Skip to main content
ARS Home » Northeast Area » Leetown, West Virginia » Cool and Cold Water Aquaculture Research » Research » Publications at this Location » Publication #328209

Research Project: Integrated Research Approaches for Improving Production Efficiency in Salmonids

Location: Cool and Cold Water Aquaculture Research

Title: A New and Improved Rainbow Trout (Oncorhynchus mykiss) Reference Genome Assembly

Author
item Gao, Guangtu

Submitted to: International Conference on Integrative Salmonid Biology
Publication Type: Abstract Only
Publication Acceptance Date: 3/15/2016
Publication Date: 4/27/2016
Citation: Gao, G. 2016. A New and Improved Rainbow Trout (Oncorhynchus mykiss) Reference Genome Assembly. International Conference on Integrative Salmonid Biology. 1: 40.

Interpretive Summary:

Technical Abstract: In an effort to improve the rainbow trout reference genome assembly, we re-sequenced the doubled-haploid Swanson line using the longest available reads from the Illumina technology; generating over 510 million paired-end shotgun reads (2x260nt), and 1 billion mate-pair reads (2x160nt) from four sequencing libraries with fragment sizes ranging from 800bp to 15Kb. We then generated a 2.17Gb genome assembly, containing 139,726 scaffolds with N50 greater than 1.7Mb using DeNovoMAGIC, the advanced genome assembly pipeline from NRGene. To generate a dense genetic map for each chromosome, we genotyped 5,716 fish from 146 full-sib families with the Affymetrix 57K SNP array. Using the information from this genetic map and two other RAD SNP based linkage maps, and from comparative sequence alignment with the Atlantic salmon genome, we anchored and ordered about 88% of the assembly scaffolds within chromosomes. The new Rainbow trout genome assembly and chromosome sequences provide major improvements over the current rainbow trout reference genome in all categories; including genome coverage, scaffold size, precision, and percent of the genome that is in chromosome sequences. We are currently working on validating and improving the assembly scaffold size using the Dovetail Chicago™ method and HiRise Scaffolder pipeline and the BioNano Genomics Irys® system for single-molecule optical genome mapping.