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One of those organisms is Streblospiobenedicti, a segmented tube-dwelling benthic polychaete which displays offspring dimorphism and is being used to study the evolutionary consequences of larval life history. Using the BeadXPress Golden Gate assay Illumina , these SNPs were validated by genotyping individuals of different developmental stages, and 84 new SNP markers resulted effective for distinguishing between geographic and phenotypic populations of S.

Given the scarcity of genomic resources for marine polychaetes, this transcriptomic approach should be very suitable for standard population genetic analyses to study the molecular and regulatory mechanisms underlying their life-history variations. Transcriptome analyses are becoming more broadly available,particularly when genome sequences are not available.

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A transcriptome analysis was performed recently on the Atlantic herring Clupeaharengus , an abundant fish found in the pelagic zone of marine waters and a critical protein source both in Europe and North America. From the biological point of view,understanding the genetic structure of C. A few studies using isozyme loci, microsatellites and SNPrevealed noticeably low levels of genetic differentiation between geographically distant and morphologically distinct forms Ryman , Limborg et al.

This analysis was further developed through examination of the skeletal muscle mRNA to assemble a transcriptome and align genomic reads to the transcripts creating an "exome assembly" Lamichhaney et al, Using this methodology it was possible to identify important genetic markers for phenotypic variation in C. A more comprehensive transcriptome analysis of other C. The full genome sequence of this large genome,on the order of Mbp,may still be a major undertaking. SNP development using a combination of next-generation sequencing NGS and a high-throughput genotyping approach, however, has the potential to make the most of efficient use of cost and time by avoiding the costly and time-intensive laboratory stages involved in genomic work for population studies in the ocean.

The wide accessibility of NGS technologies has certainly found immediate application in model marine organisms sea urchin, the polychaete Platynereisdumerilii, Amphioxus and others. Their application to the ecology and evolutionary studies of non-model organisms is being met with growing interest.

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Similarly, an integrated genomic approach that includes the construction of cDNA libraries and the generation of a large EST set for Atlantic cod Gadusmorhua have been described Bowman et al. These tools and data represent a critical resource for Atlantic cod, a valuable marine species under-represented in genomic databases. Metagenomics and proteomics. With ground-breaking advances in metagenomic sequencing and proteomic technologies, the study and characterization of uncultured biological samples are becoming more and more practical,uncovering the compositions, functions and interactions occurring in microbial communities present in different environments.

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  • Faster sequencing technologies and the ability to sequence a broad spectrum of uncultured microbes sampled directly from their habitats are maturing and revolutionizing our view of the microbial world, along with our understanding of their effects on global processes such as carbon, nitrogen and sulfur biogeochemical cycles. Analysis of microbial communities using high throughput sequencing methods for the standard 16S ribosomal RNA gene and whole genome shotgun WGS sequencing is uncovering the unique organization and identity of bacterial, archaeal and viral communities in coastal and marine environments.

    Beyond the narrow description obtained from phylogenetic surveys generally using the ribosomal gene, fingerprinting approach to biodiversity, metagenomics provides access to the functional gene composition of whole microbial communities, resulting in more reliable and comprehensive studies Edwards et al. Whole genome sequencing has been used in the last decade to sequence entire coastal and marine ecosystems.

    Similarly, by sequencing a community of DNA from a very low diversity microbiotain acid mine drainage it was possible to applya whole genome assembler algorithm to assemble the long capillary sequencing reads with great accuracy Tyson et al. Applying similar technology and using a complex bioinformatics approach, the functional potential of oceanic microbial communities in the Sargasso Sea was explored Venter et al.

    Subsequent metagenomic studies Rusch et al. Along with metagenomics, in the past few years there has been an explosion in marine environmental proteomics, the large scale characterization of proteins recovered from different coastal and marine ecosystems. While the 16S rRNA data provide essential information about the species membershipof a sample and the metagenome sequences provide an account of all possible gene products in an environmental sample, proteomics is employed to determine protein expression profiles of microbial communities, greatly expanding our knowledge of marine microorganisms and their impact on the ocean.

    Ground-breaking research in environmental proteomics hasrevealed important associations between protein diversity and ecological function in microbial communities. Proteomics can be a useful tool in determining phylogenetic relationships and resolving important questions in metapopulation biology and adaptation review in Biron et al. High-resolution capillary liquid chromatography coupled to an LTQ mass spectrometer was used to build an accurate mass and time AMT tag library as a tool to analyze protein profiles of the marine alpha-proteobacterium Candidatus pelagibacterubique, and to identify adaptation mechanisms and differentially expressed proteins from the exponential and stationary growth phases Sowell et al.

    Most proteins found in greater abundance in the stationary phase were those involved in stress response, protein refolding, transcription regulation and mitigation of oxidative damage, suggesting that these adaptive responses are important for this alphabacterium's enduring survival under conditions of limited nutrients. The determination of proteomic variations of microorganisms in response to growth conditions has become a standard approach for discovering metabolic and regulatory processes Sowell et al, ; Schwalbach et al. The study of all the metabolites present within cells, tissues and organs, as well as at the population level, has become an indispensable tool that goes beyond simply cataloguing bioactive compounds.

    Metabolomics is yielding progress in studying variations in the abundance of proteins and their subsequent post-translational modifications; and asks broader biological questions such as how metabolites reflect and affect cell function and how the environment affects the biology of marine organisms.

    Both nuclear magnetic resonance NMR and mass spectrometry MS -based or a combination of the two are increasingly more widely used to perform high throughput profiling of metabolites, as well as to investigate interactions of marine organisms with their environment, or marine metabolomics Miller, Recently published advances in this field include studies on marine fish Zhang et al.

    Targeted metabolite profiling has also been described in harbor seals and porpoises to determine contamination by chlorinated and brominated compounds Weijs et al. Similarly, NMR-based metabolic profiles have been employed to determine the metabolites responsible for the variation in the metabolic profile of pathogenic Vibrio coralliilyticus under extreme natural environments Boroujerdi et al.

    Metabolomic applications show great potential for identifying physiological responses of marine species to their changing biotic and abiotic environments. They also provide a unique opportunity to gain insight into the mechanisms behind differential effects of closely related species as well as of individuals within the same species. In addition, metabolomics along with various modern 'omics' technologies and their applications to marine biology research are providing helpful information for understanding microbial ecosystems, along with biogeography and species diversity in the ocean.

    While most genomic and post-genomic applications to marine biodiversity research are still at an early stage, exciting and innovative methodologies are emerging to discover and comprehend life history stages and new species that would otherwise be difficult to identify with traditional taxonomic methods.

    One such technique is fast large scale DNA barcoding Hebert et al. Although of unquestionable value for species identification, taxonomic approaches based on phenotypic characters have limited efficiency for ambiguous taxonomic groups or for the identification of closely related species with subtle morphological differences. DNA barcoding uses mitochondrial cytochrome c oxidase subunit I sequences to identify any species unequivocally.

    For more challenging taxonomic groups, it is clear that DNA barcoding needs to be used alongside morphology-based identification systems and include a range of molecular identification strategies based on the analysis of homologous gene regions such as ribosomal RNA molecules 16S and 18S and the internal transcribed spacer region, ITS. To date, the efficacy of molecular barcoding is finding practical applications in many taxonomic groups, including marine species, giving additional evidence for the consistency and accessibility of DNA barcoding for identifying marine organisms.

    This is a fascinating technique that is likely to find many uses in ecological studies. The user-friendliness of DNA barcodes is also finding many practical applications in developing countries Cawthorn et al. Modern biotechnology and genomics have been used to reveal unexpected features of biodiversity in the oceans.

    The application of these technologies promises far-reaching social and economic benefits in worldwide aquaculture production as well. As it applies to aquaculture and fisheries, genomics is rapidly making headway with thousands of publications appearing every year, covering cutting edge topics related to aquaculture biotechnology, genomics, epigenomics and post-genomics applications in aquaculture nutrition, stress, health and reproduction, and many other areas.

    Sequencing projects

    Choosing selected examples,we will illustrate the impact of genomics on our current understanding of genome evolution and its potential implications directly related to key traits and infectious diseases in aquaculture. Studies of adaptive evolution in population genetics of marine fish and other invertebrates are providing valuable insights into local adaptation, response to climate change and ecological impact of selective harvesting and world fisheries. This kind of research, for example transcriptomics of clams Coppe et al.

    The availability of detailed clam transcriptomics has provided new perspectives in establishing the physiological role of various biochemical processes and of population response to environmental stress. Distinctive genes involved in development or adaptation to temperature changes could be used to acquire valuable information for fishery management surveys of clam beds.

    Salmon Salmosalar is one of the most extensively studied fish and an important model species for fish genetics and evolution.

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    For instance, recent applications of restriction site-associated DNA sequencing RAD-Seq have facilitated large-scale marker discovery and genotyping Houston et al. RAD markers are valuable for association and QTL mapping as well as for population genetics and evolutionary research. They present considerable advantages over other methods and are rapidly finding application in SNP discovery and genotyping studies in non-model organisms, where they can be used in genotype-phenotype association mapping, population genetics and scaffolding genome assemblies through linkage mapping Baxter et al.

    Next Generation Sequencing

    SNP arrays have been successfully used in the assessment of population genetic structure in salmon, facilitating a better understanding of the molecular basis of adaptation to a wide range of geographical environments Bourret et al. Furthermore, some karyotype differences between European and North American Atlantic salmon via chromosomal rearrangements have been identified Brenna-Hansen et al.

    These applications may have a major impact on the aquaculture industry by providing genomic information on salmon production traits relevant to industrial development as well as for improved assessments of the sustainability of wild fish populations. Without a doubt, SNPs are becoming key markers of choice for genome research and in genetic improvement programs. Because of their practical use in the analysis of trait-genotype associations, their application in aquaculture is becoming central. Similarly, as more sequence information becomes available for marine species, other markers are increasingly being applied in aquaculture genome research.

    Having well-established genetic linkage maps at handis the basis for further genome scans for Quantitative Trait Loci, QTL, to study traits of great relevance in aquaculture. Genome-wide association studies GWAS have contributed significantly to the field in the past decade.

    GWAS examine the association between widespread genetic variants and specific traits phenotypes , usually quantitative, in the genome, transcriptome or proteome. Currently SNPs are frequently the first choice because of their considerable genome coverage, throughput of assay and quality assurance. Recent progress in SNP technology for marine species now facilitates genome-wide association studies GWAS in aquaculture to detect and pin down candidate genes for quantitative traits in various marine species.

    However, due to the shortage of SNP genotyping arrays, the first GWAS for quantitative traits in fish, for example, have only recently been published. Nevertheless, the number of genetic and biochemical processes that have been identified to explain diseases and immunity has not increased much. While QTL mapping is considered a powerful method to identify regions of the genome that co-segregate with a given trait F2 populations , a limitation is that only allelic diversity that segregates between the parents of the particular F2 cross can be assayed.

    In GWAS, on the other hand, after identifying the phenotypes of interest, it provides insights into the genetic architecture of the trait, allowing informed choice for QTL analysis and suggesting candidates for mutagenesis and transgenics. Given the most recent advances in high throughput genotyping technologies, GWAS may also stimulate the efficiency of breeding and selection in aquaculture.

    Moreover, epigenetic features such as methyl at ion and his tone deacetylation will soon be expanded in GWAS.

    The potentially negative impact on the gene pool of wild fish resulting from the unintended introduction of farmed fish can be addressed through the use of SNPs and microarrays. SNPs are now the principal tools for monitoring the interactions between natural and cultured fish populations. Providing expression information for thousands of genes simultaneously, DNA microarrays are having a profound impact on functional genomics research in marine organisms, including Atlantic salmon and common carp Rise et al.

    More recently NGS methods are being used to identify markers useful for population screening of variations in wild and farmed fishes Vera et al. Similarly, emerging NGS methods have been employed to detect mislabeling and prevent species substitution on the commercial market in a variety of settings and in a range of products. For instance, pyrosequencing has been successfully used in high-throughput identification of seafood species in different products and in species-specific PCR assays or microarrays.

    Furthermore, coupling DNA barcoding with high-throughput NGS technologies is currently being implemented in biomonitoring programs and conservation studies Hajibabaei et al. Advances in high-throughput proteomics now make it possible to compare protein content between complex biological systems. This " Frontiers in Livestock Genomics " Research Topic highlights the opportunities offered by recent develop-ments in the field of genomics, and in particular high-throughput sequencing, to contribute to addressing these challenges, with a focus on selective breeding programmes.

    Encouragingly, annual genetic gains reported for aquatic species are in general substantially higher than that of terres-trial farm animals Gjedrem et al.

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    However, the status of breeding pro-grams and the level of technology used for aquatic species production are wide-ranging, from use of wild seed stocks through to family-based selection incorporating genomic tools. In contrast, despite the global importance of mollusc species for aquaculture, few selec-tive breeding programmes exist and the state of genomic tools and knowledge for these species is typically lacking Astorga, Genomics resources such as whole genome reference sequences, high-density SNP genotyp-ing arrays and genotyping-by-sequencing are in development for several aquaculture species.

    Fuller characterisation of these resources is underway and is resulting in improved fundamen-tal knowledge of the genome structure and biology, highlighted in this issue by the analysis of repeat elements in the Asian sea bass genome Kuznetsova et al.

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    These resources will provide powerful tools for the research community and will aid in the determination of the genetic factors involved in the regulation of complex traits. Genomics in aquaculture rainbow trout Ali et al.