Genet et al. BMC Genomics 2011, 12:314 http://www.biomedcentral.com/1471-2164/12/314 databases for zebrafish (Danio_rerio.Zv9.61.pep.all.fa), stickleback (Gasterosteus_aculeatus.BROADS1.61.pep.all. fa), and medaka (Oryzias_latipes.MEDAKA1.61.pep.all.fa). BLASTN and BLASTX searches were carried out using an e-value cut off of 1e-5 with following parameters (-m9 -r1 -q-1 -G4 -E2 -W9 -F “m D” -U for BLASTN). The BLAST search results were filtered to remove non specific sequences using the following filtration steps: (1) For each BES read with BLAST hit, results were filtered to keep only the hits with the minimal e-value score; (2) BES reads with at least two hits having the same minimal e-value were filtered to keep the hits with the highest HSPs (high- scoring segment pairs; calculated as the product of % iden- tity multiplied by alignment length); and 3) keep only BES reads with single hits following filtration steps 1 and 2. For BLASTX the Ensembl protein IDs were renamed by their corresponding Ensembl gene IDs as each gene may encode several peptides due to alternative splicing. Comparative synteny analysis Identification of regions of conserved synteny between rainbow trout and model fish species were investigated using paired BAC-ends with unique hits. A region of microsynteny with the target genome was established if both BAC ends were mapped to the same chromosome with a space of 10 to 300 Kb between both ends and if they were properly oriented (tail-to-tail; the two ends in opposing orientation with 3’ ends internal) [41,48,49]. In addition, we defined regions of macro-synteny as those in which the two paired BAC-end hits were mapped to the same chromosome of the model species. Additional material Additional file 1: INRA RT rep1.0. The first Rainbow trout repeat database elements contains 735 putative elements in fasta format. 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. 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. 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. 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. Page 7 of 8 Acknowledgments and Funding The authors thank CRB GADIE (Diane Esquerre) for BAC clones handling and Brian Smith, Renee Fincham and Kristy Shewbridge for microsatellites genotyping. We are grateful to Yann Guiguen for help and precious contribution to fund raising for this study. This work was made possible by financial support of Genoscope. We acknowledge René Guyomard for his initial contribution in BAC library procurement. The microsatellites genotyping was supported by NRI Grant No. 2007-35616-17875 from the USDA National Institute of Food and Agriculture. Author details 1INRA, UMR 1313 GABI, Génétique Animale et Biologie Intégrative, 78350 Jouy-en-Josas, France. 2INRA, UMR 444 ENVT Génétique Cellulaire, 31326 Castanet-Tolosan, France. 3INRA, Sigenae, 31326 Castanet-Tolosan, France. 4National Center for Cool and Cold Water Aquaculture, ARS-USDA, 11861 Leetown Road, Kearneysville, WV 25430, USA. 5CEA Genoscope, 2 rue Gaston Crémieux, 91057 Evry Cedex, France. Authors’ contributions CG conceived the project. MB and CG supervised the project, and wrote the manuscript. MB and PD carried out bioinformatics analysis. YP performed the microsatellites genotyping analyses, provided 7,296 BAC clones for BAC end Sequencing and revised the manuscript draft. GG participated in and contributed ideas to the bioinformatics analysis. FG and PW carried out DNA extraction and DNA sequencing. 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