6533b86dfe1ef96bd12cab3b
RESEARCH PRODUCT
Whole genome semiconductor based sequencing of farmed European sea bass (Dicentrarchus labrax) Mediterranean genetic stocks using a DNA pooling approach
Maria Teresa SardinaGiuseppina SchiavoFrancesca BertoliniClaudia GeraciVincenzo ChiofaloLuca Fontanesisubject
0301 basic medicinefood.ingredientIon ProtonSNPBiologyAquatic ScienceGenomePolymorphism Single NucleotideCultivated sea baDNA sequencing03 medical and health sciencesBass (fish)Settore AGR/17 - Zootecnica Generale E Miglioramento Genetico0302 clinical medicinefoodChromosome regionsNext generation sequencingCultivated sea bass Next generation sequencing Ion Proton SNPGeneticsAnimalsSea bassGeneGeneticsGenomeCultivated sea bass; Ion Proton; Next generation sequencing; SNP; Aquatic Science; GeneticsHigh-Throughput Nucleotide SequencingIon semiconductor sequencingSequence Analysis DNA030104 developmental biologyItalyBassSelective sweepCultivated sea bass030217 neurology & neurosurgerydescription
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.
| year | journal | country | edition | language |
|---|---|---|---|---|
| 2016-01-01 |