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United States Department of Agriculture

Agricultural Research Service

Research Project: UTILIZATION OF GENOMICS FOR IMPROVING PRODUCTION TRAITS IN COOL AND COLD WATER AQUACULTURE

Location: Cool and Cold Water Aquaculture Research

Title: Rapid and accurate sequencing of the rainbow trout physical map using Illumina technology

Authors
item Miller, Michael -
item Palti, Yniv
item Luo, Ming-Cheng -
item Miller, Jeanne -
item Brunelli, Joseph -
item Wheeler, Paul -
item Rexroad, Caird
item Thorgaard, Gary -
item Doe, Chris -

Submitted to: Plant and Animal Genome Conference
Publication Type: Abstract Only
Publication Acceptance Date: November 1, 2010
Publication Date: January 15, 2011
Citation: Miller, M.R., Palti, Y., Luo, M., Miller, J.A., Brunelli, J.P., Wheeler, P.A., Rexroad III, C.E., Thorgaard, G.H., Doe, C.Q. 2011. Rapid and accurate sequencing of the rainbow trout physical map using Illumina technology. Plant and Animal Genome Conference. W045.

Technical Abstract: Rainbow trout (Oncorhynchus mykiss) are the most widely cultivated cold freshwater fish in the world and serve as an important model species for many areas of research. Despite their importance, a reference genome sequence has not yet 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 of the rainbow trout physical map. Furthermore, we have created a high-density genetic map with RAD markers that will be useful for ordering the sequence contigs. Our results indicate that this approach will produce a high quality reference genome sequence for rainbow trout and that similar strategies will be useful for sequencing other complex genomes.

Last Modified: 10/20/2014
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