Rainbow trout (Oncorhynchus mykiss) are cultivated worldwide for aquaculture production. Trout farming has been successful in North America, the species native area, as well as in many other regions, including Chile and a number of European countries where rainbow trout had been introduced since the 19th century. In 2008, total world production was about 576,000 metric tons with a total export value estimated around 2.4 billions USD (http://www.fao.org/fishery/statistics/en).
The rainbow trout is one of the most intensively studied fish species. Several features such as in vitro fertilization, ease of rearing and gamete handling and a large body size with large and clearly defined tissues, make it a particularly suited model to carry out a range of investigations. Hence, considerable amount of basic knowledge has been accumulated in many areas such as physiology, nutrition, behaviour, ecology, genetics, pathology, comparative immunology, carcinogenesis and toxicology (reviewed in ).
Combining biological and phenotypic data with genomic information can be used to increase our basic knowledge of the regulation of biological functions, and ultimately used in applied research to improve the environmental and genetic management of aquaculture production systems with focus on complex traits such as meat and carcass quality, stress tolerance or resistance to specific pathogens.
The rainbow trout genome size was estimated to be between 2.4 and 3.0 × 109 base pairs (bp) . A whole genome duplication event occurred 25 to 100 million years ago in the common ancestor of the salmonids. Since that time, re-diploidization has resulted in a semi-tetraploid state . Consequently, presence of duplicated genetic markers was reported  and many homeologous regions have been identified in the rainbow trout genome . Although the tetraploidization event increased the genome complexity, it also makes the salmonids a very pertinent group to study the differential evolution and loss of duplicated genes in the process of re-diploidization.
Several genomic resources have been developed in rainbow trout in the last decade. Seven linkage maps based on either AFLP markers [2, 6] or microsatellite markers and few SNPs [7–11] have been constructed. These maps are used for comparative mapping across salmonid species , for QTL mapping studies for various traits [13–20] or for linkage disequilibrium studies . Attempts for high throughput discovery of SNP markers are emerging but only a limited number of true SNP have been validated up to now . Large EST databases ([23, 24]; http://compbio.dfci.harvard.edu/cgi-bin/tgi/gimain.pl?gudb=r_trout and http://www.sigenae.org) are available, as well as high content DNA microarrays [25, 26]. Several bacterial artificial chromosome (BAC) libraries have also been established [4, 27, 28].
BAC libraries are a valuable genomic resource for many purposes, including clone-based sequencing, positional cloning and physical mapping. The first physical map in rainbow trout was recently built using the 10X HindIII BAC library . The map contained 4,173 contigs and 9,379 singletons. The physical length of the map contigs was estimated to be approximately 2.0 Gb, which represents almost 83% of rainbow trout genome.
BAC-end sequencing has been initially proposed to be an efficient approach for whole genome sequencing projects , for comparative physical mapping [30, 31], and for the development of molecular markers, mainly microsatellites . In the absence of whole genome sequences, BES analysis can elucidate sequence content and complexity, including gene density, potential transposable elements, and microsatellite markers . Furthermore, paired BAC-end sequences can be very useful for scaffolding in whole-genome sequencing assembly projects.
Here we report on the sequencing and characterization of BAC-end sequences (BES) from more than half of the clones from the rainbow trout 10X HindIII BAC library. The sequence content was analysed for putative genes, repetitive elements and simple sequence repeats (SSR). BES gene content was then used to establish regions of conserved synteny with other fish genomes.