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  • 1
    Online-Ressource
    Online-Ressource
    San Diego :Elsevier Science & Technology,
    Schlagwort(e): Fish culture. ; Electronic books.
    Materialart: Online-Ressource
    Seiten: 1 online resource (306 pages)
    Ausgabe: 1st ed.
    ISBN: 9780128016909
    DDC: 576.5
    Sprache: Englisch
    Anmerkung: Cover -- Title page -- Copyright page -- Contents -- List of Contributors -- 1 - The new era of genome sequencing using high-throughput sequencing technology: generation of the first version of th... -- Introduction -- The first version of the Atlantic cod genome -- The sequencing of a wild-caught cod specimen -- The challenges of assembling large, outbred genomes -- Assembling the first version of the cod genome -- Annotating the first version of the cod genome -- Synteny with other teleost genomes -- Ongoing efforts to improve the Atlantic cod genome assembly -- The impact of combining different sequencing technologies -- Software developments for de novo assembly -- Goals for a new reference genome -- Acknowledgments -- Glossary -- References -- 2 - The rainbow trout genome, an important landmark for aquaculture and genome evolution -- Rainbow trout -- Rainbow trout and Salmonids commercial importance -- Rainbow trout: a freshwater laboratory rat -- Rainbow trout life cycle -- Genomic aspects -- The rainbow trout genome: diversity, structure, organization -- Genomic resources preexisting before the first genome sequence in rainbow trout -- Rainbow trout genome sequencing -- Rainbow trout genome structure -- A genome for genetic and functional investigations -- Deciphering the genetic architecture of traits -- Functional insights in Rainbow trout nutrition -- Selected examples of nutritional regulation of transcript levels -- Nutrition and flesh quality: molecular LC-PUFA biosynthesis pathway is functional -- Functional but atypically regulated glucose metabolism -- Linking nutrition to metabolism: hormonal and nutrient sensor roles -- The 21st century or the "omics" boom in nutritional studies -- Nutritional regulation of hepatic glucose-6-phosphatase genes expression in rainbow trout: how the trout genome sequencing. , Trout genomics for health -- The rainbow trout immunome: the added value of a full repertoire of fish immunity genes -- Toward the definition of a trout immunome -- The case of antigen specific receptors, Igs and TCRs -- Interest of a genome assembly for linkage studies: gene clusters and linkage studies -- Rainbow trout reproduction with a genome sequence -- Future directions and concluding remarks: resources are still expending -- References -- 3 - An improved version of the Atlantic cod genome and advancements in functional genomics: implications for the future... -- The Atlantic cod fisheries-and the rebirth of cod aquaculture -- Immunogenomics-the unusual immune system of Atlantic cod -- Atlantic cod functional genomics research -- Immunity and/or stress -- Reproduction and development -- Nutrigenomics -- Toxicogenomics -- Generation of a new version of the Atlantic cod genome -- Annotation using MAKER2 -- Tandem repeat content-assembly and biological implications -- An improved Atlantic cod genome-a valuable resource for biological inferences, fisheries management and the future cod aqua... -- References -- 4 - Catfish genomic studies: progress and perspectives -- Introduction -- The genome: structure and organization -- Development of molecular markers -- Linkage mapping -- Physical mapping -- Whole genome sequencing -- Genome evolution and comparative genomics -- The transcriptome: expression and function -- Early efforts of EST sequencing -- RNA-Seq based transcriptome analysis -- Protein-coding genes -- Long noncoding RNAs -- MicroRNAs -- Analysis of gene expression under various stress conditions -- Gene pathways, networks, and their regulation -- The genome: single nucleotide polymorphisms and genomic variations -- Single nucleotide polymorphisms -- Strain and population level genomic variations. , Historical application of molecular markers for the analysis of populations -- Development of high-density SNP arrays -- The genome: its relationship with phenome -- QTL analysis -- Genome-wide association studies -- Sex determination and progress toward understanding of sex in catfish -- Gene expression and regulation in control of phenotypes -- Future directions -- Functional analysis of genes -- Gene knockout systems and their potential use in catfish -- Concluding remarks -- References -- 5 - Tilapia genomic studies -- Introduction -- Life history -- The genome: structure and organization -- Development of molecular markers -- Linkage mapping -- Repetitive sequences in the tilapia genome -- Physical mapping -- Whole genome sequencing -- Genome evolution and comparative genomics -- Transcriptome: expression and function -- Expressed sequence tags (ESTs) -- RNA-seq -- microRNAs -- Gene expression under different conditions -- Liver transcriptome response to variation in dietary fat level -- Response to pathogen infection -- Functional and applied aspects -- Reproduction-sex determination and differentiation -- Salinity -- Future direction and aspects -- Whole genome sequence -- Genetic improvement based on genomics -- Conclusions -- Acknowledgments -- References -- 6 - Turbot (Scophthalmus maximus) genomic resources: application for boosting aquaculture production -- Biology and aquaculture -- Turbot biology -- Turbot production: aquaculture -- Main problems of turbot production -- Breeding programs -- Impact of turbot aquaculture on wild populations -- Genomic resources -- Introduction -- Transcriptome -- Genetic map -- Whole genome sequencing -- Genetic architecture and function of productive traits -- Growth-related traits -- Molecular genomics of growth -- QTL screening: growth-related QTL -- QTL methodology -- Growth-related QTL. , Identification of candidate genes through comparative mapping -- Genomics of the resistance of turbot to the main industrial diseases -- Main diseases in turbot farms -- High-throughput gene expression: microarrays and RNAseq -- Functional genomics of the response to the main turbot diseases -- Furunculosis versus scuticociliatosis -- VHSV -- Enteromyxosis -- QTL screening: disease resistance related QTL -- Crossing information from functional and association studies -- Reproduction and sex control: general revision, QTL, functional genomics, and ongoing research -- Sex differentiation in fish -- Genetic architecture of sex determination in turbot -- Gonad development and differentiation in turbot -- Concluding remarks and perspectives -- References -- 7 - Zebrafish offer aquaculture research their services -- Introduction -- The Genome: diversity, structure and organization -- The Genome and the corresponding transcriptome -- Comparative perspectives -- DNA and genome sequencing -- Expressing the genome-the transcriptome defines all transcripts produced -- Epigenetics-three levels of non-Mendelian heritage -- Level 1: DNA methylation and hydroxymethylation -- Level 2: histone protein modifications are dynamic -- Level 3: Noncoding RNAs dominate the transcriptomes -- Levels 1, 2, and 3 cross-talk in epigenetic landscapes -- The toolbox: a set of advanced methods -- Genome and epigenome editing -- High-throughput imaging-screening -- Functional and applied aspects of systems biology -- Breeding model and reproduction control -- What can we learn from history? -- Reproduction control -- Fish health -- Bacterial infections and vaccine development -- Viral infection genomics -- Husbandry and nutrition -- Husbandry guidelines -- Nutritional omics -- Effects of stressors -- Zebrafish embryo toxicity test. , High-throughput screening and transgenic reporter fish -- Transgenerational effects -- Future directions future perspectives -- Acknowledgments -- References -- 8 - Current status in other finfish species -- Introduction -- Transcriptome resources and their main characteristics in gilthead seabream and soles -- Current genetic maps and genome drafts in gilthead seabream and soles -- Genetic maps and QTLs -- Toward the first draft of Senegalese sole genome -- Superscaffolds as putative chromosomes of Senegalese sole -- Databases for genomic resources in gilthead seabream and soles -- Functional and applied aspects using genomic approaches -- Transcriptomic studies in larval stages and metamorphosis -- Transcriptomic studies in nutrition -- Transcriptomic studies in health and welfare -- Future directions -- Concluding remarks -- Acknowledgments -- References -- 9 - Molluscs -- Life history and biology -- Genomes: diversity, structure, and organization -- Functional and applied aspects -- Growth -- Immune function -- Reproduction -- Future directions -- References -- 10 - Genomics in the common carp -- Common carp biology and aquaculture -- The genome: diversity, structure, organization, and evolution -- BAC-based genomics -- Tetraploidized genome: genome structure, organization, and whole genome duplication -- Genetic diversity studies -- Genome evolution and gene fate of tetraploidization -- Functional genomics research and applications in the common carp -- Skin color -- Immunity and disease resistance -- Response to environmental stress -- Toxicology -- Genetic tool development -- Future directions -- Toward the perfect genome: updating the genome and annotation -- Construction of comprehensive genome databases -- Further develop genome resources from diverse populations -- Unveiling the genetic basis of important traits for breeding applications. , Concluding remarks.
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  • 2
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    PANGAEA
    In:  Supplement to: Mittermayer, Felix H; Stiasny, Martina H; Clemmesen, Catriona; Bayer, Till; Puvanendran, Velmurugu; Chierici, Melissa; Jentoft, Sissel; Reusch, Thorsten B H (2019): Transcriptome profiling reveals exposure to predicted end-of-century ocean acidification as a stealth stressor for Atlantic cod larvae. Scientific Reports, 9(1), https://doi.org/10.1038/s41598-019-52628-1
    Publikationsdatum: 2024-01-26
    Beschreibung: Exposure of larvea from Atlantic cod ( Gadus morhua) to predicted end-of-century ocean acidification levels. Dry weight was measured at 5 and 15 days-post-hatch For information on the experimental set-up please consult the material and methods section and the supplementary material.
    Schlagwort(e): Age; Experimental treatment; Gadus morhua, larvae, dry mass; Identification; Sample, optional label/labor no; Species; Standard deviation; Treatment: partial pressure of carbon dioxide
    Materialart: Dataset
    Format: text/tab-separated-values, 832 data points
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  • 3
    Publikationsdatum: 2024-03-15
    Beschreibung: Ocean acidification (OA), a direct consequence of increasing atmospheric CO2 concentration dissolving in ocean waters, is impacting many fish species. Little is known about the molecular mechanisms underlying the observed physiological impacts in fish. We used RNAseq to characterize the transcriptome of 3 different larval stages of Atlantic cod (Gadus morhua) exposed to simulated OA at levels (1179 µatm CO2) representing end-of-century predictions compared to controls (503 µatm CO2), which were shown to induce tissue damage and elevated mortality in G. morhua. Only few genes were differentially expressed in 6 and 13 days-post-hatching (dph) (3 and 16 genes, respectively), during a period when maximal mortality as a response to elevated pCO2 occurred. At 36 dph, 1413 genes were differentially expressed, most likely caused by developmental asynchrony between the treatment groups, with individuals under OA growing faster. A target gene analysis revealed only few genes of the universal and well-defined cellular stress response to be differentially expressed. We thus suggest that predicted ocean acidification levels constitute a “stealth stress” for early Atlantic cod larvae, with a rapid breakdown of cellular homeostasis leading to organismal death that was missed even with an 8-fold replication implemented in this study.
    Schlagwort(e): Age; Alkalinity, total; Animalia; Aragonite saturation state; Barents_Sea; Bicarbonate ion; Calcite saturation state; Calculated using seacarb after Nisumaa et al. (2010); Carbon, inorganic, dissolved; Carbonate ion; Carbonate system computation flag; Carbon dioxide; Chordata; Coast and continental shelf; Containers and aquaria (20-1000 L or 〈 1 m**2); EXP; Experiment; Fugacity of carbon dioxide (water) at sea surface temperature (wet air); Gadus morhua; Growth/Morphology; Identification; Laboratory experiment; Larvae, dry mass; Nekton; North Atlantic; OA-ICC; Ocean Acidification International Coordination Centre; Partial pressure of carbon dioxide, standard deviation; Partial pressure of carbon dioxide (water) at sea surface temperature (wet air); Pelagos; pH; Polar; Registration number of species; Salinity; Sample, optional label/labor no; Single species; Species; Temperature, water; Treatment; Type; Uniform resource locator/link to reference
    Materialart: Dataset
    Format: text/tab-separated-values, 2496 data points
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  • 4
    Publikationsdatum: 2022-05-25
    Beschreibung: Author Posting. © The Authors, 2005. This is the author's version of the work. It is posted here by permission of Elsevier B. V. for personal use, not for redistribution. The definitive version was published in Aquaculture 250 (2005): 471-479, doi:10.1016/j.aquaculture.2005.03.019.
    Beschreibung: The effect of exogenous growth hormone (GH) treatment on the growth of juvenile yellow perch (Perca flavescens) was investigated in four experiments. In the first two experiments, juvenile yellow perch were reared at either 13°C or 21°C, and injected weekly with bovine GH (bGH) at 0.1, 1.0 or 10.0 μg/g body weight for 84 days. No significant growth enhancement in GH-treated fish was measured in fish in either of the experiments. In the third experiment, juvenile yellow perch were treated with estradiol-17β (E2, 15 μg/g of diet), bGH (1.0 μg/g body weight) injected weekly or both hormones for 70 days at 21°C. E2 alone stimulated growth, but no further growth stimulation occurred in the E2 + bGH-treated fish. In addition, no growth enhancement was found in fish treated with bGH alone. We measured no difference in serum insulin-like growth factor-I (IGF-I) levels between the treatment groups at 12 and 24 h after the final injection of GH; however, a drop in IGF-I levels after 24 h was observed. In a fourth study, the effect of recombinant yellow perch GH (rypGH, 0.2 or 1.0 μg/g body weight) injected weekly was evaluated in yellow perch juveniles. The fish were reared for 42 days at 18°C. Neither GH dosages improved growth compared to control-injected and non-injected fish. Taken together, the lack of effect of mammalian GH or rypGH in our experiments suggests (1) low binding affinity between these hormones and the GH receptor in yellow perch, (2) that the endogenous GH levels were already at biologically maximal levels or (3) that other endocrine factors are needed in order for GH to promote yellow perch growth. The reduction in IGF-I levels 24 h after handling suggests a negative effect of handling stress on the GH-IGF-I axis in yellow perch.
    Beschreibung: This work was supported by the University of Wisconsin-Madison College of Agricultural and Life Sciences and School of Natural Resources; the Wisconsin Department of Natural Resources; the University of Wisconsin Sea Grant College Program, National Oceanic and Atmospheric Administration, US Department of Commerce; the State of Wisconsin (Federal Grant NA46RG0481, Project No. R/AQ-38); and the USDA NOAA Project R/A-05-99, grant #NA86RG0048 to FG and SR. This study was also funded by the Norwegian Research Council (NFR).
    Schlagwort(e): Yellow perch ; GH ; Growth ; IGF-I ; E2
    Repository-Name: Woods Hole Open Access Server
    Materialart: Preprint
    Format: 112359 bytes
    Format: application/pdf
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  • 5
    Publikationsdatum: 2020-02-06
    Beschreibung: Knowledge of the range and chronology of historic trade and long-distance transport of natural resources is essential for determining the impacts of past human activities on marine environments. However, the specific biological sources of imported fauna are often difficult to identify, in particular if species have a wide spatial distribution and lack clear osteological or isotopic differentiation between populations. Here, we report that ancient fish-bone remains, despite being porous, brittle, and light, provide an excellent source of endogenous DNA (15–46%) of sufficient quality for whole-genome reconstruction. By comparing ancient sequence data to that of modern specimens, we determine the biological origin of 15 Viking Age (800–1066 CE) and subsequent medieval (1066–1280 CE) Atlantic cod (Gadus morhua) specimens from excavation sites in Germany, Norway, and the United Kingdom. Archaeological context indicates that one of these sites was a fishing settlement for the procurement of local catches, whereas the other localities were centers of trade. Fish from the trade sites show a mixed ancestry and are statistically differentiated from local fish populations. Moreover, Viking Age samples from Haithabu, Germany, are traced back to the North East Arctic Atlantic cod population that has supported the Lofoten fisheries of Norway for centuries. Our results resolve a long-standing controversial hypothesis and indicate that the marine resources of the North Atlantic Ocean were used to sustain an international demand for protein as far back as the Viking Age.
    Materialart: Article , PeerReviewed
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  • 6
    Publikationsdatum: 2023-02-08
    Beschreibung: A fundamental problem for the evolution of pregnancy, the most specialized form of parental investment among vertebrates, is the rejection of the nonself-embryo. Mammals achieve immunological tolerance by down-regulating both major histocompatibility complex pathways (MHC I and II). Although pregnancy has evolved multiple times independently among vertebrates, knowledge of associated immune system adjustments is restricted to mammals. All of them (except monotremata) display full internal pregnancy, making evolutionary reconstructions within the class mammalia meaningless. Here, we study the seahorse and pipefish family (syngnathids) that have evolved male pregnancy across a gradient from external oviparity to internal gestation. We assess how immunological tolerance is achieved by reconstruction of the immune gene repertoire in a comprehensive sample of 12 seahorse and pipefish genomes along the “male pregnancy” gradient together with expression patterns of key immune and pregnancy genes in reproductive tissues. We found that the evolution of pregnancy coincided with a modification of the adaptive immune system. Divergent genomic rearrangements of the MHC II pathway among fully pregnant species were identified in both genera of the syngnathids: The pipefishes (Syngnathus) displayed loss of several genes of the MHC II pathway while seahorses (Hippocampus) featured a highly divergent invariant chain (CD74). Our findings suggest that a trade-off between immunological tolerance and embryo rejection accompanied the evolution of unique male pregnancy. That pipefishes survive in an ocean of microbes without one arm of the adaptive immune defense suggests a high degree of immunological flexibility among vertebrates, which may advance our understanding of immune-deficiency diseases.
    Materialart: Article , PeerReviewed , info:eu-repo/semantics/article
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  • 7
    Publikationsdatum: 2022-01-31
    Beschreibung: Genetic divergence among populations arises through natural selection or drift and is counteracted by connectivity and gene flow. In sympatric populations, isolating mechanisms are thus needed to limit the homogenizing effects of gene flow to allow for adaptation and speciation. Chromosomal inversions act as an important mechanism maintaining isolating barriers, yet their role in sympatric populations and divergence with gene flow is not entirely understood. Here, we revisit the question of whether inversions play a role in the divergence of connected populations of the marine fish Atlantic cod (Gadus morhua), by exploring a unique data set combining whole-genome sequencing data and behavioural data obtained with acoustic telemetry. Within a confined fjord environment, we find three genetically differentiated Atlantic cod types belonging to the oceanic North Sea population, the western Baltic population and a local fjord-type cod. Continuous behavioural tracking over 4 year revealed temporally stable sympatry of these types within the fjord. Despite overall weak genetic differentiation consistent with high levels of gene flow, we detected significant frequency shifts of three previously identified inversions, indicating an adaptive barrier to gene flow. In addition, behavioural data indicated that North Sea cod and individuals homozygous for the LG12 inversion had lower fitness in the fjord environment. However, North Sea and fjord-type cod also occupy different depths, possibly contributing to prezygotic reproductive isolation and representing a behavioural barrier to gene flow. Our results provide the first insights into a complex interplay of genomic and behavioural isolating barriers in Atlantic cod and establish a new model system towards an understanding of the role of genomic structural variants in adaptation and diversification.
    Materialart: Article , PeerReviewed , info:eu-repo/semantics/article
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  • 8
    Publikationsdatum: 2022-01-31
    Beschreibung: Atlantic cod (Gadus morhua) is a species of great ecological and economical importance in the Baltic Sea. Here, two genetically differentiated stocks, the western and the eastern Baltic cod, display substantial mechanical mixing, hampering our understanding of cod ecology and impeding stock assessments and management. Based on whole-genome re-sequencing data from reference samples obtained from the study area, we designed two different panels of Single Nucleotide Polymorphisms markers (SNPs), which take into account the exceptional genome architecture of cod. A minimum panel of 20 diagnostic SNPs and an extended panel (20 diagnostic and 18 biologically informative SNPs, 38 in total) were developed and validated to distinguish unambiguously between the western and the eastern Baltic cod stocks and to enable studies of local adaptation to the specific environment in the Baltic Sea, respectively. We tested both panels on cod sampled from the southern Baltic Sea (n = 603) caught in 2015 and 2016. Genotyping results showed that catches from the mixing zone in the Arkona Sea, were composed of similar proportions of individuals of the western and the eastern stock. Catches from adjacent areas to the east, the Bornholm Basin and Gdańsk Deep, were exclusively composed of eastern Baltic cod, whereas catches from adjacent western areas (Belt Sea and Öresund) were composed of western Baltic cod. Interestingly, the two Baltic cod stocks showed strong genetic differences at loci associated with life-history trait candidate genes, highlighting the species’ potential for ecological adaptation even at small geographical scales. The minimum and the extended panel of SNP markers presented in this study provide powerful tools for future applications in research and fisheries management to further illuminate the mixing dynamics of cod in the Baltic Sea and to better understand Baltic cod ecology.
    Materialart: Article , PeerReviewed
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  • 9
    Publikationsdatum: 2024-02-07
    Beschreibung: The unique male pregnancy in pipefishes and seahorses ranges from basic attachment (pouch-less species: Nerophinae) of maternal eggs to specialized internal gestation in pouched species (e.g. Syngnathus and Hippocampus) with many transitions in between. Due to this diversity, male pregnancy offers a unique platform for assessing physiological and molecular adaptations in pregnancy evolution. These insights will contribute to answering long-standing questions of why and how pregnancy evolved convergently in so many vertebrate systems. To understand the molecular congruencies and disparities in male pregnancy evolution, we compared transcriptome-wide differentially expressed genes in four syngnathid species, at four pregnancy stages (nonpregnant, early, late and parturition). Across all species and pregnancy forms, metabolic processes and immune dynamics defined pregnancy stages, especially pouched species shared expression features akin to female pregnancy. The observed downregulation of adaptive immune genes in early-stage pregnancy and its reversed upregulation during late/parturition in pouched species, most notably in Hippocampus, combined with directionless expression in the pouch-less species, suggests immune modulation to be restricted to pouched species that evolved placenta-like systems. We propose that increased foeto-paternal intimacy in pouched syngnathids commands immune suppression processes in early gestation, and that the elevated immune response during parturition coincides with pouch opening and reduced progeny reliance. Immune response regulation in pouched species supports the recently described functional MHC II pathway loss as critical in male pregnancy evolution. The independent co-option of similar genes and pathways both in male and female pregnancy highlights immune modulation as crucial for the evolutionary establishment of pregnancy.
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  • 10
    Publikationsdatum: 2024-02-07
    Beschreibung: Teleost adaptive immune systems have evolved with more flexibility than previously assumed. A particularly enigmatic system to address immune system modifications in the evolutionary past is represented by the Syngnathids, the family of pipefishes, seahorses and seadragons. These small fishes with their unique male pregnancy have lost the spleen as an important immune organ as well as a functional major histocompatibility class II (MHC II) pathway. How these evolutionary changes have impacted immune cell population dynamics have up to this point remained unexplored. Here, we present the first immune cell repertoire characterization of a syngnathid fish (Syngnathus typhle) using single-cell transcriptomics. Gene expression profiles of individual cells extracted from blood and head-kidney clustered in twelve putative cell populations with eight belonging to those with immune function. Upregulated cell marker genes identified in humans and teleosts were used to define cell clusters. While the suggested loss of CD4+ T-cells accompanied the loss of the MHC II pathway was supported, the upregulation of specific subtype markers within the T-cell cluster indicates subpopulations of regulatory T-cells (il2rb) and cytotoxic T-cells (gzma). Utilizing single-cell RNA sequencing this report is the first to characterize immune cell populations in syngnathids and provides a valuable foundation for future cellular classification and experimental work within the lineage.
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