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.

Bertolini, F., Geraci, C., Schiavo, G., Sardina, M., Chiofalo, V., Fontanesi, L. (2016). Whole genome semiconductor based sequencing of farmed European sea bass (Dicentrarchus labrax) Mediterranean genetic stocks using a DNA pooling approach. MARINE GENOMICS, 28, 63-70 [10.1016/j.margen.2016.03.007].

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

BERTOLINI, FRANCESCA;GERACI, CLAUDIA;SCHIAVO, GIUSEPPINA;FONTANESI, LUCA
2016

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.
2016
Bertolini, F., Geraci, C., Schiavo, G., Sardina, M., Chiofalo, V., Fontanesi, L. (2016). Whole genome semiconductor based sequencing of farmed European sea bass (Dicentrarchus labrax) Mediterranean genetic stocks using a DNA pooling approach. MARINE GENOMICS, 28, 63-70 [10.1016/j.margen.2016.03.007].
Bertolini, F.; Geraci, C.; Schiavo, G.; Sardina, M.T.; Chiofalo, V.; Fontanesi, L
File in questo prodotto:
Eventuali allegati, non sono esposti

I documenti in IRIS sono protetti da copyright e tutti i diritti sono riservati, salvo diversa indicazione.

Utilizza questo identificativo per citare o creare un link a questo documento: https://hdl.handle.net/11585/590138
 Attenzione

Attenzione! I dati visualizzati non sono stati sottoposti a validazione da parte dell'ateneo

Citazioni
  • ???jsp.display-item.citation.pmc??? 3
  • Scopus 10
  • ???jsp.display-item.citation.isi??? 10
social impact