European sea bass genome and its variation provide insights into adaptation to euryhalinity and speciation

Mbaye Tine, Heiner Kuhl, Pierre-Alexandre Gagnaire, Bruno Louro, Erick Desmarais, Rute S.T. Martins, Jochen Hecht, Florian Knaust, Khalid Belkhir, Sven Klages, Roland Dieterich, Kurt Stueber, Francesc Piferrer, Bruno Guinand, Nicolas Bierne, Filip A. M. Volckaert, Luca Bargelloni, Deborah M. Power, François Bonhomme (), Adelino V. M. Canario () and Richard Reinhardt ()
Additional contact information
Mbaye Tine: Max Planck Genome-centre Cologne, Carl-von-Linné-Weg 10, D-50829 Köln, Germany
Heiner Kuhl: Max Planck Institute for Molecular Genetics, Ihnestrasse 63, D-14195 Berlin, Germany
Pierre-Alexandre Gagnaire: Institut des Sciences de l'Evolution (UMR 5554), CNRS-UM2-IRD, Place Eugène Bataillon
Bruno Louro: CCMAR-Centre of Marine Sciences, University of Algarve, Building 7, Campus de Gambelas, 8005-139 Faro, Portugal
Erick Desmarais: Institut des Sciences de l'Evolution (UMR 5554), CNRS-UM2-IRD, Place Eugène Bataillon
Rute S.T. Martins: CCMAR-Centre of Marine Sciences, University of Algarve, Building 7, Campus de Gambelas, 8005-139 Faro, Portugal
Jochen Hecht: Max Planck Institute for Molecular Genetics, Ihnestrasse 63, D-14195 Berlin, Germany
Florian Knaust: Max Planck Institute for Molecular Genetics, Ihnestrasse 63, D-14195 Berlin, Germany
Khalid Belkhir: Institut des Sciences de l'Evolution (UMR 5554), CNRS-UM2-IRD, Place Eugène Bataillon
Sven Klages: Max Planck Institute for Molecular Genetics, Ihnestrasse 63, D-14195 Berlin, Germany
Roland Dieterich: Max Planck Genome-centre Cologne, Carl-von-Linné-Weg 10, D-50829 Köln, Germany
Kurt Stueber: Max Planck Genome-centre Cologne, Carl-von-Linné-Weg 10, D-50829 Köln, Germany
Francesc Piferrer: Institut de Ciències del Mar, Consejo Superior de Investigaciones Científicas (CSIC), Passeig Marítim, 37-49
Bruno Guinand: Institut des Sciences de l'Evolution (UMR 5554), CNRS-UM2-IRD, Place Eugène Bataillon
Nicolas Bierne: Institut des Sciences de l'Evolution (UMR 5554), CNRS-UM2-IRD, Place Eugène Bataillon
Filip A. M. Volckaert: Laboratory of Biodiversity and Evolutionary Genomics, University of Leuven, Charles Deberiotstraat 32, B-3000 Leuven, Belgium
Luca Bargelloni: Università di Padova
Deborah M. Power: CCMAR-Centre of Marine Sciences, University of Algarve, Building 7, Campus de Gambelas, 8005-139 Faro, Portugal
François Bonhomme: Institut des Sciences de l'Evolution (UMR 5554), CNRS-UM2-IRD, Place Eugène Bataillon
Adelino V. M. Canario: CCMAR-Centre of Marine Sciences, University of Algarve, Building 7, Campus de Gambelas, 8005-139 Faro, Portugal
Richard Reinhardt: Max Planck Genome-centre Cologne, Carl-von-Linné-Weg 10, D-50829 Köln, Germany

Nature Communications, 2014, vol. 5, issue 1, 1-10

Abstract: Abstract The European sea bass (Dicentrarchus labrax) is a temperate-zone euryhaline teleost of prime importance for aquaculture and fisheries. This species is subdivided into two naturally hybridizing lineages, one inhabiting the north-eastern Atlantic Ocean and the other the Mediterranean and Black seas. Here we provide a high-quality chromosome-scale assembly of its genome that shows a high degree of synteny with the more highly derived teleosts. We find expansions of gene families specifically associated with ion and water regulation, highlighting adaptation to variation in salinity. We further generate a genome-wide variation map through RAD-sequencing of Atlantic and Mediterranean populations. We show that variation in local recombination rates strongly influences the genomic landscape of diversity within and differentiation between lineages. Comparing predictions of alternative demographic models to the joint allele-frequency spectrum indicates that genomic islands of differentiation between sea bass lineages were generated by varying rates of introgression across the genome following a period of geographical isolation.

Date: 2014
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DOI: 10.1038/ncomms6770

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