Biology

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Author: search.filters.author.Baroiller, Jean-Francois

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    An EST resource for tilapia based on 17 normalized libraries and assembly of 116,899 sequence tags
    (Springer Nature, 2010-04-30) Lee, Bo-Young; Howe, Aimee E; Conte, Matthew A; D'Cotta, Helena; Pepey, Elodie; Baroiller, Jean-Francois; di Palma, Federica; Carleton, Karen L; Kocher, Thomas D
    Large collections of expressed sequence tags (ESTs) are a fundamental resource for analysis of gene expression and annotation of genome sequences. We generated 116,899 ESTs from 17 normalized and two non-normalized cDNA libraries representing 16 tissues from tilapia, a cichlid fish widely used in aquaculture and biological research. The ESTs were assembled into 20,190 contigs and 36,028 singletons for a total of 56,218 unique sequences and a total assembled length of 35,168,415 bp. Over the whole project, a unique sequence was discovered for every 2.079 sequence reads. 17,722 (31.5%) of these unique sequences had significant BLAST hits (e-value < 10-10) to the UniProt database. Normalization of the cDNA pools with double-stranded nuclease allowed us to efficiently sequence a large collection of ESTs. These sequences are an important resource for studies of gene expression, comparative mapping and annotation of the forthcoming tilapia genome sequence.
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    Comparative physical maps derived from BAC end sequences of tilapia (Oreochromis niloticus)
    (2010-11-16) 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.
    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.