Abstract
BackgroundThe release of oil resulting from the blowout of the Deepwater Horizon (DH) drilling platform was one of the largest in history discharging more than 189 million gallons of oil and subject to widespread application of oil dispersants. This event impacted a wide range of ecological habitats with a complex mix of pollutants whose biological impact is still not yet fully understood. To better understand the effects on a vertebrate genome, we studied gene expression in the salt marsh minnow Fundulus grandis, which is local to the northern coast of the Gulf of Mexico and is a sister species of the ecotoxicological model Fundulus heteroclitus. To assess genomic changes, we quantified mRNA expression using high throughput sequencing technologies (RNA-Seq) in F. grandis populations in the marshes and estuaries impacted by DH oil release. This application of RNA-Seq to a non-model, wild, and ecologically significant organism is an important evaluation of the technology to quickly assess similar events in the future.ResultsOur de novo assembly of RNA-Seq data produced a large set of sequences which included many duplicates and fragments. In many cases several of these could be associated with a common reference sequence using blast to query a reference database. This reduced the set of significant genes to 1,070 down-regulated and 1,251 up-regulated genes. These genes indicate a broad and complex genomic response to DH oil exposure including the expected AHR-mediated response and CYP genes. In addition a response to hypoxic conditions and an immune response are also indicated. Several genes in the choriogenin family were down-regulated in the exposed group; a response that is consistent with AH exposure. These analyses are in agreement with oligonucleotide-based microarray analyses, and describe only a subset of significant genes with aberrant regulation in the exposed set.ConclusionRNA-Seq may be successfully applied to feral and extremely polymorphic organisms that do not have an underlying genome sequence assembly to address timely environmental problems. Additionally, the observed changes in a large set of transcript expression levels are indicative of a complex response to the varied petroleum components to which the fish were exposed.
Highlights
The release of oil resulting from the blowout of the Deepwater Horizon (DH) drilling platform was one of the largest in history discharging more than 189 million gallons of oil and subject to widespread application of oil dispersants
We have leveraged the body of existing scientific work surrounding F. heteroclitus in the analysis of high throughput sequencing techniques applied to natural Fundulus grandis populations, a closely-related sister species inhabiting DH-impacted sites in the Gulf of Mexico [9]
Illumina short read data have recently been shown to be more resilient to fragmentary, incomplete sequences as targets for alignment for digital gene expression [11] as would likely be the case in non-model organisms
Summary
The release of oil resulting from the blowout of the Deepwater Horizon (DH) drilling platform was one of the largest in history discharging more than 189 million gallons of oil and subject to widespread application of oil dispersants. In April of 2010, the explosion of the Deepwater Horizon oil drilling platform initiated the largest deep water oil release in the history of the petroleum industry culminating in more than 189 million gallons of crude oil released into the environment [1,2] This incident has greatly impacted the natural and economic resources of many Gulf of Mexico coastal areas [3,4,5,6,7]. We have leveraged the body of existing scientific work surrounding F. heteroclitus in the analysis of high throughput sequencing techniques applied to natural Fundulus grandis populations, a closely-related sister species inhabiting DH-impacted sites in the Gulf of Mexico [9] This application holds promise for revealing induction of environmental stress with genome-wide molecular genetic response patterns. We provide methodological detail and results of transcriptome expression comparisons between populations of F. grandis sampled directly from the environment affected by the DH oil release versus those from unaffected populations
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