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ARS Home » Northeast Area » Leetown, West Virginia » Cool and Cold Water Aquaculture Research » Research » Publications at this Location » Publication #347675

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

Location: Cool and Cold Water Aquaculture Research

Title: Evaluation of the utility of the new rainbow trout genome assembly for analyzing RNA-seq data from stress response experiments

item Gao, Guangtu
item Weber, Gregory - Greg
item Liu, Sixin
item Palti, Yniv
item Rexroad, Caird

Submitted to: Plant and Animal Genome Conference
Publication Type: Abstract Only
Publication Acceptance Date: 11/1/2017
Publication Date: 1/13/2018
Citation: Gao, G., Weber, G.M., Liu, S., Palti, Y., Rexroad Iii, C.E. 2018. Evaluation of the utility of the new rainbow trout genome assembly for analyzing RNA-seq data from stress response experiments. Plant and Animal Genome Conference. International Plant and Animal Genome XXVI. Paper No. 102.

Interpretive Summary:

Technical Abstract: The newly released rainbow trout genome assembly in NCBI RefSeq has greatly expanded our abilities for analyzing rainbow trout sequencing data. In this poster, we evaluate the utility of this genome assembly for analyzing RNA sequencing (RNA-seq) data of rainbow trout responses to various stressors, including high temperature, low temperature, re-use water quality, salinity, and confinement. A spliced-alignment software, STAR was used to align the RNA-seq reads to the reference genome. Aligned reads were counted using htseq-count, and DESeq2 was used in comparing the treatments with the controls. A total of 90% of the RNA-seq reads were mapped to the reference genome with ~75% and ~15% of the reads uniquely and multiply mapped to the genome, respectively. This is a major improvement from previous RNA-seq studies in rainbow trout that mapped the RNA-seq reads to a reference transcriptome and would typically have only ~ 55% of the reads aligned to the reference. The majority of the reads were mapped to genome locations annotated by RefSeq gene models, but there was also a substantial amount of the reads that were mapped to genomic regions that are currently not annotated. Comparing with the control samples, differentially expressed genes (DEG) were found in the responses to all stressors but the confinement stress experiment. Functional annotations of the DEGs was conducted to identify molecular and biological pathways that may be involved in the rainbow trout stress response.