Genet et al. BMC Genomics 2011, 12:314 http://www.biomedcentral.com/1471-2164/12/314 Table 4 Rainbow trout BAC end sequences BlastX statistics Medaka Stickleback Zebrafish Total BES with hits BES with unique hitsa BACs BAC with one end Paired BAC-ends Paired BAC-ends with unique hits Unique hits paired BAC-ends matched on the same chromosome Also identified by BlastN Microsynteny identified 9,312 9,125 8,700 306 293 132 85 40 9,308 9,058 8,674 317 305 148 105 45 10,487 9,983 9,717 385 355 155 105 30 a The bioinformatic filtering criteria used for identifying ‘unique’ hits are described in the methods section. most likely due to the large evolutionary distance between the salmonids and the model species. Multiple gene hits may be caused by gene duplications or by the presence of conserved sequences among mem- bers of gene families. BLASTX searches revealed hits with some genes existing in large copy numbers as exemplified by protocadherin members families (53 hits) and odorant receptor members families (48 hits) (Addi- tional file 3). The others gene hits showed identity to transposable elements such as piggybac transposable ele- ment 4 or LINE-1 type transposase domain containing 1 or transposase (data not shown) which revealed that these transposable elements were not masked by the INRA RT rep1.0 database. Identification of regions of microsynteny The sequence homology searches were conducted using both BlastN and BlastX alignment tools. For BlastN searches, we identified 792, 812, and 632 BACs with both ends having significant unique hits to the medaka, stickleback, and zebrafish genomes, respec- tively (Table 3). Out of those, 418 (53%), 566 (70%), and 360 (57%) unique paired BAC-end hits matched on the same chromosome (macro-synteny) in medaka, stickle- back and zebrafish, respectively. Of those, we identified 307 (73%), 421 (74%) and 176 (49%) regions of micro- synteny between rainbow trout and medaka, stickleback, and zebrafish, respectively (additional file 4). For BLASTX analysis, we identified 293, 305, and 355 BACs with both ends having significant gene hits to the medaka, stickleback, and zebrafish genomes, respectively (Table 4). Further analysis revealed that 132 (45%; medaka), 148 (48%; stickleback), and 155 (43%; zebra- fish) paired BAC-end gene hits were in macro-synteny. Of those, we identified 40 (30%), 45 (30%) and 30 (30%) regions of microsynteny between rainbow trout and Page 5 of 8 medaka, stickleback, and zebrafish, respectively (addi- tional file 5). Finally, our BlastN analyses identified 85 (medaka), 105 (stickleback), and 105 (zebrafish) unique paired BAC end hits in macrosynteny that were also detected using BlastX analyses (Table 3). As expected, our analysis revealed moderate macro- synteny between rainbow trout and the three model spe- cies and even lower level of microsynteny likely due to chromosomal rearrangements that have occurred since the divergent of those species from a common teleost ancestor. The strongest decline in number of microsyn- teny regions was observed for zebrafish, which is indeed more distant from rainbow trout than the medaka and stickleback [42]. While the number of significant BES hits with BlastN was between 1.78 (zebrafish) to 2.7 (stickleback) times greater than those with BlastX hits, the difference in identifying microsynteny was even greater. The number of microsynteny regions identified with BlastN was 5.8 (zebrafish) to 9.3 (stickleback) times greater than BlastX. This can be explained by several factors including incomplete annotations of the model fish genomes and the presence of pseudogenes and con- served non-coding sequences that were not included in the peptide databases. BlastN also appears to be more accurate for estimating microsynteny as it provides the exact points of sequence matches on the chromosomes of the reference genomes (instead of the ORF bound- aries for BlastX). However, it is also important to note that 17% (stickleback) to 33% (zebrafish) of the macro- synteny BAC paired ends identified by BlastX were not revealed by BlastN. This may be caused by non- or less- conserved peptides whose coding sequences are not under strong selection pressure and have evolved enough to escape detection as significant unique hits by BlastN. The comparative genome analyses reported here pro- vide a survey of conserved synteny between rainbow trout and three model fish species. The results of our analyses suggest that for many regions in the rainbow trout genome comparative mapping might serve as a useful genomic resource for identifying candidate genes in QTL detection studies. Nevertheless, further assess- ment of regions of conserved synteny by direct sequen- cing of full-length BAC clones and by evaluating gene content and orthology revealed that gene order, orienta- tions, and gene length are highly variable across fish species (manuscript in preparation). Conclusions In the present study, we sequenced and subsequently characterized more than half of BAC ends from the rainbow trout Swanson YY double haploid male 10X HindIII BAC library. These genomic sequences were used to generate the first rainbow trout specific repeat