Email updates

Keep up to date with the latest news and content from BMC Genomics and BioMed Central.

Open Access Research article

The European sea bass Dicentrarchus labrax genome puzzle: comparative BAC-mapping and low coverage shotgun sequencing

Heiner Kuhl1*, Alfred Beck1, Grzegorz Wozniak1, Adelino VM Canario2, Filip AM Volckaert3 and Richard Reinhardt1

Author Affiliations

1 Max Planck Institute for Molecular Genetics, Ihnestr. 63, D-14195 Berlin, Germany

2 Centre of Marine Sciences (CCMAR), University of Algarve, Gambelas, 8005-139 Faro, Portugal

3 Laboratory of Animal Diversity and Systematics, Katholieke Universiteit Leuven, Ch. Deberiotstraat 32, B-3000 Leuven, Belgium

For all author emails, please log on.

BMC Genomics 2010, 11:68  doi:10.1186/1471-2164-11-68

Published: 27 January 2010

Abstract

Background

Food 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.

Results

End 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.

Conclusions

The 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.