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ARS Home » Northeast Area » Leetown, West Virginia » Cool and Cold Water Aquaculture Research » Research » Publications at this Location » Publication #323548

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

Location: Cool and Cold Water Aquaculture Research

Title: A new rainbow trout (Oncorhynchus mykiss) reference genome assembly

item Gao, Guangtu
item LIEN, SIGBJORN - Centre For Integrative Genetics (CIGENE)
item MOEN, THOMAS - Aquagen
item MILLER, MICHAEL - Uc Davis Medical Center
item Liu, Sixin
item HERNANDEZ, ALVARO - University Of Illinois
item THORGAARD, GARY - Washington State University
item KENT, MATTHEW - Centre For Integrative Genetics (CIGENE)
item Palti, Yniv

Submitted to: Plant and Animal Genome
Publication Type: Abstract Only
Publication Acceptance Date: 12/1/2015
Publication Date: 1/10/2016
Citation: Gao, G., Lien, S., Baranski, M., Moen, T., Miller, M., Liu, S., Hernandez, A., Thorgaard, G., Kent, M., Palti, Y. 2016. A new rainbow trout (Oncorhynchus mykiss) reference genome assembly [abstract]. Plant and Animal Genome. P0467.

Interpretive Summary:

Technical Abstract: In an effort to improve the rainbow trout reference genome assembly, we have re-sequenced the doubled-haploid Swanson line using the longest available reads from the Illumina technology. Overall we generated over 510 million 260nt paired-end shotgun reads, and 1 billion 160nt mate-pair reads from four fragment size libraries (800bp - 15Kb). The sequences were assembled using DeNovoMAGIC, the advanced genome assembly pipeline from NRGene, which generated a 2.17 Gb genome assembly, containing 139,726 scaffolds with N50 greater than 1.7 Mb. To generate chromosome maps we genotyped more than 4,000 pedigreed fish with the 57K SNP chip and with RAD SNPs and generated dense genetic maps. We found that ~80% of the new assembly can be anchored and ordered onto chromosomes based on the new genetic maps. Our initial analysis shows that the new physical genome sequence assembly and its integration with the new genetic maps provide major improvements to the rainbow trout reference genome in all categories; including genome coverage, scaffold size, precision and anchoring and ordering of the scaffolds onto chromosome maps. The assembly can be further improved by merging of neighboring scaffolds using overlapping long sequences from other trout assemblies or long reads sequencing technologies.