Reduced-representation bisulfite sequencing finds novel epigenome-wide response to oil pollution in the foundation plant Spartina alterniflora

The application of genomics technology in ecological contexts allows for examination of how rapid environmental change may shape standing molecular level variation and organismal response in natural populations. We previously demonstrated an effect of the Deepwater Horizon oil spill on gene expression patterns and genetic variation, but not methylation variation, in oil-exposed populations of the foundation salt marsh grass, Spartina alterniflora . Here, we used a reduced representation bisulfite sequencing approach, epigenotyping by sequencing (epiGBS), in an attempt to find correlations among DNA sequence, DNA methylation, gene expression, and exposure of S. alterniflora to the Deepwater Horizon oil spill. We also compare the results of anonymous markers (MS-AFLP) and a reduced representation sequencing approach (epiGBS), providing insight into the trade-offs in these technologies for ecological epigenetics studies. With the increased resolution of the epiGBS data set, we document genetic and methylation differentiation between oil-exposed and unexposed populations, both genome-wide and at single nucleotides. We also found a strong correlation of genome-wide methylation patterns and gene expression, independent of population genetic structure. Overall, these findings demonstrate that variation in DNA methylation is abundant, responsive, and correlated to gene expression in natural populations, and may represent an important component of the response to environmental stress.