Comparative physical maps derived from BAC end sequences of tilapia (<it>Oreochromis niloticus</it>)

BMC Genomics. 2010;11(1):636 DOI 10.1186/1471-2164-11-636


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Journal Title: BMC Genomics

ISSN: 1471-2164 (Online)

Publisher: BMC

LCC Subject Category: Technology: Chemical technology: Biotechnology | Science: Biology (General): Genetics

Country of publisher: United Kingdom

Language of fulltext: English

Full-text formats available: PDF, HTML



Lindblad-Toh Kerstin
Di Palma Federica
Johnson Jeremy
Poulain Julie
Dossat Carole
Stuart Andrew
Amemiya Chris
Lee Bo-Young
Howe Aimee E
Katagiri Takayuki
Conte Matthew A
Soler Lucile
Baroiller Jean-Francois
D'Cotta Helena
Ozouf-Costaz Catherine
Kocher Thomas D


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Time From Submission to Publication: 17 weeks


Abstract | Full Text

<p>Abstract</p> <p>Background</p> <p>The Nile tilapia is the second most important fish in aquaculture. It is an excellent laboratory model, and is closely related to the African lake cichlids famous for their rapid rates of speciation. A suite of genomic resources has been developed for this species, including genetic maps and ESTs. Here we analyze BAC end-sequences to develop comparative physical maps, and estimate the number of genome rearrangements, between tilapia and other model fish species.</p> <p>Results</p> <p>We obtained sequence from one or both ends of 106,259 tilapia BACs. BLAST analysis against the genome assemblies of stickleback, medaka and pufferfish allowed identification of homologies for approximately 25,000 BACs for each species. We calculate that rearrangement breakpoints between tilapia and these species occur about every 3 Mb across the genome. Analysis of 35,000 clones previously assembled into contigs by restriction fingerprints allowed identification of longer-range syntenies.</p> <p>Conclusions</p> <p>Our data suggest that chromosomal evolution in recent teleosts is dominated by alternate loss of gene duplicates, and by intra-chromosomal rearrangements (~one per million years). These physical maps are a useful resource for comparative positional cloning of traits in cichlid fishes. The paired BAC end sequences from these clones will be an important resource for scaffolding forthcoming shotgun sequence assemblies of the tilapia genome.</p>