Whole genome sequencing of turbot (Scophthalmus maximus; Pleuronectiformes): a fish adapted to demersal life
| Autor: | Beatriz Novoa, José Antonio Álvarez-Dios, Jèssica Gómez-Garrido, Antonio Figueras, Patricia Pereiro, Laia Carreté, Marina Marcet-Houben, Toni Gabaldón, José Luis García, J. L. Abal-Fabeiro, Paulino Martínez, Anna Vlasova, Ivo Gut, Antonio Hermoso-Pulido, Carlos Fernández, Antonio Gómez-Tato, Diego Robledo, Ana Viñas, André Corvelo, Carmen Bouza, Xulio Maside, Tyler Alioto, Beatriz Galán, Juan A. Rubiolo, Xoana Taboada, Miguel Hermida, Marta Gut, Roderic Guigó, Xabier Bello, Belén G. Pardo, Gabriel Forn-Cuní |
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| Přispěvatelé: | Universidade de Santiago de Compostela. Centro de Investigación en Medicina Molecular e Enfermidades Crónicas, Universidade de Santiago de Compostela. Departamento de Anatomía Patolóxica e Ciencias Forenses, Universidade de Santiago de Compostela. Departamento de Matemática Aplicada, Universidade de Santiago de Compostela. Departamento de Matemáticas, Universidade de Santiago de Compostela. Departamento de Zooloxía, Xenética e Antropoloxía Física, Ministerio de Economía y Competitividad (España) |
| Rok vydání: | 2016 |
| Předmět: |
Fish Proteins
0301 basic medicine Candidate gene Genome evolution ved/biology.organism_classification_rank.species genome evolution Percomorpha Genome sequencing Genome Evolution Molecular Open Reading Frames 03 medical and health sciences Genetic map Flatfish Flatfishes/genetics Genetics Animals genetic map Fish Proteins/genetics Molecular Biology Repetitive Sequences Nucleic Acid Synteny Whole genome sequencing biology ved/biology Molecular Sequence Annotation 04 agricultural and veterinary sciences General Medicine Turbot Full Papers productive traits biology.organism_classification Adaptation Physiological turbot genome sequencing 030104 developmental biology Productive traits Flatfishes 040102 fisheries 0401 agriculture forestry and fisheries |
| Zdroj: | DNA Research: An International Journal for Rapid Publication of Reports on Genes and Genomes Figueras, A, Robledo, D, Corvelo, A, Hermida, M, Pereiro, P, Rubiolo, J A, Gómez-Garrido, J, Carreté, L, Bello, X, Gut, M, Gut, I G, Marcet-Houben, M, Forn-Cuní, G, Galán, B, García, J L, Abal-Fabeiro, J L, Pardo, B G, Taboada, X, Fernández, C, Vlasova, A, Hermoso-Pulido, A, Guigó, R, Álvarez-Dios, J A, Gómez-Tato, A, Viñas, A, Maside, X, Gabaldón, T, Novoa, B, Bouza, C, Alioto, T & Martínez, P 2016, ' Whole genome sequencing of turbot (Scophthalmus maximus; Pleuronectiformes) : a fish adapted to demersal life ', DNA Research, vol. 23, no. 3, pp. 181-92 . https://doi.org/10.1093/dnares/dsw007 Recercat. Dipósit de la Recerca de Catalunya instname Minerva: Repositorio Institucional de la Universidad de Santiago de Compostela Universidad de Santiago de Compostela (USC) Minerva. Repositorio Institucional de la Universidad de Santiago de Compostela Digital.CSIC. Repositorio Institucional del CSIC |
| ISSN: | 1756-1663 1340-2838 |
| DOI: | 10.1093/dnares/dsw007 |
| Popis: | 12 páginas, 5 figuras.-- Antonio Figueras ... et al.-- This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/4.0/), which permits non-commercial re-use, distribution, and reproduction in any medium, provided the original work is properly cited 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 This work was funded by the Spanish Government: projects Consolider Ingenio: Aquagenomics (CSD2007-00002) and Metagenoma de la Península Ibérica (CSD2007-00005), Ministerio de Economía y Competitividad and European Regional Development Funds (AGL2012-35904), and Ministerio de Economía y Competitividad (AGL2014-51773 and AGL2014-57065-R); and Local Government Xunta de Galicia (GRC2014/010). P.P. and D.R. gratefully acknowledge the Spanish Ministerio de Educación for their FPU fellowships (AP2010-2408, AP2012-0254). Funding to pay the Open Access publication charges for this article was provided by the Ministerio de Economía y Competitividad (AGL2014-51773) and Xunta de Galicia (GRC2014/010) |
| Databáze: | OpenAIRE |
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