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

Tine, Mbaye ... et. al.-- 10 pages, 5 figures, supplementary information https://doi.org/10.1038/ncomms6770

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

This work was initiated during the MARINE GENOMICS EUROPE project EU-FP6 505403 and was supported by grants from the Max Planck Society (MPG for genome sequencing, assembly and annotation), LIFECYCLE EU-FP7 222719 and BMBF-01GS0805 to R.R., and the French ANR grants LABRAD-SEQ 11-PDOC-009-01 to P.-A.G. and REGULBASS 09-GENM-003 to B.G. M.T. received a fellowship from the MPG, H.K. was partly financed by LIFECYCLE EU-FP7 222719 and F.K. by the BMBF-01GS0805 grant. L.B. was supported by the grant Progetto 12/MI/2004 from the Veneto Region. R.S.T.M. and B.L. were in receipt of fellowships SFRH/BPD/66742/2009 and SFRH/BPD/89889/2012 from the Foundation for Science and Technology of Portugal

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