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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: Progress of the rainbow trout reference genome assembly project

Authors
item Palti, Yniv
item Miller, Michael -

Submitted to: International Conference on Integrative Salmonid Biology
Publication Type: Abstract Only
Publication Acceptance Date: May 1, 2014
Publication Date: June 10, 2014
Citation: Palti, Y., Miller, M. 2014. Progress of the rainbow trout reference genome assembly project [abstract]. International Conference on Integrative Salmonid Biology. Paper No. 21425.

Technical Abstract: Rainbow trout are the most widely cultivated cold freshwater fish in the world and an important model species for many research areas. Despite this importance, the complex nature of the rainbow trout genome (pseudotetraploid and high repeat content) has hindered the production of a high-quality reference genome assembly. Our genome sequencing strategy utilized a bacterial artificial chromosome (BAC) clone based physical map to reduce sequence and assembly complexity. DNA was extracted from individual minimal tiling path (MTP) clones, and approximately 1,200 pools of 12 BAC clones each were generated. Each pool was individually indexed and sequenced at approximately 50-100X coverage with paired-end Illumina sequencing. In addition, seven high-quality mate-pair libraries were generated from genomic DNA to aid in BAC clone assembly and scaffolding. The mate-pair libraries have unique insert-sizes ranging from 2.5 to 16 kb, and each represents 1-2X genomic coverage. Lastly, we generated 50X whole genome shotgun coverage with paired-end Illumina sequencing. Assembling a combination the BAC-based paired-end, genomic mate-pair, and genomic paired-end sequence data results in the majority of BAC clones being completely scaffolded. The current version of the draft genome assembly can be downloaded or searched for BLAST sequence homology on the AnimalGenome.org web site. Despite our progress to date, the resulting assembly has limitations including many gaps in each scaffolds and poor coverage of regions not represented in the MTP. These factors have limited the utility and widespread release of the reference genome assembly. To improve the assembly by closing gaps in the current scaffolds we plan to explore long range reads technologies from Illumina and Pac Bio. We are currently utilizing SNP genotype data from the new rainbow trout 57K SNP chip (about 46K SNPs were polymorphic in 10 full-sib families). The genetic map in combination with BAC physical map will be used to guide the assembly of the sequence scaffolds from the individual BACs.

Last Modified: 10/22/2014
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