Open Access Research article

Analysis of BAC-end sequences in rainbow trout: Content characterization and assessment of synteny between trout and other fish genomes

Carine Genet1*, Patrice Dehais23, Yniv Palti4, Guangtu Gao4, Frederick Gavory5, Patrick Wincker5, Edwige Quillet1 and Mekki Boussaha1

Author Affiliations

1 INRA, UMR 1313 GABI, Génétique Animale et Biologie Intégrative, 78350 Jouy-en-Josas, France

2 INRA, UMR 444 ENVT Génétique Cellulaire, 31326 Castanet-Tolosan, France

3 INRA, Sigenae, 31326 Castanet-Tolosan, France

4 National Center for Cool and Cold Water Aquaculture, ARS-USDA, 11861 Leetown Road, Kearneysville, WV 25430, USA

5 CEA Genoscope, 2 rue Gaston Crémieux, 91057 Evry Cedex, France

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BMC Genomics 2011, 12:314  doi:10.1186/1471-2164-12-314

Published: 14 June 2011

Additional files

Additional file 1:

INRA RT rep1.0. The first Rainbow trout repeat database elements contains 735 putative elements in fasta format.

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Additional file 2:

PCR conditions, allele size range, number of alleles and GenBank accession numbers for tested microsatellites. Duplicated markers are in bold. ND indicates that for these duplicated microsatellite it was not possible to determine the allele numbers. * indicates monomorphic or non informative microsatellites in the mapping panel. Abbreviations: Atp: Annealing temperature.

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Additional file 3:

An example of multiple gene hits corresponding to odorant receptor gene family (sheet 1) or protocadherin gene family (sheet 2) in zebrafish.

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Additional file 4:

Summary of conserved microsyntenies identified by Blastn analysis with medaka (sheet 1), stickleback (sheet 2) and zebrafish (sheet 3). BAC, Forward and reverse hits indicate the orientation of the BES using the forward T7 and the reverse Sp6 sequencing primers, respectively. Span indicates the average distance between the two genes in the corresponding species.

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Additional file 5:

Summary of conserved microsyntenies identified by BlastX analysis with medaka (sheet 1), stickleback (sheet 2) and zebrafish (sheet 3) gene hits. Putative identities of mate paired genes were provided as ENSEMBL protein ID. Forward and reverse hits indicate the orientation of the BES using the forward T7 and the reverse Sp6 sequencing primers, respectively. Span indicates the average distance between the two genes in the corresponding species.

Format: XLS Size: 81KB Download file

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