NDLI: Whole genome semiconductor based sequencing of farmed European sea bass (Dicentrarchus labrax) Mediterranean genetic stocks using a DNA pooling approach.

Content Provider	World Health Organization (WHO)-Global Index Medicus
Author	Bertolini, Francesca Geraci, Claudia Schiavo, Giuseppina Sardina, Maria Teresa Chiofalo, Vincenzo Fontanesi, Luca
Description	Country affiliation: Italy Author Affiliation: Bertolini F ( Department of Agricultural and Food Sciences, Division of Animal Sciences, University of Bologna, Viale Fanin 46, 40127 Bologna, Italy.); Geraci C ( Department of Agricultural and Food Sciences, Division of Animal Sciences, University of Bologna, Viale Fanin 46, 40127 Bologna, Italy.); Schiavo G ( Department of Agricultural and Food Sciences, Division of Animal Sciences, University of Bologna, Viale Fanin 46, 40127 Bologna, Italy.); Sardina MT ( Department of Agricultural and Forestry Sciences, University of Palermo, Viale delle Scienze, 90128 Palermo, Italy.); Chiofalo V ( Department of Veterinary Medicine, Division of Animal Production, University of Messina, Polo Universitario dell'Annunziata, 98168 Messina, Italy.); Fontanesi L ( 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.)
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.
File Format	HTM / HTML
ISSN	18747787
Journal	Marine Genomics
Volume Number	28
e-ISSN	18767478
Language	English
Publisher	Elsevier
Publisher Date	2016-08-01
Publisher Place	Netherlands
Access Restriction	One Nation One Subscription (ONOS)
Subject Keyword	Discipline Genetics Discipline Biology
Content Type	Text
Resource Type	Article
Subject	Genetics Aquatic Science

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