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

Kuhl, H., Beck, A., Wozniak, G., Canario, A. V. M., Volckaert, F. A. M., & Reinhardt, R. (2010). The European sea bass Dicentrarchus labrax genome puzzle: comparative BAC-mapping and low coverage shotgun sequencing. BMC Genomics, 11, 11:68-11:68. doi:0.1186/1471-2164-11-68.

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Item Permalink: http://hdl.handle.net/11858/00-001M-0000-0010-7C0B-9 Version Permalink: http://hdl.handle.net/11858/00-001M-0000-0010-7C0C-7
Genre: Journal Article

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 Creators:
Kuhl, Heiner1, Author              
Beck, Alfred2, Author              
Wozniak, Grzegorz3, Author              
Canario, Adelino V. M., Author
Volckaert, Filip A. M., Author
Reinhardt, Richard4, Author              
Affiliations:
1Sequencing (Head: Bernd Timmermann), Scientific Service (Head: Manuela B. Urban), Max Planck Institute for Molecular Genetics, Max Planck Society, ou_1479670              
2Computing (Head: Donald Buczek/Peter Marquardt), Scientific Service (Head: Christoph Krukenkamp), Max Planck Institute for Molecular Genetics, Max Planck Society, ou_1479667              
3Independent Junior Research Groups (OWL), Max Planck Institute for Molecular Genetics, Max Planck Society, ou_1433554              
4High Throughput Technologies, Max Planck Institute for Molecular Genetics, Max Planck Society, ou_1433552              

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 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.

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Language(s): eng - English
 Dates: 2010-01-27
 Publication Status: Published in print
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Title: BMC Genomics
Source Genre: Journal
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Pages: - Volume / Issue: 11 Sequence Number: - Start / End Page: 11:68 - 11:68 Identifier: ISSN: 1471-2164