title: Directed sequencing and annotation of three Dicentrarchus labrax L. chromosomes by applying Sanger- and pyrosequencing technologies on pooled DNA of comparatively mapped BAC clones.
abstract: Dicentrarchus labrax is one of the major marine aquaculture species in the European Union. In this study, we have developed a directed-sequencing strategy to sequence three sea bass chromosomes and compared results with other teleosts. Three BAC DNA pools were created from sea bass BAC clones that mapped to stickleback chromosomes/groups V, XVII and XXI. The pools were sequenced to 17-39x coverage by pyrosequencing. Data assembly was supported by Sanger reads and mate pair data and resulted in superscaffolds of 13.2 Mb, 17.5 Mb and 13.7 Mb respectively. Annotation features of the superscaffolds include 1477 genes. We analyzed size change of exon, intron and intergenic sequence between teleost species and deduced a simple model for the evolution of genome composition in teleost lineage. Combination of second generation sequencing technologies, Sanger sequencing and genome partitioning strategies allows "high-quality draft assemblies" of chromosome-sized superscaffolds, which are crucial for the prediction and annotation of complete genes.
authors.affiliation: Max Planck Institute for Molecular Genetics, Ihnestrasse 63, D-14195 Berlin, Germany. kuhl@molgen.mpg.de
authors.forename: Heiner
authors.initials: H
authors.lastname: Kuhl
authors.forename: Mbaye
authors.initials: M
authors.lastname: Tine
authors.forename: Alfred
authors.initials: A
authors.lastname: Beck
authors.forename: Bernd
authors.initials: B
authors.lastname: Timmermann
authors.forename: Chinnappa
authors.initials: C
authors.lastname: Kodira
authors.forename: Richard
authors.initials: R
authors.lastname: Reinhardt
mesh_terms: D000818:Animals; D001492:Bass / Q000235:genetics*; D002874:Chromosome Mapping; D002875:Chromosomes / Q000235:genetics*; D022202:Chromosomes, Artificial, Bacterial / Q000235:genetics*; D003001:Cloning, Molecular; D005091:Exons; D008040:Genetic Linkage; D016678:Genome; D007438:Introns; D016415:Sequence Alignment; D017422:Sequence Analysis, DNA / Q000379:methods*