Background. Oil spills are major environmental disasters. Dispersants help control spills, as they emulsify oil into droplets to speed bioremediation. Although dispersant toxicity is controversial, the genetic consequences and damages of dispersed oil exposure are poorly understood. We used RNA-seq to measure gene expression of flatback mudcrabs (Eurypanopeus depressus, Decapoda, Brachyura, Panopeidae) exposed to dispersed oil.
Methods. Our experimental design included two control types, oil-only, and oil-dispersant treatments with three replicates each. We prepared 100 base pair-ended libraries from total RNA and sequenced them in one Illumina HiSeq2000 lane. We assembled a reference transcriptome with all replicates per treatment, assessed quality with novel metrics, identified transcripts, and quantified gene expression with open source software.
Results. Our mudcrab transcriptome included 500,008 transcripts from 347,082,962 pair-end raw reads. In oil-only treatments, we found few significant differences. However, in oil-dispersant treatments, over 4000 genes involved with cellular differentiation, primordial cellular component upkeep, apoptosis, and immune response were downregulated. A few muscle structure and development genes were upregulated.
Discussion. Our results provide evidence that exposure to chemically dispersed oil causes a generalized cellular shutdown and muscular repair attempts. Our results suggest current oil-spill treatment procedures could be detrimental to crustaceans and indicate additional research is needed to evaluate the impact of oil spills in gene expression. Finally, traditional quality metrics such as N50s have limitations to explain the nature of RNA-seq compared to new methods in non-model decapod crustaceans.
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Vazquez-Miranda, H., Thoma, B., Wong, J., Felder, D., Crandall, K. A., & Bracken-Grissom, H. (2017). Transcriptomic effects of dispersed oil in a non-model decapod crustacean. PeerJ Preprints, 5 (). http://dx.doi.org/10.7287/peerj.preprints.2977v1