Sequencing Salmonid Genomes Using Next Generation Technologies

Salmonids are important from an environmental, economic, biomedical, and cultural standpoint. Despite their importance, a reference genome sequence has not been generated for any salmonid due in large part to the complex nature of their genomes. A bacterial artificial chromosome (BAC) clone based physical map has been generated for rainbow trout that allows genomic complexity to be reduced by analyzing individual BAC clones. Here we show that a combination of short-fragment paired-end Illumina sequencing of indexed BAC clones and long-fragment mate-pair Illumina sequencing of genomic DNA can produce high quality assemblies of entire BAC clones.  We have used this approach to sequence 14,000 BAC clones that constitute a minimal tilling path of the rainbow trout physical map. Furthermore, we have used RAD Sequencing to create a high-density genetic map for ordering the sequence scaffolds. Our results indicate that this approach has produced a high quality reference genome sequence for rainbow trout, and that this reference will facilitate rapid genome sequencing of other salmonids.