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

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.

Difference in responses of two coastal species to fluctuating salinities and temperatures: Potential modification of specific distribution areas in the context of global change

“…Moreover, these different reactions to environmental changes may lead to the current speciation, as recently observed for seabass (Tine et al, 2014). (Tine et al, 2014).…”

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

“…A Python script was used to assign SNPs to coding or non-coding regions using the annotation map data of the European sea bass reference genome obtained by Tine et al (2014) and available at http://seabass.mpipz.mpg.de/DOWNLOADS/.…”

“…mpipz.mpg.de/DOWNLOADS/; Tine et al, 2014) and analyzed with the Enrichr platform (http://amp.pharm.mssm.edu/Enrichr/enrich) for gene functional enrichment analyses (Chen et al, 2013) using the GO Biological Process and the Kyoto Encyclopedia of Genes and Genomes (http://www.genome.jp/kegg/; KEGG 2015) and PANTHER (http:// www.pantherdb.org/pathway/) pathway analyses.…”

“…Then, a Python script was used to retain for subsequent analyses only trimmed reads with length ≥ 30. Alignment to the reference sequence of D. labrax (accession number: GCA_000689215.1; Tine et al, 2014) was carried out using the option mem of BurrowsWheeler Aligner (BWA; Li, 2013), with default parameters. The resulted sam file was converted into binary files, and duplicated reads were removed with Samtools software (Li et al, 2009).…”

“…A radiation hybrid map was obtained by Guyon et al (2010) and BAC sequencing data and preliminary single nucleotide polymorphism discovery were reported (Kuhl et al, 2010(Kuhl et al, , 2011a(Kuhl et al, , 2011b. Only recently, the publication of the first version of the assembled D. labrax whole genome has opened new opportunities to evaluate and monitor genetic stock variability (Tine et al, 2014).…”