Using WGCNA to Examine RNASeq Expression Data in the Annual Killifish Austrofundulus Limnaeus

Annual killifish (Austrofundulus limnaeus) live in ephemeral ponds of Venezuela. They have evolved a unique life history that includes experience embryonic diapause; a period of developmental dormancy and metabolic arrest that supports survival during the dry season. Developing and diapausing embryos are extremely resistant to environmental stresses; for example, they can survive for months without oxygen (anoxia). A. limnaeus’ tolerance to anoxia is an important survival mechanism as they can spend months buried in anoxic soil during development. I hypothesize that this extreme anoxia tolerance is supported by gene expression networks that are different from typical vertebrates. To evaluate this hypothesis, I will use weighted gene correlation network analysis (WGCNA) to evaluate RNAseq data from embryos exposed to anoxia, and recovery from anoxia. WGCNA describes patterns of correlation among genes across the experimental treatments, and creates modules of statistically correlated genes. These modules can be compared to one another and across different developmental stages that have differing tolerances of anoxia. I hope to discover unique gene expression modules involved with anoxia tolerance. Understanding how cells can survive without oxygen could lead to critical breakthroughs in medicine and emerging biotechnologies, such as treatments to mitigate damage from heart attacks or strokes.