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.

Figure 1

Distribution of BLAST scores for type 2, 3 and 4 hits of the Broad Institute tilapia BAC end sequences on the stickleback genome assembly. The distribution was truncated at e^-10.

Figure 2

Comparative mapping of tilapia data mapped on the stickleback genome assembly displayed in GBrowse at http://www.BouillaBase.org. a) Type 1 and 2 BLAST hits, b) Type 3 BLAST hits, c) FPC contigs.