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Title: Status of the rainbow trout genome reference sequence assembly

item Palti, Yniv
item Rexroad, Caird

Submitted to: Government Publication/Report
Publication Type: Government Publication
Publication Acceptance Date: 11/1/2010
Publication Date: 11/1/2010
Citation: Palti, Y., Rexroad III, C.E. 2010. Status of the rainbow trout genome reference sequence assembly. Government Publication/Report. 1:1-9.

Interpretive Summary:

Technical Abstract: Rainbow trout (Oncorhynchus mykiss) are the most cultivated cold water fish in the U.S. In addition to interests associated with aquaculture and sport fisheries, the rainbow trout serves as a model research organism for studies related to carcinogenesis, toxicology, comparative immunology, disease ecology, physiology and nutrition. Current genomic resources available for rainbow trout research include multiple bacterial artificial chromosome (BAC) libraries; doubled haploid (DH) clonal lines; multiple genetic maps based on clonal lines and outbred populations; a BAC fingerprinting physical map; a database of ~200,000 BAC end sequences (BES); large EST and transcriptome databases and several DNA microarrays. Two complementing genome assembly projects are currently underway in France and in the U.S. In the first project, a similar approach to the turkey genome assembly using multi-platform nextgen technologies for de-novo sequencing of the rainbow trout genome is employed by INRA and The Genoscope in France (expected release of genome assembly in Dec. 2011). In the second project, a pooling and tagging scheme is used for sequencing of the ~15,000 clones of the BAC physical map minimal tilling path (MTP) with the Illumina sequencing platform at the University of Oregon. This is a modification of the classic clone-by-clone approach. The source of DNA for the INRA de-novo assembly project is the Swanson double haploid homozygous line of Gary Thorgaard. The same source of genomic DNA was also used for producing the BAC libraries used to generate the physical map. We propose the following approach to obtaining a genome reference sequence for rainbow trout: 1) Sequencing of all the clones in the physical map MTP using nextgen platforms. 2) High density SNP map based on the reference Swanson line to aid in the genome assembly. 3) 1X-2X Sanger whole genome sequencing to fill in gaps in the assembly and cover long repetitive sequences. 4) SNP discovery efforts like RRLs and RADs for developing genotyping platforms that will enable genome variation analyses. Expected Value and Impact: A reference genome sequence and a commercial high density SNP chip for rainbow trout will be produced. The high-throughput genotyping platform will enhance genomic analyses in this economically important species and will enable direct and rapid linking of phenotypes to genotypes. The draft reference genome sequence will facilitate functional genomics and proteomic approaches. Methods for genomic analysis in a complex and duplicated vertebrate genome will be established.