Dataset Information

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.

SUBMITTER: Tine M

PROVIDER: S-EPMC4284805 | biostudies-literature | 2014

REPOSITORIES: biostudies-literature

ACCESS DATA

Publications

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

Tine Mbaye M Kuhl Heiner H Gagnaire Pierre-Alexandre PA Louro Bruno B Desmarais Erick E Martins Rute S T RS Hecht Jochen J Knaust Florian F Belkhir Khalid K Klages Sven S Dieterich Roland R Stueber Kurt K Piferrer Francesc F Guinand Bruno B Bierne Nicolas N Volckaert Filip A M FA Bargelloni Luca L Power Deborah M DM Bonhomme François F Canario Adelino V M AV Reinhardt Richard R

Nature communications 20141223

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 associ ...[more]

PMID: 25534655

Similar Datasets

Project description:Several studies have attempted to understand the origin and evolution of single-exon genes (SEGs) in eukaryotic organisms, including fishes, but few have examined the functional and evolutionary relationships between SEGs and multiple-exon gene (MEG) paralogs, in particular the conservation of promoter regions. Given that SEGs originate via the reverse transcription of mRNA from a "parental" MEGs, such comparisons may enable identifying evolutionarily-related SEG/MEG paralogs, which might fulfill equivalent physiological functions. Here, the relationship of SEG proportion with MEG count, gene density, intron count, and chromosome size was assessed for the genome of the European sea bass, Dicentrarchus labrax. Then, SEGs with an MEG parent were identified, and promoter sequences of SEG/MEG paralogs were compared, to identify highly conserved functional motifs. The results revealed a total count of 1,585 (8.3% of total genes) SEGs in the European sea bass genome, which was correlated with MEG count but not with gene density. The significant correlation of SEG content with the number of MEGs suggests that SEGs were continuously and independently generated over evolutionary time following species divergence through retrotranscription events, followed by tandem duplications. Functional annotation showed that the majority of SEGs are functional, as is evident from their expression in RNA-seq data used to support homology-based genome annotation. Differences in 5'UTR and 3'UTR lengths between SEG/MEG paralogs observed in this study may contribute to gene expression divergence between them and therefore lead to the emergence of new SEG functions. The comparison of nonsynonymous to synonymous changes (Ka/Ks) between SEG/MEG parents showed that 74 of them are under positive selection (Ka/Ks > 1; p = .0447). An additional fifteen SEGs with an MEG parent have a common promoter, which implies that they are under the influence of common regulatory networks.

Dataset Information

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

Publications

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

Similar Datasets

OmicsDI is part of the ELIXIR infrastructure

Tweets