title: Comparative physical maps derived from BAC end sequences of tilapia (Oreochromis niloticus).
abstract: 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 end-sequences 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.
authors.affiliation: CIRAD-PERSYST, Aquaculture Research Unit, TA B-20/A, Campus International de Baillarguet, 34398 Montpellier cedex 5, France.
authors.forename: Lucile
authors.initials: L
authors.lastname: Soler
authors.forename: Matthew A
authors.initials: MA
authors.lastname: Conte
authors.forename: Takayuki
authors.initials: T
authors.lastname: Katagiri
authors.forename: Aimee E
authors.initials: AE
authors.lastname: Howe
authors.forename: Bo-Young
authors.initials: BY
authors.lastname: Lee
authors.forename: Chris
authors.initials: C
authors.lastname: Amemiya
authors.forename: Andrew
authors.initials: A
authors.lastname: Stuart
authors.forename: Carole
authors.initials: C
authors.lastname: Dossat
authors.forename: Julie
authors.initials: J
authors.lastname: Poulain
authors.forename: Jeremy
authors.initials: J
authors.lastname: Johnson
authors.forename: Federica
authors.initials: F
authors.lastname: Di Palma
authors.forename: Kerstin
authors.initials: K
authors.lastname: Lindblad-Toh
authors.forename: Jean-Francois
authors.initials: JF
authors.lastname: Baroiller
authors.forename: Helena
authors.initials: H
authors.lastname: D'Cotta
authors.forename: Catherine
authors.initials: C
authors.lastname: Ozouf-Costaz
authors.forename: Thomas D
authors.initials: TD
authors.lastname: Kocher
mesh_terms: D000818:Animals; D022202:Chromosomes, Artificial, Bacterial / Q000235:genetics*; D023681:Cichlids / Q000235:genetics*; D017124:Conserved Sequence / Q000235:genetics; D029941:Fish Proteins / Q000235:genetics; D015723:Gene Library; D023061:Gene Order / Q000235:genetics; D016678:Genome / Q000235:genetics; D018895:Microsatellite Repeats / Q000235:genetics; D008969:Molecular Sequence Data; D020161:Physical Chromosome Mapping; D017422:Sequence Analysis, DNA / Q000379:methods*; D023701:Smegmamorpha / Q000235:genetics
chemical_list: D029941:Fish Proteins