ARS | Publication request: Rapid and accurate sequencing of the rainbow trout physical map using Illumina technology

Submitted to: Meeting Abstract
Publication Type: Abstract Only
Publication Acceptance Date: January 25, 2011
Publication Date: March 11, 2011
Citation: Palti, Y. 2011. Rapid and accurate sequencing of the rainbow trout physical map using Illumina technology [abstract]. Fish Genome Meeting, Hinxton,UK. p. 241.

Technical Abstract: Rainbow trout (Oncorhynchus mykiss) are the most widely cultivated cold freshwater fish in the world and an important model species for many areas of research. Despite their importance, a reference genome sequence has not been generated for rainbow trout due in large part to the complex nature of their genome. A bacterial artificial chromosome (BAC) clone based physical map has been generated that allows genomic complexity to be reduced by analyzing individual BAC clones. To test the feasibility of highly parallel sequencing of rainbow trout BAC clones, we used a combination short fragment paired-end Illumina sequencing of indexed BAC clones and long fragment mate-pair Illumina sequencing of genomic DNA. Strikingly, we found that this approach can produce high quality assemblies of entire BAC clones with relatively low sequencing coverage, and we are currently using it to sequence 14,766 BAC clones that constitute a minimal tilling path (MTP) of the rainbow trout physical map. Furthermore, we have created a high-density genetic map with RAD (restricted site associated DNA) markers that will be useful for ordering the sequence contigs. We believe that our MTP sequence in combination with the INRA and Genoscope deep coverage shotgun sequencing of the same doubled haploid line will provide the necessary building blocks for the rainbow trout reference genome sequence assembly and that similar strategy will be useful for sequencing other complex genomes.