title: Whole genome sequencing of turbot (Scophthalmus maximus; Pleuronectiformes): a fish adapted to demersal life.
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.
authors.affiliation: Instituto de Investigaciones Marinas (IIM), Consejo Superior de Investigaciones Científicas (CSIC), Vigo 36208, Spain antoniofigueras@iim.csic.es paulino.martinez@usc.es.
authors.forename: Antonio
authors.initials: A
authors.lastname: Figueras
authors.affiliation: Departamento de Xenética, Facultade de Bioloxía (CIBUS), Universidade de Santiago de Compostela, Santiago de Compostela 15782, Spain.
authors.forename: Diego
authors.initials: D
authors.lastname: Robledo
authors.affiliation: 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.
authors.forename: André
authors.initials: A
authors.lastname: Corvelo
authors.affiliation: Departamento de Xenética, Facultade de Veterinaria, Universidade de Santiago de Compostela, Lugo 27002, Spain.
authors.forename: Miguel
authors.initials: M
authors.lastname: Hermida
authors.affiliation: Instituto de Investigaciones Marinas (IIM), Consejo Superior de Investigaciones Científicas (CSIC), Vigo 36208, Spain.
authors.forename: Patricia
authors.initials: P
authors.lastname: Pereiro
authors.affiliation: Departamento de Xenética, Facultade de Veterinaria, Universidade de Santiago de Compostela, Lugo 27002, Spain.
authors.forename: Juan A
authors.initials: JA
authors.lastname: Rubiolo
authors.affiliation: Centre Nacional d'Anàlisi Genòmica (CNAG-CRG), Centre de Regulació Genómica, Parc Científic de Barcelona, Barcelona 08028, Spain.
authors.forename: Jèssica
authors.initials: J
authors.lastname: Gómez-Garrido
authors.affiliation: Centre Nacional d'Anàlisi Genòmica (CNAG-CRG), Centre de Regulació Genómica, Parc Científic de Barcelona, Barcelona 08028, Spain.
authors.forename: Laia
authors.initials: L
authors.lastname: Carreté
authors.affiliation: 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.
authors.forename: Xabier
authors.initials: X
authors.lastname: Bello
authors.affiliation: Centre Nacional d'Anàlisi Genòmica (CNAG-CRG), Centre de Regulació Genómica, Parc Científic de Barcelona, Barcelona 08028, Spain.
authors.forename: Marta
authors.initials: M
authors.lastname: Gut
authors.affiliation: Centre Nacional d'Anàlisi Genòmica (CNAG-CRG), Centre de Regulació Genómica, Parc Científic de Barcelona, Barcelona 08028, Spain.
authors.forename: Ivo Glynne
authors.initials: IG
authors.lastname: Gut
authors.affiliation: Centre Nacional d'Anàlisi Genòmica (CNAG-CRG), Centre de Regulació Genómica, Parc Científic de Barcelona, Barcelona 08028, Spain.
authors.forename: Marina
authors.initials: M
authors.lastname: Marcet-Houben
authors.affiliation: Instituto de Investigaciones Marinas (IIM), Consejo Superior de Investigaciones Científicas (CSIC), Vigo 36208, Spain.
authors.forename: Gabriel
authors.initials: G
authors.lastname: Forn-Cuní
authors.affiliation: Centro de Investigaciones Biológicas (CIB), Consejo Superior de Investigaciones Científicas, Madrid 28040, Spain.
authors.forename: Beatriz
authors.initials: B
authors.lastname: Galán
authors.affiliation: Centro de Investigaciones Biológicas (CIB), Consejo Superior de Investigaciones Científicas, Madrid 28040, Spain.
authors.forename: José Luis
authors.initials: JL
authors.lastname: García
authors.affiliation: 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.
authors.forename: José Luis
authors.initials: JL
authors.lastname: Abal-Fabeiro
authors.affiliation: Departamento de Xenética, Facultade de Veterinaria, Universidade de Santiago de Compostela, Lugo 27002, Spain.
authors.forename: Belen G
authors.initials: BG
authors.lastname: Pardo
authors.affiliation: Departamento de Xenética, Facultade de Bioloxía (CIBUS), Universidade de Santiago de Compostela, Santiago de Compostela 15782, Spain.
authors.forename: Xoana
authors.initials: X
authors.lastname: Taboada
authors.affiliation: Departamento de Xenética, Facultade de Veterinaria, Universidade de Santiago de Compostela, Lugo 27002, Spain.
authors.forename: Carlos
authors.initials: C
authors.lastname: Fernández
authors.affiliation: Centre Nacional d'Anàlisi Genòmica (CNAG-CRG), Centre de Regulació Genómica, Parc Científic de Barcelona, Barcelona 08028, Spain.
authors.forename: Anna
authors.initials: A
authors.lastname: Vlasova
authors.affiliation: Centre Nacional d'Anàlisi Genòmica (CNAG-CRG), Centre de Regulació Genómica, Parc Científic de Barcelona, Barcelona 08028, Spain.
authors.forename: Antonio
authors.initials: A
authors.lastname: Hermoso-Pulido
authors.affiliation: Centre Nacional d'Anàlisi Genòmica (CNAG-CRG), Centre de Regulació Genómica, Parc Científic de Barcelona, Barcelona 08028, Spain.
authors.forename: Roderic
authors.initials: R
authors.lastname: Guigó
authors.affiliation: Departamento de Matemática Aplicada, Facultade de Matemáticas, Universidade de Santiago de Compostela, 15782 Santiago de Compostela, Spain.
authors.forename: José Antonio
authors.initials: JA
authors.lastname: Álvarez-Dios
authors.affiliation: Departamento de Xeometría e Topoloxía, Facultade de Matemáticas, Universidade de Santiago de Compostela, 15782 Santiago de Compostela, Spain.
authors.forename: Antonio
authors.initials: A
authors.lastname: Gómez-Tato
authors.affiliation: Departamento de Xenética, Facultade de Bioloxía (CIBUS), Universidade de Santiago de Compostela, Santiago de Compostela 15782, Spain.
authors.forename: Ana
authors.initials: A
authors.lastname: Viñas
authors.affiliation: 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.
authors.forename: Xulio
authors.initials: X
authors.lastname: Maside
authors.affiliation: 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.
authors.forename: Toni
authors.initials: T
authors.lastname: Gabaldón
authors.affiliation: Instituto de Investigaciones Marinas (IIM), Consejo Superior de Investigaciones Científicas (CSIC), Vigo 36208, Spain.
authors.forename: Beatriz
authors.initials: B
authors.lastname: Novoa
authors.affiliation: Departamento de Xenética, Facultade de Veterinaria, Universidade de Santiago de Compostela, Lugo 27002, Spain.
authors.forename: Carmen
authors.initials: C
authors.lastname: Bouza
authors.affiliation: Centre Nacional d'Anàlisi Genòmica (CNAG-CRG), Centre de Regulació Genómica, Parc Científic de Barcelona, Barcelona 08028, Spain.
authors.forename: Tyler
authors.initials: T
authors.lastname: Alioto
authors.affiliation: Departamento de Xenética, Facultade de Veterinaria, Universidade de Santiago de Compostela, Lugo 27002, Spain antoniofigueras@iim.csic.es paulino.martinez@usc.es.
authors.forename: Paulino
authors.initials: P
authors.lastname: Martínez
mesh_terms: D000222:Adaptation, Physiological; D000818:Animals; D019143:Evolution, Molecular; D029941:Fish Proteins / Q000235:genetics; D005412:Flatfishes / Q000235:genetics*; D016678:Genome; D058977:Molecular Sequence Annotation; D016366:Open Reading Frames; D012091:Repetitive Sequences, Nucleic Acid
chemical_list: D029941:Fish Proteins
keywords: genetic map; genome evolution; genome sequencing; productive traits; turbot