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

Soler Lucile, Conte Matthew A., Katagiri Takayuki, Howe Aimée E., Lee Bo-Young, Amemiya Chris, Stuart Andrew, Dossat Carole, Poulain Julie, Johnson Jeremy, Di Palma Frederica, Lindblad-Toh Kerstin, Baroiller Jean-François, D'Cotta Helena, Ozouf-Costaz Catherine, Kocher Thomas D.. 2010. Comparative physical maps derived from BAC end sequences of tilapia (Oreochromis niloticus). BMC Genomics, 11 (636), 8 p.

Quartile : Q1, Sujet : BIOTECHNOLOGY & APPLIED MICROBIOLOGY / Quartile : Q1, Sujet : GENETICS & HEREDITY

Résumé : 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.

Mots-clés Agrovoc : Oreochromis niloticus, carte génétique, génome, évolution, génomique, microsatellite, marqueur génétique, séquence nucléotidique

Mots-clés complémentaires : BAC, Séquencage

Classification Agris : L10 - Génétique et amélioration des animaux
M12 - Production de l'aquaculture
L60 - Taxonomie et géographie animales

Champ stratégique Cirad : Axe 1 (2005-2013) - Intensification écologique

Auteurs et affiliations

• Soler Lucile, CIRAD-PERSYST-UPR Aquaculture (FRA)
• Conte Matthew A., University of Maryland (USA)
• Katagiri Takayuki, Tokyo University of Marine Science and Technology (JPN)
• Howe Aimée E., University of Maryland (USA)
• Lee Bo-Young, University of Maryland (USA)
• Amemiya Chris, Benaroya Research Institute at Virginia Mason (USA)
• Stuart Andrew, Benaroya Research Institute at Virginia Mason (USA)
• Dossat Carole, Institut de génomique (FRA)
• Poulain Julie, Institut de génomique (FRA)
• Johnson Jeremy, Broad Institut (USA)
• Di Palma Frederica, Broad Institut (USA)
• Lindblad-Toh Kerstin, Broad Institut (USA)
• Baroiller Jean-François, CIRAD-PERSYST-UPR Aquaculture (FRA) ORCID: 0000-0002-0992-1725
• D'Cotta Helena, CIRAD-PERSYST-UPR Aquaculture (FRA) ORCID: 0000-0003-2739-3476
• Ozouf-Costaz Catherine, MNHN (FRA)
• Kocher Thomas D., University of Maryland (USA)

Source : Cirad - Agritrop (https://agritrop.cirad.fr/558037/)

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