarian differentiation (e.g., cd98, gpd1 and cry2), and 12 with testicular differentiation (e.g., ace, capn8 and nxph1). To identify putative sex determining genes, ∼4.000 DEG in juvenile gonads were mapped and their positions compared with that of previously identified sex- and growth-related quantitative trait loci (QTL). Although no genes mapped to the previously identified sex-related QTLs, two genes (foxl2 and 17βhsd) of the canonical reproduction-related genes mapped to growth-QTLs in linkage group (LG) 15 and LG6, respectively, suggesting that these genes are related to the growth dimorphism in this species.
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Affiliation(s)
- L Ribas
- Institut de Ciències del Mar, Consejo Superior de Investigaciones Científicas (CSIC), 08003, Barcelona, Spain
| | - D Robledo
- Departamento de Genética. Facultad de Veterinaria, Universidad de Santiago de Compostela, 27002, Lugo, Spain
| | - A Gómez-Tato
- Departamento de Matemática Aplicada, Facultad de Matemáticas, Universidad de Santiago de Compostela, 15781, Santiago de Compostela, Spain
| | - A Viñas
- Departamento de Genética. Facultad de Veterinaria, Universidad de Santiago de Compostela, 27002, Lugo, Spain
| | - P Martínez
- Departamento de Genética. Facultad de Veterinaria, Universidad de Santiago de Compostela, 27002, Lugo, Spain
| | - F Piferrer
- Institut de Ciències del Mar, Consejo Superior de Investigaciones Científicas (CSIC), 08003, Barcelona, Spain.
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17
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Diopere E, Maes GE, Komen H, Volckaert FAM, Groenen MAM. A genetic linkage map of sole (Solea solea): a tool for evolutionary and comparative analyses of exploited (flat)fishes. PLoS One 2014; 9:e115040. [PMID: 25541971 PMCID: PMC4277273 DOI: 10.1371/journal.pone.0115040] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2014] [Accepted: 09/12/2014] [Indexed: 11/19/2022] Open
Abstract
Linkage maps based on markers derived from genes are essential evolutionary tools for commercial marine fish to help identify genomic regions associated with complex traits and subject to selective forces at play during exploitation or selective breeding. Additionally, they allow the use of genomic information from other related species for which more detailed information is available. Sole (solea solea L.) is a commercially important flatfish species in the North Sea, subject to overexploitation and showing evidence of fisheries-induced evolutionary changes in growth- and maturation-related traits. Sole would definitely benefit from a linkage map to better understand how evolution has shaped its genome structure. This study presents a linkage map of sole based on 423 single nucleotide polymorphisms derived from expressed sequence tags and 8 neutral microsatellite markers. The total map length is 1233.8 cM and consists of 38 linkage groups with a size varying between 0 to 92.1 cM. Being derived from expressed sequence tags allowed us to align the map with the genome of four model fish species, namely medaka (Oryzias latipes), Nile tilapia (Oreochromis niloticus), three-spined stickleback (Gasterosteus aculeatus) and green spotted pufferfish (Tetraodon nigroviridis). This comparison revealed multiple conserved syntenic regions with all four species, and suggested that the linkage groups represent 21 putative sole chromosomes. The map was also compared to the linkage map of turbot (Scophthalmus maximus), another commercially important flatfish species and closely related to sole. For all putative sole chromosomes (except one) a turbot homolog was detected, confirming the even higher degree of synteny between these two flatfish species.
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Affiliation(s)
- Eveline Diopere
- Laboratory of Biodiversity and Evolutionary Genomics, University of Leuven, Ch. Deberiotstraat 32, B-3000 Leuven, Belgium
- * E-mail:
| | - Gregory E. Maes
- Laboratory of Biodiversity and Evolutionary Genomics, University of Leuven, Ch. Deberiotstraat 32, B-3000 Leuven, Belgium
- Centre for Sustainable Tropical Fisheries and Aquaculture, James Cook University, 4811 QLD Townsville, Australia
| | - Hans Komen
- Animal Breeding and Genomics Centre, Wageningen University, Marijkeweg 40, NL-6700 AH Wageningen, the Netherlands
| | - Filip A. M. Volckaert
- Laboratory of Biodiversity and Evolutionary Genomics, University of Leuven, Ch. Deberiotstraat 32, B-3000 Leuven, Belgium
| | - Martien A. M. Groenen
- Animal Breeding and Genomics Centre, Wageningen University, Marijkeweg 40, NL-6700 AH Wageningen, the Netherlands
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Hachero-Cruzado I, Rodríguez-Rua A, Román-Padilla J, Ponce M, Fernández-Díaz C, Manchado M. Characterization of the genomic responses in early Senegalese sole larvae fed diets with different dietary triacylglycerol and total lipids levels. COMPARATIVE BIOCHEMISTRY AND PHYSIOLOGY D-GENOMICS & PROTEOMICS 2014; 12:61-73. [DOI: 10.1016/j.cbd.2014.09.005] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/05/2014] [Revised: 09/29/2014] [Accepted: 09/30/2014] [Indexed: 12/16/2022]
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Benzekri H, Armesto P, Cousin X, Rovira M, Crespo D, Merlo MA, Mazurais D, Bautista R, Guerrero-Fernández D, Fernandez-Pozo N, Ponce M, Infante C, Zambonino JL, Nidelet S, Gut M, Rebordinos L, Planas JV, Bégout ML, Claros MG, Manchado M. De novo assembly, characterization and functional annotation of Senegalese sole (Solea senegalensis) and common sole (Solea solea) transcriptomes: integration in a database and design of a microarray. BMC Genomics 2014; 15:952. [PMID: 25366320 PMCID: PMC4232633 DOI: 10.1186/1471-2164-15-952] [Citation(s) in RCA: 51] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2014] [Accepted: 10/15/2014] [Indexed: 12/26/2022] Open
Abstract
Background Senegalese sole (Solea senegalensis) and common sole (S. solea) are two economically and evolutionary important flatfish species both in fisheries and aquaculture. Although some genomic resources and tools were recently described in these species, further sequencing efforts are required to establish a complete transcriptome, and to identify new molecular markers. Moreover, the comparative analysis of transcriptomes will be useful to understand flatfish evolution. Results A comprehensive characterization of the transcriptome for each species was carried out using a large set of Illumina data (more than 1,800 millions reads for each sole species) and 454 reads (more than 5 millions reads only in S. senegalensis), providing coverages ranging from 1,384x to 2,543x. After a de novo assembly, 45,063 and 38,402 different transcripts were obtained, comprising 18,738 and 22,683 full-length cDNAs in S. senegalensis and S. solea, respectively. A reference transcriptome with the longest unique transcripts and putative non-redundant new transcripts was established for each species. A subset of 11,953 reference transcripts was qualified as highly reliable orthologs (>97% identity) between both species. A small subset of putative species-specific, lineage-specific and flatfish-specific transcripts were also identified. Furthermore, transcriptome data permitted the identification of single nucleotide polymorphisms and simple-sequence repeats confirmed by FISH to be used in further genetic and expression studies. Moreover, evidences on the retention of crystallins crybb1, crybb1-like and crybb3 in the two species of soles are also presented. Transcriptome information was applied to the design of a microarray tool in S. senegalensis that was successfully tested and validated by qPCR. Finally, transcriptomic data were hosted and structured at SoleaDB. Conclusions Transcriptomes and molecular markers identified in this study represent a valuable source for future genomic studies in these economically important species. Orthology analysis provided new clues regarding sole genome evolution indicating a divergent evolution of crystallins in flatfish. The design of a microarray and establishment of a reference transcriptome will be useful for large-scale gene expression studies. Moreover, the integration of transcriptomic data in the SoleaDB will facilitate the management of genomic information in these important species. Electronic supplementary material The online version of this article (doi:10.1186/1471-2164-15-952) contains supplementary material, which is available to authorized users.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | - Manuel Manchado
- IFAPA Centro El Toruño, IFAPA, Consejeria de Agricultura y Pesca, 11500 El Puerto de Santa María, Cádiz, Spain.
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Hemmer-Hansen J, Therkildsen NO, Pujolar JM. Population genomics of marine fishes: next-generation prospects and challenges. THE BIOLOGICAL BULLETIN 2014; 227:117-132. [PMID: 25411371 DOI: 10.1086/bblv227n2p117] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
Over the past few years, technological advances have facilitated giant leaps forward in our ability to generate genome-wide molecular data, offering exciting opportunities for gaining new insights into the ecology and evolution of species where genomic information is still limited. Marine fishes are valuable organisms for advancing our understanding of evolution on historical and contemporary time scales, and here we highlight areas in which research on these species is likely to be particularly important in the near future. These include possibilities for gaining insights into processes on ecological time scales, identifying genomic signatures associated with population divergence under gene flow, and determining the genetic basis of phenotypic traits. We also consider future challenges pertaining to the implementation of genome-wide coverage through next-generation sequencing and genotyping methods in marine fishes. Complications associated with fast decay of linkage disequilibrium, as expected for species with large effective population sizes, and the possibility that adaptation is associated with both soft selective sweeps and polygenic selection, leaving complex genomic signatures in natural populations, are likely to challenge future studies. However, the combination of high genome coverage and new statistical developments offers promising solutions. Thus, the next generation of studies is likely to truly facilitate the transition from population genetics to population genomics in marine fishes. This transition will advance our understanding of basic evolutionary processes and will offer new possibilities for conservation and management of valuable marine resources.
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Affiliation(s)
- Jakob Hemmer-Hansen
- Section for Marine Living Resources, National Institute of Aquatic Resources, Technical University of Denmark, Vejlsøvej 39, DK-8600 Silkeborg, Denmark;
| | | | - José Martin Pujolar
- Department of Bioscience, Aarhus University, Ny Munkegade 114, DK-8000 Aarhus C, Denmark
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21
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Santos CA, Blanck DV, de Freitas PD. RNA-seq as a powerful tool for penaeid shrimp genetic progress. Front Genet 2014; 5:298. [PMID: 25221571 PMCID: PMC4147233 DOI: 10.3389/fgene.2014.00298] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2014] [Accepted: 08/11/2014] [Indexed: 11/27/2022] Open
Abstract
The sequences of all different RNA transcripts present in a cell or tissue that are related to the gene expression and its functional control represent what it is called a transcriptome. The transcripts vary between cells, tissues, ontogenetic and environmental conditions, and the knowledge that can be gained through them is of a solid relevance for genetic applications in aquaculture. Some of the techniques used in transcriptome studies, such as microarrays, are being replaced for next-generation sequencing approaches. RNA-seq emerges as a new possibility for the transcriptome complexity analysis as well as for the candidate genes and polymorphisms identification of penaeid species. Thus, it may also help to understand the determination of complex traits mechanisms and genetic improvement of stocks. In this review, it is first introduced an overview of transcriptome analysis by RNA-seq, followed by a discussion of how this approach may be applied in genetic progress within penaeid stocks.
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Affiliation(s)
- Camilla A Santos
- Laboratory of Molecular Biodiversity and Conservation, Department of Genetics and Evolution, Federal University of São Carlos São Carlos, Brazil
| | - Danielly V Blanck
- Laboratory of Molecular Biodiversity and Conservation, Department of Genetics and Evolution, Federal University of São Carlos São Carlos, Brazil
| | - Patrícia D de Freitas
- Laboratory of Molecular Biodiversity and Conservation, Department of Genetics and Evolution, Federal University of São Carlos São Carlos, Brazil
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22
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Braasch I, Peterson SM, Desvignes T, McCluskey BM, Batzel P, Postlethwait JH. A new model army: Emerging fish models to study the genomics of vertebrate Evo-Devo. JOURNAL OF EXPERIMENTAL ZOOLOGY PART B-MOLECULAR AND DEVELOPMENTAL EVOLUTION 2014; 324:316-41. [PMID: 25111899 DOI: 10.1002/jez.b.22589] [Citation(s) in RCA: 84] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/16/2014] [Revised: 06/19/2014] [Accepted: 06/25/2014] [Indexed: 01/08/2023]
Abstract
Many fields of biology--including vertebrate Evo-Devo research--are facing an explosion of genomic and transcriptomic sequence information and a multitude of fish species are now swimming in this "genomic tsunami." Here, we first give an overview of recent developments in sequencing fish genomes and transcriptomes that identify properties of fish genomes requiring particular attention and propose strategies to overcome common challenges in fish genomics. We suggest that the generation of chromosome-level genome assemblies--for which we introduce the term "chromonome"--should be a key component of genomic investigations in fish because they enable large-scale conserved synteny analyses that inform orthology detection, a process critical for connectivity of genomes. Orthology calls in vertebrates, especially in teleost fish, are complicated by divergent evolution of gene repertoires and functions following two rounds of genome duplication in the ancestor of vertebrates and a third round at the base of teleost fish. Second, using examples of spotted gar, basal teleosts, zebrafish-related cyprinids, cavefish, livebearers, icefish, and lobefin fish, we illustrate how next generation sequencing technologies liberate emerging fish systems from genomic ignorance and transform them into a new model army to answer longstanding questions on the genomic and developmental basis of their biodiversity. Finally, we discuss recent progress in the genetic toolbox for the major fish models for functional analysis, zebrafish, and medaka, that can be transferred to many other fish species to study in vivo the functional effect of evolutionary genomic change as Evo-Devo research enters the postgenomic era.
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Affiliation(s)
- Ingo Braasch
- Institute of Neuroscience, University of Oregon, Eugene, Oregon
| | | | | | | | - Peter Batzel
- Institute of Neuroscience, University of Oregon, Eugene, Oregon
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23
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Fine mapping and evolution of the major sex determining region in turbot (Scophthalmus maximus). G3-GENES GENOMES GENETICS 2014; 4:1871-80. [PMID: 25106948 PMCID: PMC4199694 DOI: 10.1534/g3.114.012328] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Fish sex determination (SD) systems are varied, suggesting evolutionary changes including either multiple evolution origins of genetic SD from nongenetic systems (such as environmental SD) and/or turnover events replacing one genetic system by another. When genetic SD is found, cytological differentiation between the two members of the sex chromosome pair is often minor or undetectable. The turbot (Scophthalmus maximus), a valuable commercial flatfish, has a ZZ/ZW system and a major SD region on linkage group 5 (LG5), but there are also other minor genetic and environmental influences. We here report refined mapping of the turbot SD region, supported by comparative mapping with model fish species, to identify the turbot master SD gene. Six genes were located to the SD region, two of them associated with gonad development (sox2 and dnajc19). All showed a high association with sex within families (P = 0), but not at the population level, so they are probably partially sex-linked genes, but not SD gene itself. Analysis of crossovers in LG5 using two families confirmed a ZZ/ZW system in turbot and suggested a revised map position for the master gene. Genetic diversity and differentiation for 25 LG5 genetic markers showed no differences between males and females sampled from a wild population, suggesting a recent origin of the SD region in turbot. We also analyzed associations with markers of the most relevant sex-related linkage groups in brill (S. rhombus), a closely related species to turbot; the data suggest that an ancient XX/XY system in brill changed to a ZZ/ZW mechanism in turbot.
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24
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Robledo D, Hernández-Urcera J, Cal RM, Pardo BG, Sánchez L, Martínez P, Viñas A. Analysis of qPCR reference gene stability determination methods and a practical approach for efficiency calculation on a turbot (Scophthalmus maximus) gonad dataset. BMC Genomics 2014; 15:648. [PMID: 25091330 PMCID: PMC4133071 DOI: 10.1186/1471-2164-15-648] [Citation(s) in RCA: 84] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2013] [Accepted: 07/25/2014] [Indexed: 01/26/2023] Open
Abstract
Background Gene expression analysis by reverse transcription quantitative PCR (qPCR) is the most widely used method for analyzing the expression of a moderate number of genes and also for the validation of microarray results. Several issues are crucial for a successful qPCR study, particularly the selection of internal reference genes for normalization and efficiency determination. There is no agreement on which method is the best to detect the most stable genes neither on how to perform efficiency determination. In this study we offer a comprehensive evaluation of the characteristics of reference gene selection methods and how to decide which one is more reliable when they show discordant outcomes. Also, we analyze the current efficiency calculation controversy. Our dataset is composed by gonad samples of turbot at different development times reared at different temperatures. Turbot (Scophthalmus maximus) is a relevant marine aquaculture European species with increasing production in the incoming years. Since females largely outgrow males, identification of genes related to sex determination, gonad development and reproductive behavior, and analysis of their expression profiles are of primary importance for turbot industry. Results We analyzed gene stability of six reference genes: RPS4, RPL17, GAPDH, ACTB, UBQ and B2M using the comparative delta-CT method, Bestkeeper, NormFinder and GeNorm approaches in gonad samples of turbot. Supported by descriptive statistics, we found NormFinder to be the best method, while on the other side, GeNorm results proved to be unreliable. According to our analysis, UBQ and RPS4 were the most stable genes, while B2M was the least stable gene. We also analyzed the efficiency calculation softwares LinRegPCR, LREanalyzer, DART and PCR-Miner and we recommend LinRegPCR for research purposes since it does not systematically overestimate efficiency. Conclusion Our results indicate that NormFinder and LinRegPCR are the best approaches for reference gene selection and efficiency determination, respectively. We also recommend the use of UBQ and RPS4 for normalization of gonad development samples in turbot. Electronic supplementary material The online version of this article (doi:10.1186/1471-2164-15-648) contains supplementary material, which is available to authorized users.
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Affiliation(s)
| | | | | | | | | | | | - Ana Viñas
- Departamento de Genética, Facultad de Biología (CIBUS), Universidad de Santiago de Compostela, 15782 Santiago de Compostela, Spain.
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25
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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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26
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Xing M, Hou Z, Yuan J, Liu Y, Qu Y, Liu B. Taxonomic and functional metagenomic profiling of gastrointestinal tract microbiome of the farmed adult turbot (Scophthalmus maximus). FEMS Microbiol Ecol 2013; 86:432-43. [DOI: 10.1111/1574-6941.12174] [Citation(s) in RCA: 117] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2012] [Revised: 06/10/2013] [Accepted: 06/18/2013] [Indexed: 11/27/2022] Open
Affiliation(s)
- Mengxin Xing
- Institute of Oceanology; Chinese Academy of Sciences; Qingdao China
- University of Chinese Academy of Sciences; Beijing China
| | - Zhanhui Hou
- Institute of Oceanology; Chinese Academy of Sciences; Qingdao China
| | - Jianbo Yuan
- Institute of Oceanology; Chinese Academy of Sciences; Qingdao China
- University of Chinese Academy of Sciences; Beijing China
| | - Yuan Liu
- Institute of Oceanology; Chinese Academy of Sciences; Qingdao China
| | - Yanmei Qu
- Institute of Oceanology; Chinese Academy of Sciences; Qingdao China
| | - Bin Liu
- Institute of Oceanology; Chinese Academy of Sciences; Qingdao China
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27
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Capozzi F, Bordoni A. Foodomics: a new comprehensive approach to food and nutrition. GENES & NUTRITION 2013; 8:1-4. [PMID: 22933238 PMCID: PMC3535000 DOI: 10.1007/s12263-012-0310-x] [Citation(s) in RCA: 129] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/31/2012] [Accepted: 08/02/2012] [Indexed: 12/26/2022]
Abstract
In the past 20 years, the scientific community has faced a great development in different fields due to the development of high-throughput, omics technologies. Starting from the four major types of omics measurements (genomics, transcriptomics, proteomics, and metabolomics), a variety of omics subdisciplines (epigenomics, lipidomics, interactomics, metallomics, diseasomics, etc.) has emerged. Thanks to the omics approach, researchers are now facing the possibility of connecting food components, foods, the diet, the individual, the health, and the diseases, but this broad vision needs not only the application of advanced technologies, but mainly the ability of looking at the problem with a different approach, a "foodomics approach". Foodomics is the comprehensive, high-throughput approach for the exploitation of food science in the light of an improvement of human nutrition. Foodomics is a new approach to food and nutrition that studies the food domain as a whole with the nutrition domain to reach the main objective, the optimization of human health and well-being.
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Affiliation(s)
- Francesco Capozzi
- Department of Food Sciences, University of Bologna, Piazza Goidanich, 60, 47521 Cesena, FC Italy
| | - Alessandra Bordoni
- Department of Food Sciences, University of Bologna, Piazza Goidanich, 60, 47521 Cesena, FC Italy
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