Abstract
BackgroundFood supply from the ocean is constrained by the shortage of domesticated and selected fish. Development of genomic models of economically important fishes should assist with the removal of this bottleneck. European sea bass Dicentrarchus labrax L. (Moronidae, Perciformes, Teleostei) is one of the most important fishes in European marine aquaculture; growing genomic resources put it on its way to serve as an economic model.ResultsEnd sequencing of a sea bass genomic BAC-library enabled the comparative mapping of the sea bass genome using the three-spined stickleback Gasterosteus aculeatus genome as a reference. BAC-end sequences (102,690) were aligned to the stickleback genome. The number of mappable BACs was improved using a two-fold coverage WGS dataset of sea bass resulting in a comparative BAC-map covering 87% of stickleback chromosomes with 588 BAC-contigs. The minimum size of 83 contigs covering 50% of the reference was 1.2 Mbp; the largest BAC-contig comprised 8.86 Mbp. More than 22,000 BAC-clones aligned with both ends to the reference genome. Intra-chromosomal rearrangements between sea bass and stickleback were identified. Size distributions of mapped BACs were used to calculate that the genome of sea bass may be only 1.3 fold larger than the 460 Mbp stickleback genome.ConclusionsThe BAC map is used for sequencing single BACs or BAC-pools covering defined genomic entities by second generation sequencing technologies. Together with the WGS dataset it initiates a sea bass genome sequencing project. This will allow the quantification of polymorphisms through resequencing, which is important for selecting highly performing domesticated fish.
Highlights
Food supply from the ocean is constrained by the shortage of domesticated and selected fish
Sequences from model teleost fish genomes are a valuable tool for comparative approaches to elucidate the genomics of phylogenetically related non-model teleost [14,15,16,17], they are selected for the opposite reasons of aquaculture species, which generally have large body mass and long reproductive cycles
The genomic sequence of T. rubripes [8]] was not used as the genome assembly has not been assigned to chromosomes
Summary
Food supply from the ocean is constrained by the shortage of domesticated and selected fish. Teleost fishes are the most diverse group of vertebrates, with approximately 28,000 species, which have colonized a range of aquatic environments and display a variety of biochemical, physiological and morphological adaptations [1,2]. Because of this diversity and their position at the base of the vertebrate phylogeny, some species are considered good models of evolution, development and human diseases [3,4,5,6]. Sequences from model teleost fish genomes are a valuable tool for comparative approaches to elucidate the genomics of phylogenetically related non-model teleost [14,15,16,17], they are selected for the opposite reasons of aquaculture species, which generally have large body mass and long reproductive cycles
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