title: Whole genome semiconductor based sequencing of farmed European sea bass (Dicentrarchus labrax) Mediterranean genetic stocks using a DNA pooling approach.
abstract: European sea bass (Dicentrarchus labrax) is an important marine species for commercial and sport fisheries and aquaculture production. Recently, the European sea bass genome has been sequenced and assembled. This resource can open new opportunities to evaluate and monitor variability and identify variants that could contribute to the adaptation to farming conditions. In this work, two DNA pools constructed from cultivated European sea bass were sequenced using a next generation semiconductor sequencing approach based on Ion Proton sequencer. Using the first draft version of the D. labrax genome as reference, sequenced reads obtained a total of about 1.6 million of single nucleotide polymorphisms (SNPs), spread all over the chromosomes. Transition/transversion (Ti/Tv) was equal to 1.28, comparable to what was already reported in Salmon species. A pilot homozygosity analysis across the D. labrax genome using DNA pool sequence datasets indicated that this approach can identify chromosome regions with putative signatures of selection, including genes involved in ion transport and chloride channel functions, amino acid metabolism and circadian clock and related neurological systems. This is the first study that reported genome wide polymorphisms in a fish species obtained with the Ion Proton sequencer. Moreover, this study provided a methodological approach for selective sweep analysis in this species.
authors.affiliation: Department of Agricultural and Food Sciences, Division of Animal Sciences, University of Bologna, Viale Fanin 46, 40127 Bologna, Italy.
authors.forename: Francesca
authors.initials: F
authors.lastname: Bertolini
authors.affiliation: Department of Agricultural and Food Sciences, Division of Animal Sciences, University of Bologna, Viale Fanin 46, 40127 Bologna, Italy.
authors.forename: Claudia
authors.initials: C
authors.lastname: Geraci
authors.affiliation: Department of Agricultural and Food Sciences, Division of Animal Sciences, University of Bologna, Viale Fanin 46, 40127 Bologna, Italy.
authors.forename: Giuseppina
authors.initials: G
authors.lastname: Schiavo
authors.affiliation: Department of Agricultural and Forestry Sciences, University of Palermo, Viale delle Scienze, 90128 Palermo, Italy.
authors.forename: Maria Teresa
authors.initials: MT
authors.lastname: Sardina
authors.affiliation: Department of Veterinary Medicine, Division of Animal Production, University of Messina, Polo Universitario dell'Annunziata, 98168 Messina, Italy.
authors.forename: Vincenzo
authors.initials: V
authors.lastname: Chiofalo
authors.affiliation: Department of Agricultural and Food Sciences, Division of Animal Sciences, University of Bologna, Viale Fanin 46, 40127 Bologna, Italy. Electronic address: luca.fontanesi@unibo.it.
authors.forename: Luca
authors.initials: L
authors.lastname: Fontanesi
mesh_terms: D000818:Animals; D001492:Bass / Q000235:genetics*; D016678:Genome; D059014:High-Throughput Nucleotide Sequencing / Q000662:veterinary; D007558:Italy; D020641:Polymorphism, Single Nucleotide; D017422:Sequence Analysis, DNA / Q000662:veterinary
keywords: Cultivated sea bass; Ion Proton; Next generation sequencing; SNP