Comparative physical maps derived from BAC end sequences of tilapia (Oreochromis niloticus)

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https://doi.org/10.1186/1471-2164-11-636Date
2010-11-16Author
Soler, Lucile
Conte, Matthew A.
Katagiri, Takayuki
Howe, Aimee E.
Lee, Bo-Young
Amemiya, Chris
Stuart, Andrew
Dossat, Carole
Poulain, Julie
Johnson, Jeremy
Di Palma, Federica
Lindblad-Toh, Kerstin
Baroiller, Jean-Francois
D'Cotta, Helena
Ozouf-Costaz, Catherine
Kocher, Thomas D.
Citation
Soler, L., Conte, M.A., Katagiri, T. et al. Comparative physical maps derived from BAC end sequences of tilapia (Oreochromis niloticus). BMC Genomics 11, 636 (2010).
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Show full item recordAbstract
Background: 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 endsequences to develop comparative physical maps, and estimate the number of genome rearrangements, between
tilapia and other model fish species.
Results: 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.
Conclusions: 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.