ArticleBMC genomics2010
The European sea bass Dicentrarchus labrax genome puzzle: comparative BAC-mapping and low coverage shotgun sequencing.
Article in BMC genomics, 2010. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 25 papers.
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Who cites it
25 citing papers in PubMed, 77 citations in OpenAlex.
- Article
- Early innate immune responses in European sea bass (Frontiers in immunology · 2023Article
- Acute Inflammation Induces Neuroendocrine and Opioid Receptor Genes Responses in the SeabassBiology · 2022Article
- Inventory of European Sea Bass (Frontiers in genetics · 2019Article
- Comparative mapping for bighead carp (Aristichthys nobilis) against model and non-model fishes provides insights into the genomic evolution of cyprinids.Molecular genetics and genomics : MGG · 2015Article
- European sea bass genome and its variation provide insights into adaptation to euryhalinity and speciation.Nature communications · 2014Article
- Consolidation of the genetic and cytogenetic maps of turbot (Scophthalmus maximus) using FISH with BAC clones.Chromosoma · 2014Article
- Construction of a high-coverage bacterial artificial chromosome library and comprehensive genetic linkage map of yellowtail Seriola quinqueradiata.BMC research notes · 2014Article
- Genetic inactivation of European sea bass (Dicentrarchus labrax L.) eggs using UV-irradiation: observations and perspectives.PloS one · 2014Article
- Whole genome comparative analysis of channel catfish (Ictalurus punctatus) with four model fish species.BMC genomics · 2013Article
- Comparative genomic analysis of catfish linkage group 8 reveals two homologous chromosomes in zebrafish and other teleosts with extensive inter-chromosomal rearrangements.BMC genomics · 2013Article
- Filtering duplicate reads from 454 pyrosequencing data.Bioinformatics (Oxford, England) · 2013Article
- Genomic approaches to study genetic and environmental influences on fish sex determination and differentiation.Marine biotechnology (New York, N.Y.) · 2012Review
- A second generation integrated map of the rainbow trout (Oncorhynchus mykiss) genome: analysis of conserved synteny with model fish genomes.Marine biotechnology (New York, N.Y.) · 2012Article
- Fast skeletal muscle transcriptome of the gilthead sea bream (Sparus aurata) determined by next generation sequencing.BMC genomics · 2012Article
- Genomic characterization of the European sea bass Dicentrarchus labrax reveals the presence of a novel uncoupling protein (UCP) gene family member in the teleost fish lineage.BMC evolutionary biology · 2012Article
- A microsatellite linkage map of striped bass (Morone saxatilis) reveals conserved synteny with the three-spined stickleback (Gasterosteus aculeatus).Marine biotechnology (New York, N.Y.) · 2012Article
- Systematic exploration of error sources in pyrosequencing flowgram data.Bioinformatics (Oxford, England) · 2011Article
- Analysis of BAC-end sequences in rainbow trout: content characterization and assessment of synteny between trout and other fish genomes.BMC genomics · 2011Article
- Natural history of SLC11 genes in vertebrates: tales from the fish world.BMC evolutionary biology · 2011Article
Corrections and comments
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Authors and funding
6 authors at 3 institutions in 3 countries.
Funding
No grant is acknowledged in the PubMed record.
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.
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.