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Exploring a Nonmodel Teleost Genome Through RAD Sequencing—Linkage Mapping in Common Pandora, Pagellus erythrinus and Comparative Genomic Analysis

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      Abstract

      Common pandora ( Pagellus erythrinus) is a benthopelagic marine fish belonging to the teleost family Sparidae, and a newly recruited species in Mediterranean aquaculture. The paucity of genetic information relating to sparids, despite their growing economic value for aquaculture, provides the impetus for exploring the genomics of this fish group. Genomic tool development, such as genetic linkage maps provision, lays the groundwork for linking genotype to phenotype, allowing fine-mapping of loci responsible for beneficial traits. In this study, we applied ddRAD methodology to identify polymorphic markers in a full-sib family of common pandora. Employing the Illumina MiSeq platform, we sampled and sequenced a size-selected genomic fraction of 99 individuals, which led to the identification of 920 polymorphic loci. Downstream mapping analysis resulted in the construction of 24 robust linkage groups, corresponding to the karyotype of the species. The common pandora linkage map showed varying degrees of conserved synteny with four other teleost genomes, namely the European seabass ( Dicentrarchus labrax), Nile tilapia ( Oreochromis niloticus), stickleback ( Gasterosteus aculeatus), and medaka ( Oryzias latipes), suggesting a conserved genomic evolution in Sparidae. Our work exploits the possibilities of genotyping by sequencing to gain novel insights into genome structure and evolution. Such information will boost the study of cultured species and will set the foundation for a deeper understanding of the complex evolutionary history of teleosts.

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        MAFFT Multiple Sequence Alignment Software Version 7: Improvements in Performance and Usability

        We report a major update of the MAFFT multiple sequence alignment program. This version has several new features, including options for adding unaligned sequences into an existing alignment, adjustment of direction in nucleotide alignment, constrained alignment and parallel processing, which were implemented after the previous major update. This report shows actual examples to explain how these features work, alone and in combination. Some examples incorrectly aligned by MAFFT are also shown to clarify its limitations. We discuss how to avoid misalignments, and our ongoing efforts to overcome such limitations.
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          Circos: an information aesthetic for comparative genomics.

          We created a visualization tool called Circos to facilitate the identification and analysis of similarities and differences arising from comparisons of genomes. Our tool is effective in displaying variation in genome structure and, generally, any other kind of positional relationships between genomic intervals. Such data are routinely produced by sequence alignments, hybridization arrays, genome mapping, and genotyping studies. Circos uses a circular ideogram layout to facilitate the display of relationships between pairs of positions by the use of ribbons, which encode the position, size, and orientation of related genomic elements. Circos is capable of displaying data as scatter, line, and histogram plots, heat maps, tiles, connectors, and text. Bitmap or vector images can be created from GFF-style data inputs and hierarchical configuration files, which can be easily generated by automated tools, making Circos suitable for rapid deployment in data analysis and reporting pipelines.
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            Author and article information

            Affiliations
            [* ]Institute of Marine Biology, Biotechnology and Aquaculture, Hellenic Centre for Marine Research, Heraklion, 71500, Greece
            []Department of Biology, University of Crete, Heraklion, 70013, Greece
            []Institute of Aquaculture, School of Natural Sciences, University of Stirling, Scotland, FK9 4LA, United Kingdom
            [§ ]Laboratory of Agrobiotechnology and Inspection of Agricultural Products, Department of Agricultural Technology, School of Agricultural Technology Food Technology and Nutrition, Alexander Technological Educational Institute of Thessaloniki, Sindos, 57400, Greece
            Author notes
            [1 ]Corresponding author: Institute of Marine Biology, Biotechnology and Aquaculture, Hellenic Centre for Marine Research, Gournes Thalassocosmos, Gournes Pediados, Heraklion, 71003, Greece. E-mail: tsigeno@ 123456hcmr.gr
            Journal
            G3 (Bethesda)
            Genetics
            G3: Genes, Genomes, Genetics
            G3: Genes, Genomes, Genetics
            G3: Genes, Genomes, Genetics
            G3: Genes|Genomes|Genetics
            Genetics Society of America
            2160-1836
            28 December 2015
            March 2016
            : 6
            : 3
            : 509-519
            26715088 4777114 GGG_023432 10.1534/g3.115.023432
            Copyright © 2016 Manousaki et al.

            This is an open-access article distributed under the terms of the Creative Commons Attribution 4.0 International License ( http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.

            Counts
            Figures: 5, Tables: 2, Equations: 0, References: 56, Pages: 11
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            Investigations

            Genetics

            aquaculture, synteny, ddrad, rad sequencing, sparidae

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