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

Authors :
Volckaert Filip AM
Canario Adelino VM
Wozniak Grzegorz
Beck Alfred
Kuhl Heiner
Reinhardt Richard
Source :
BMC Genomics, Vol 11, Iss 1, p 68 (2010)
Publication Year :
2010
Publisher :
BMC, 2010.

Abstract

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.

Details

Language :
English
ISSN :
14712164
Volume :
11
Issue :
1
Database :
Directory of Open Access Journals
Journal :
BMC Genomics
Publication Type :
Academic Journal
Accession number :
edsdoj.3e074683751744f4ab0806ceb9e296ec
Document Type :
article
Full Text :
https://doi.org/10.1186/1471-2164-11-68