title: Integrating genomic resources of flatfish (Pleuronectiformes) to boost aquaculture production.
abstract: Flatfish have a high market acceptance thus representing a profitable aquaculture production. The main farmed species is the turbot (Scophthalmus maximus) followed by Japanese flounder (Paralichthys olivaceous) and tongue sole (Cynoglossus semilaevis), but other species like Atlantic halibut (Hippoglossus hippoglossus), Senegalese sole (Solea senegalensis) and common sole (Solea solea) also register an important production and are very promising for farming. Important genomic resources are available for most of these species including whole genome sequencing projects, genetic maps and transcriptomes. In this work, we integrate all available genomic information of these species within a common framework, taking as reference the whole assembled genomes of turbot and tongue sole (>210× coverage). New insights related to the genetic basis of productive traits and new data useful to understand the evolutionary origin and diversification of this group were obtained. Despite a general 1:1 chromosome syntenic relationship between species, the comparison of turbot and tongue sole genomes showed huge intrachromosomic reorganizations. The integration of available mapping information supported specific chromosome fusions along flatfish evolution and facilitated the comparison between species of previously reported genetic associations for productive traits. When comparing transcriptomic resources of the six species, a common set of ~2500 othologues and ~150 common miRNAs were identified, and specific sets of putative missing genes were detected in flatfish transcriptomes, likely reflecting their evolutionary diversification.
authors.affiliation: Department of Zoology, Genetics and Physical Anthropology, Faculty of Biology (CIBUS), Universidade de Santiago de Compostela, 15782 Santiago de Compostela, Spain.
authors.forename: Diego
authors.initials: D
authors.lastname: Robledo
authors.affiliation: Department of Zoology, Genetics and Physical Anthropology, Faculty of Veterinary, Universidade de Santiago de Compostela, 27002 Lugo, Spain.
authors.forename: Miguel
authors.initials: M
authors.lastname: Hermida
authors.affiliation: Department of Zoology, Genetics and Physical Anthropology, Faculty of Veterinary, Universidade de Santiago de Compostela, 27002 Lugo, Spain.
authors.forename: Juan A
authors.initials: JA
authors.lastname: Rubiolo
authors.affiliation: Department of Zoology, Genetics and Physical Anthropology, Faculty of Veterinary, Universidade de Santiago de Compostela, 27002 Lugo, Spain.
authors.forename: Carlos
authors.initials: C
authors.lastname: Fernández
authors.affiliation: Department of Zoology, Genetics and Physical Anthropology, Faculty of Veterinary, Universidade de Santiago de Compostela, 27002 Lugo, Spain.
authors.forename: Andrés
authors.initials: A
authors.lastname: Blanco
authors.affiliation: Department of Zoology, Genetics and Physical Anthropology, Faculty of Veterinary, Universidade de Santiago de Compostela, 27002 Lugo, Spain.
authors.forename: Carmen
authors.initials: C
authors.lastname: Bouza
authors.affiliation: Department of Zoology, Genetics and Physical Anthropology, Faculty of Veterinary, Universidade de Santiago de Compostela, 27002 Lugo, Spain. Electronic address: paulino.martinez@usc.es.
authors.forename: Paulino
authors.initials: P
authors.lastname: Martínez
mesh_terms: D000818:Animals; D017756:Aquaculture; D019295:Computational Biology; D019143:Evolution, Molecular; D005412:Flatfishes / Q000235:genetics*; D020869:Gene Expression Profiling; D016678:Genome / Q000235:genetics*; D023281:Genomics; D059014:High-Throughput Nucleotide Sequencing; D035683:MicroRNAs / Q000235:genetics*; D058977:Molecular Sequence Annotation; D010802:Phylogeny; D040641:Quantitative Trait Loci; D059467:Transcriptome
chemical_list: D035683:MicroRNAs
keywords: Aquaculture; Comparative mapping; Evolution; Genetic map; Genome; Pleuronectiformes; Transcriptome