Genomics Research Group (GRG): Elucidating the Effects of the Deepwater Horizon Oil Spill on the Atlantic Oyster Using Global Transcriptome Analysis

• Main Authors: Raghavachari, Nalini, Showmaker, Kurt, Liu, Poching, Jafari, Nadereh, Barker, Natalie, Willett, Kristine L., Corrales, Jone, Patterson, Heather K., Carmichael, Ruth H., Baldwin, Don, Reyero, Natalia G.
• Format: Text
• Language: English
• Published: Association of Biomolecular Resource Facilities 2013
• Subjects: Poster Session Abstracts; Pacific; Pacific oyster
• Online Access: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3635446

Global transcriptome analysis is of growing importance in understanding how altered expression of genetic variants contributes to complex diseases such as cancer, diabetes, and heart disease as well as the effect of environmental pollutants to living organisms. The Genomics Research Group applied next generation sequencing technologies to study the effects of Deep Water Horizon oil spill on the transcriptome of atlantic oysters. The Deep Water Horizon oil spill resulted in the release of over 200 million gallons of crude oil into the waters of the Gulf of Mexico. Over two million gallons of chemical were used to emulsify and disperse oil plumes posing further risks to the environment in addition to the direct impacts of crude oil. Biota such as the commercially important Atlantic oyster Crassostrea virginica, were inevitably exposed to spill-related contaminants in the Gulf. The potential effects of oiled water and sediments on oysters range from non-detectable to reduced settlement to impaired immune function, acute intoxication, and death due to bioaccumulation of contaminants. Oil also may affect oxygen diffusion through the water column, and in some cases lead to hypoxic conditions that prompt avoidance migration by mobile species. Sedentary organisms such as oysters are even more susceptible to these negative effects of oil contamination. The mechanisms of toxicity of the oil and spill-related compounds are not well understood. In order to understand these mechanisms, we used RNAsequencing of oyster samples from before and after the spill. As the C. virginica genome is not available, we used two different approaches. First, the sequences were mapped to the Pacific oyster genome, recently released. Secondly, a de novo transcriptome assembly was performed. The de novo transcriptome assembly returned a 66-70% alignment rate. Finally, 9,469 transcripts were identified as homologs between the Atlantic and the Pacific oyster.